H ANDN920101 D alpha-CH chemical shifts (Andersen et al., 1992) R LIT:1810048b PMID:1575719 A Andersen, N.H., Cao, B. and Chen, C. T Peptide/protein structure analysis using the chemical shift index method: upfield alpha-CH values reveal dynamic helices and aL sites J Biochem. and Biophys. Res. Comm. 184, 1008-1014 (1992) C BUNA790102 0.949 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.35 4.38 4.75 4.76 4.65 4.37 4.29 3.97 4.63 3.95 4.17 4.36 4.52 4.66 4.44 4.50 4.35 4.70 4.60 3.95 // H ARGP820101 D Hydrophobicity index (Argos et al., 1982) R LIT:0901079b PMID:7151796 A Argos, P., Rao, J.K.M. and Hargrave, P.A. T Structural prediction of membrane-bound proteins J Eur. J. Biochem. 128, 565-575 (1982) C JOND750101 1.000 SIMZ760101 0.967 GOLD730101 0.936 TAKK010101 0.906 MEEJ810101 0.891 CIDH920105 0.867 LEVM760106 0.865 CIDH920102 0.862 MEEJ800102 0.855 MEEJ810102 0.853 CIDH920103 0.827 PLIV810101 0.820 CIDH920104 0.819 LEVM760107 0.806 NOZY710101 0.800 PARJ860101 -0.835 WOLS870101 -0.838 BULH740101 -0.854 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.61 0.60 0.06 0.46 1.07 0. 0.47 0.07 0.61 2.22 1.53 1.15 1.18 2.02 1.95 0.05 0.05 2.65 1.88 1.32 // H ARGP820102 D Signal sequence helical potential (Argos et al., 1982) R LIT:0901079b PMID:7151796 A Argos, P., Rao, J.K.M. and Hargrave, P.A. T Structural prediction of membrane-bound proteins J Eur. J. Biochem. 128, 565-575 (1982) C ARGP820103 0.961 KYTJ820101 0.803 JURD980101 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.18 0.20 0.23 0.05 1.89 0.72 0.11 0.49 0.31 1.45 3.23 0.06 2.67 1.96 0.76 0.97 0.84 0.77 0.39 1.08 // H ARGP820103 D Membrane-buried preference parameters (Argos et al., 1982) R LIT:0901079b PMID:7151796 A Argos, P., Rao, J.K.M. and Hargrave, P.A. T Structural prediction of membrane-bound proteins J Eur. J. Biochem. 128, 565-575 (1982) C ARGP820102 0.961 MIYS850101 0.822 NAKH900106 0.810 EISD860103 0.810 KYTJ820101 0.806 JURD980101 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.56 0.45 0.27 0.14 1.23 0.51 0.23 0.62 0.29 1.67 2.93 0.15 2.96 2.03 0.76 0.81 0.91 1.08 0.68 1.14 // H BEGF750101 D Conformational parameter of inner helix (Beghin-Dirkx, 1975) R LIT:1309065 PMID:50789 A Beghin, F. and Dirkx, J. T Une methode statistique simple de prediction des conformations proteiques J Arch. Int. Physiol. Biochim. 83, 167-168 (1975) C KANM800103 0.893 AURR980113 0.857 ROBB760103 0.852 CHOP780201 0.841 QIAN880105 0.833 AURR980109 0.821 QIAN880107 0.815 PALJ810102 0.811 AURR980108 0.810 CHOP780101 -0.803 CHOP780210 -0.804 CRAJ730103 -0.812 ROBB760108 -0.819 ROBB760113 -0.826 CHAM830101 -0.854 PALJ810106 -0.859 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1. 0.52 0.35 0.44 0.06 0.44 0.73 0.35 0.60 0.73 1. 0.60 1. 0.60 0.06 0.35 0.44 0.73 0.44 0.82 // H BEGF750102 D Conformational parameter of beta-structure (Beghin-Dirkx, 1975) R LIT:1309065 PMID:50789 A Beghin, F. and Dirkx, J. T Une methode statistique simple de prediction des conformations proteiques J Arch. Int. Physiol. Biochim. 83, 167-168 (1975) C LEVM780102 0.834 PRAM900103 0.834 PALJ810110 0.834 NAGK730102 0.833 QIAN880120 0.829 QIAN880119 0.811 ROBB760106 0.809 PTIO830102 0.807 LIFS790101 0.807 MIYS850101 0.806 PONP800107 0.803 PALJ810104 0.801 MEIH800101 -0.832 RACS770101 -0.840 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.77 0.72 0.55 0.65 0.65 0.72 0.55 0.65 0.83 0.98 0.83 0.55 0.98 0.98 0.55 0.55 0.83 0.77 0.83 0.98 // H BEGF750103 D Conformational parameter of beta-turn (Beghin-Dirkx, 1975) R LIT:1309065 PMID:50789 A Beghin, F. and Dirkx, J. T Une methode statistique simple de prediction des conformations proteiques J Arch. Int. Physiol. Biochim. 83, 167-168 (1975) C ROBB760113 0.924 ROBB760108 0.922 ROBB760110 0.903 CHOP780101 0.885 CRAJ730103 0.874 PALJ810106 0.859 TANS770110 0.834 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.37 0.84 0.97 0.97 0.84 0.64 0.53 0.97 0.75 0.37 0.53 0.75 0.64 0.53 0.97 0.84 0.75 0.97 0.84 0.37 // H BHAR880101 D Average flexibility indices (Bhaskaran-Ponnuswamy, 1988) R LIT:1414112 A Bhaskaran, R. and Ponnuswamy, P.K. T Positional flexibilities of amino acid residues in globular proteins J Int. J. Peptide Protein Res. 32, 241-255 (1988) C VINM940103 0.869 KARP850102 0.806 WERD780101 -0.803 RICJ880111 -0.813 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.357 0.529 0.463 0.511 0.346 0.493 0.497 0.544 0.323 0.462 0.365 0.466 0.295 0.314 0.509 0.507 0.444 0.305 0.420 0.386 // H BIGC670101 D Residue volume (Bigelow, 1967) R LIT:2004108b PMID:6048539 A Bigelow, C.C. T On the average hydrophobicity of proteins and the relation between it and protein structure J J. Theor. Biol. 16, 187-211 (1967) * (Asn Gln 5.0) C GOLD730102 1.000 KRIW790103 0.993 TSAJ990101 0.993 TSAJ990102 0.992 CHOC750101 0.990 GRAR740103 0.984 FAUJ880103 0.972 CHAM820101 0.966 CHOC760101 0.960 FASG760101 0.919 LEVM760105 0.913 ROSG850101 0.910 DAWD720101 0.903 LEVM760102 0.896 LEVM760106 0.876 CHAM830106 0.870 LEVM760107 0.863 FAUJ880106 0.860 RADA880106 0.856 MCMT640101 0.814 RADA880103 -0.865 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 52.6 109.1 75.7 68.4 68.3 89.7 84.7 36.3 91.9 102.0 102.0 105.1 97.7 113.9 73.6 54.9 71.2 135.4 116.2 85.1 // H BIOV880101 D Information value for accessibility; average fraction 35% (Biou et al., 1988) R LIT:1413106b PMID:3237683 A Biou, V., Gibrat, J.F., Levin, J.M., Robson, B. and Garnier, J. T Secondary structure prediction: combination of three different methods J Protein Engineering 2, 185-191 (1988) C RADA880108 0.981 ROSG850102 0.981 NISK860101 0.972 BIOV880102 0.968 MIYS850101 0.960 WERD780101 0.951 FAUJ830101 0.942 NADH010103 0.939 NADH010104 0.937 MEIH800103 0.934 CIDH920104 0.933 PONP800103 0.926 PONP800102 0.926 NADH010102 0.921 NISK800101 0.920 PONP800101 0.918 CIDH920105 0.912 PONP930101 0.912 PONP800108 0.907 PLIV810101 0.899 MANP780101 0.899 ROBB790101 0.890 CIDH920103 0.887 DESM900102 0.878 JANJ780102 0.875 NADH010105 0.867 CIDH920102 0.864 EISD860103 0.864 MEEJ810101 0.855 JANJ790102 0.848 CIDH920101 0.847 JURD980101 0.840 GUOD860101 0.839 SWER830101 0.839 NADH010101 0.838 KYTJ820101 0.829 EISD860101 0.828 JANJ790101 0.827 MEEJ810102 0.824 CHOC760103 0.823 PONP800107 0.816 EISD840101 0.811 DESM900101 0.807 KRIW710101 -0.813 PARS000101 -0.819 FUKS010102 -0.820 KARP850101 -0.825 JANJ780103 -0.829 WOEC730101 -0.829 ROSM880101 -0.830 LEVM760101 -0.831 KUHL950101 -0.834 FUKS010103 -0.840 HOPT810101 -0.848 WOLS870101 -0.854 ROSM880102 -0.854 RACS770103 -0.856 OOBM770101 -0.858 KRIW790102 -0.869 FUKS010104 -0.873 VINM940102 -0.876 KARP850102 -0.880 PARJ860101 -0.889 RACS770101 -0.893 VINM940103 -0.901 GRAR740102 -0.910 KRIW790101 -0.910 OOBM770103 -0.920 GUYH850101 -0.929 RACS770102 -0.937 VINM940101 -0.941 MEIH800101 -0.949 MEIH800102 -0.956 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 16. -70. -74. -78. 168. -73. -106. -13. 50. 151. 145. -141. 124. 189. -20. -70. -38. 145. 53. 123. // H BIOV880102 D Information value for accessibility; average fraction 23% (Biou et al., 1988) R LIT:1413106b PMID:3237683 A Biou, V., Gibrat, J.F., Levin, J.M., Robson, B. and Garnier, J. T Secondary structure prediction: combination of three different methods J Protein Engineering 2, 185-191 (1988) C BIOV880101 0.968 ROSG850102 0.960 RADA880108 0.942 NISK860101 0.939 MIYS850101 0.930 WERD780101 0.929 MEIH800103 0.916 NADH010102 0.914 NADH010103 0.913 FAUJ830101 0.911 NADH010104 0.900 CIDH920104 0.890 CIDH920105 0.882 PONP800103 0.879 PONP930101 0.877 DESM900102 0.876 NISK800101 0.873 PONP800102 0.867 JANJ780102 0.862 PONP800101 0.860 CIDH920103 0.860 PLIV810101 0.858 JANJ790102 0.856 PONP800108 0.854 WARP780101 0.853 MANP780101 0.847 EISD860103 0.845 CIDH920102 0.837 EISD860101 0.832 NAKH900110 0.829 MEEJ810101 0.822 DESM900101 0.821 ROBB790101 0.821 CIDH920101 0.819 GUOD860101 0.817 PONP800107 0.814 EISD840101 0.814 JURD980101 0.805 NADH010101 0.804 KARP850101 -0.804 KUHL950101 -0.809 JANJ780101 -0.809 FUKS010102 -0.810 PARS000101 -0.813 WOEC730101 -0.819 ROSM880101 -0.824 VINM940102 -0.826 ROSM880102 -0.837 WOLS870101 -0.842 LEVM760101 -0.847 KARP850102 -0.859 JANJ780103 -0.860 HOPT810101 -0.864 PARJ860101 -0.875 RACS770101 -0.875 KRIW790101 -0.876 OOBM770101 -0.877 KRIW790102 -0.878 GRAR740102 -0.881 GUYH850101 -0.885 FUKS010104 -0.887 VINM940103 -0.889 RACS770103 -0.906 OOBM770103 -0.925 VINM940101 -0.929 RACS770102 -0.932 MEIH800101 -0.937 MEIH800102 -0.951 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 44. -68. -72. -91. 90. -117. -139. -8. 47. 100. 108. -188. 121. 148. -36. -60. -54. 163. 22. 117. // H BROC820101 D Retention coefficient in TFA (Browne et al., 1982) R LIT:0809229 PMID:7125223 A Browne, C.A., Bennett, H.P.J. and Solomon, S. T The isolation of peptides by high-performance liquid chromatography using predicted elution positions J Anal. Biochem. 124, 201-208 (1982) C BROC820102 0.925 ZIMJ680105 0.896 MEEJ800102 0.877 TAKK010101 0.836 GUOD860101 0.832 NAKH900110 0.830 NOZY710101 0.829 MEEJ810102 0.820 RADA880102 0.811 BULH740101 -0.815 PARJ860101 -0.849 WOLS870101 -0.871 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.3 -3.6 -5.7 -2.9 -9.2 -0.3 -7.1 -1.2 -2.1 6.6 20.0 -3.7 5.6 19.2 5.1 -4.1 0.8 16.3 5.9 3.5 // H BROC820102 D Retention coefficient in HFBA (Browne et al., 1982) R LIT:0809229 PMID:7125223 A Browne, C.A., Bennett, H.P.J. and Solomon, S. T The isolation of peptides by high-performance liquid chromatography using predicted elution positions J Anal. Biochem. 124, 201-208 (1982) C BROC820101 0.925 ZIMJ680105 0.865 MEEJ800102 0.857 MEEJ800101 0.840 TAKK010101 0.839 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 3.9 3.2 -2.8 -2.8 -14.3 1.8 -7.5 -2.3 2.0 11.0 15.0 -2.5 4.1 14.7 5.6 -3.5 1.1 17.8 3.8 2.1 // H BULH740101 D Transfer free energy to surface (Bull-Breese, 1974) R PMID:4839053 A Bull, H.B. and Breese, K. T Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues J Arch. Biochem. Biophys. 161, 665-670 (1974) C WOLS870101 0.929 PARJ860101 0.909 GRAR740102 0.822 ROBB790101 -0.813 BROC820101 -0.815 LEVM760106 -0.818 CIDH920104 -0.829 FAUJ830101 -0.830 EISD860101 -0.833 MIYS850101 -0.838 WILM950101 -0.845 CIDH920103 -0.848 CIDH920102 -0.851 JOND750101 -0.853 ARGP820101 -0.854 RADA880102 -0.856 TAKK010101 -0.865 CIDH920105 -0.871 GOLD730101 -0.874 MEEJ800102 -0.875 MEEJ810101 -0.876 ZIMJ680105 -0.879 MEEJ810102 -0.880 NOZY710101 -0.892 SIMZ760101 -0.894 VENT840101 -0.907 PLIV810101 -0.912 GUOD860101 -0.922 SWER830101 -0.923 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.20 -0.12 0.08 -0.20 -0.45 0.16 -0.30 0.00 -0.12 -2.26 -2.46 -0.35 -1.47 -2.33 -0.98 -0.39 -0.52 -2.01 -2.24 -1.56 // H BULH740102 D Apparent partial specific volume (Bull-Breese, 1974) R PMID:4839053 A Bull, H.B. and Breese, K. T Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues J Arch. Biochem. Biophys. 161, 665-670 (1974) * (Tyr !) C COHE430101 0.923 ZIMJ680102 0.825 GOLD730101 0.825 SIMZ760101 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.691 0.728 0.596 0.558 0.624 0.649 0.632 0.592 0.646 0.809 0.842 0.767 0.709 0.756 0.730 0.594 0.655 0.743 0.743 0.777 // H BUNA790101 D alpha-NH chemical shifts (Bundi-Wuthrich, 1979) R LIT:0503064b A Bundi, A. and Wuthrich, K. T 1H-nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH J Biopolymers 18, 285-297 (1979) * (Pro !) C BLAM930101 0.945 ONEK900101 0.902 ROBB760104 0.823 FAUJ880113 0.818 CHOP780213 -0.822 ISOY800104 -0.842 MUNV940104 -0.865 TANS770104 -0.867 MUNV940105 -0.874 AVBF000104 -0.922 ONEK900102 -0.949 FINA910102 -0.992 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.249 8.274 8.747 8.410 8.312 8.411 8.368 8.391 8.415 8.195 8.423 8.408 8.418 8.228 0. 8.380 8.236 8.094 8.183 8.436 // H BUNA790102 D alpha-CH chemical shifts (Bundi-Wuthrich, 1979) R LIT:0503064b A Bundi, A. and Wuthrich, K. T 1H-nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH J Biopolymers 18, 285-297 (1979) C ANDN920101 0.949 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.349 4.396 4.755 4.765 4.686 4.373 4.295 3.972 4.630 4.224 4.385 4.358 4.513 4.663 4.471 4.498 4.346 4.702 4.604 4.184 // H BUNA790103 D Spin-spin coupling constants 3JHalpha-NH (Bundi-Wuthrich, 1979) R LIT:0503064b A Bundi, A. and Wuthrich, K. T 1H-nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH J Biopolymers 18, 285-297 (1979) * (Met Pro Trp !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.5 6.9 7.5 7.0 7.7 6.0 7.0 5.6 8.0 7.0 6.5 6.5 0. 9.4 0. 6.5 6.9 0. 6.8 7.0 // H BURA740101 D Normalized frequency of alpha-helix (Burgess et al., 1974) R LIT:2004075b A Burgess, A.W., Ponnuswamy, P.K. and Scheraga, H.A. T Analysis of conformations of amino acid residues and prediction of backbone topography in proteins J Isr. J. Chem. 12, 239-286 (1974) C CHOP780201 0.917 TANS770101 0.917 ROBB760101 0.912 CRAJ730101 0.900 PALJ810102 0.900 NAGK730101 0.883 GEIM800101 0.858 KANM800101 0.855 MAXF760101 0.852 PALJ810101 0.850 ISOY800101 0.839 LEVM780104 0.833 GEIM800104 0.819 KANM800103 0.810 RACS820108 0.809 AURR980108 0.808 PRAM900102 0.805 LEVM780101 0.805 NAGK730103 -0.830 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.486 0.262 0.193 0.288 0.200 0.418 0.538 0.120 0.400 0.370 0.420 0.402 0.417 0.318 0.208 0.200 0.272 0.462 0.161 0.379 // H BURA740102 D Normalized frequency of extended structure (Burgess et al., 1974) R LIT:2004075b A Burgess, A.W., Ponnuswamy, P.K. and Scheraga, H.A. T Analysis of conformations of amino acid residues and prediction of backbone topography in proteins J Isr. J. Chem. 12, 239-286 (1974) C ROBB760105 0.821 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.288 0.362 0.229 0.271 0.533 0.327 0.262 0.312 0.200 0.411 0.400 0.265 0.375 0.318 0.340 0.354 0.388 0.231 0.429 0.495 // H CHAM810101 D Steric parameter (Charton, 1981) R LIT:2004112b PMID:7300379 A Charton, M. T Protein folding and the genetic code: An alternative quantitative model J J. Theor. Biol. 91, 115-123 (1981) * (Pro !) C FAUJ880102 0.881 LEVM760104 -0.818 KIMC930101 -0.848 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.52 0.68 0.76 0.76 0.62 0.68 0.68 0.00 0.70 1.02 0.98 0.68 0.78 0.70 0.36 0.53 0.50 0.70 0.70 0.76 // H CHAM820101 D Polarizability parameter (Charton-Charton, 1982) R LIT:0902079b PMID:7183857 A Charton, M. and Charton, B.I. T The structural dependence of amino acid hydrophobicity parameters J J. Theor. Biol. 99, 629-644 (1982) * (Pro 0.018) C FAUJ880103 0.992 CHOC750101 0.982 TSAJ990102 0.978 TSAJ990101 0.977 GOLD730102 0.967 CHOC760101 0.966 BIGC670101 0.966 KRIW790103 0.963 FASG760101 0.962 GRAR740103 0.951 ROSG850101 0.917 LEVM760102 0.915 LEVM760105 0.915 FAUJ880106 0.902 CHAM830106 0.899 LEVM760107 0.891 MCMT640101 0.871 DAWD720101 0.865 RADA880106 0.847 LEVM760106 0.818 HUTJ700102 0.815 CHAM830105 0.809 SNEP660103 0.808 RADA880103 -0.912 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.046 0.291 0.134 0.105 0.128 0.180 0.151 0.000 0.230 0.186 0.186 0.219 0.221 0.290 0.131 0.062 0.108 0.409 0.298 0.140 // H CHAM820102 D Free energy of solution in water, kcal/mole (Charton-Charton, 1982) R LIT:0902079b PMID:7183857 A Charton, M. and Charton, B.I. T The structural dependence of amino acid hydrophobicity parameters J J. Theor. Biol. 99, 629-644 (1982) * (Asn His Lys Thr !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.368 -1.03 0. 2.06 4.53 0.731 1.77 -0.525 0. 0.791 1.07 0. 0.656 1.06 -2.24 -0.524 0. 1.60 4.91 0.401 // H CHAM830101 D The Chou-Fasman parameter of the coil conformation (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) C CHOP780101 0.946 CHOP780216 0.942 PALJ810106 0.939 GEIM800111 0.938 CHOP780203 0.931 QIAN880132 0.925 TANS770110 0.917 GEIM800108 0.916 QIAN880133 0.913 LEVM780103 0.909 PRAM900104 0.909 CHOP780210 0.905 LEVM780106 0.900 ISOY800103 0.881 QIAN880131 0.860 NAGK730103 0.857 ROBB760113 0.841 QIAN880134 0.841 PALJ810105 0.826 CRAJ730103 0.821 QIAN880135 0.814 ROBB760108 0.812 ROBB760110 0.804 AVBF000102 -0.803 QIAN880105 -0.803 PALJ810102 -0.808 FAUJ880102 -0.809 ISOY800101 -0.815 RICJ880109 -0.826 CHOP780201 -0.828 AURR980113 -0.828 ROBB760101 -0.828 AURR980108 -0.834 PTIO830101 -0.841 AURR980114 -0.842 BEGF750101 -0.854 QIAN880106 -0.856 QIAN880107 -0.858 ROBB760103 -0.878 KANM800103 -0.889 SUEM840101 -0.891 AURR980109 -0.896 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.71 1.06 1.37 1.21 1.19 0.87 0.84 1.52 1.07 0.66 0.69 0.99 0.59 0.71 1.61 1.34 1.08 0.76 1.07 0.63 // H CHAM830102 D A parameter defined from the residuals obtained from the best correlation of the Chou-Fasman parameter of beta-sheet (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.118 0.124 0.289 0.048 0.083 -0.105 -0.245 0.104 0.138 0.230 -0.052 0.032 -0.258 0.015 0. 0.225 0.166 0.158 0.094 0.513 // H CHAM830103 D The number of atoms in the side chain labelled 1+1 (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C AVBF000101 0.843 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 1. 1. 1. 1. 1. 1. 0. 1. 2. 1. 1. 1. 1. 0. 1. 2. 1. 1. 2. // H CHAM830104 D The number of atoms in the side chain labelled 2+1 (Charton-Charton, 1983) R LIT:0907093b PMID: A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 1. 1. 1. 0. 1. 1. 0. 1. 1. 2. 1. 1. 1. 0. 0. 0. 1. 1. 0. // H CHAM830105 D The number of atoms in the side chain labelled 3+1 (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C CHAM830106 0.874 LEVM760102 0.843 FASG760101 0.839 CHOC760101 0.833 LEVM760105 0.829 FAUJ880103 0.813 CHAM820101 0.809 RADA880103 -0.808 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 1. 0. 0. 0. 1. 1. 0. 1. 0. 0. 1. 1. 1. 0. 0. 0. 1.5 1. 0. // H CHAM830106 D The number of bonds in the longest chain (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C LEVM760102 0.962 LEVM760105 0.958 FASG760101 0.943 CHOC760101 0.937 FAUJ880103 0.927 RADA880106 0.922 CHOC750101 0.906 CHAM820101 0.899 TSAJ990102 0.896 GRAR740103 0.890 TSAJ990101 0.889 KRIW790103 0.876 CHAM830105 0.874 BIGC670101 0.870 GOLD730102 0.869 OOBM770102 0.858 FAUJ880106 0.845 FAUJ880104 0.817 RADA880103 -0.901 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 5. 2. 2. 1. 3. 3. 0. 3. 2. 2. 4. 3. 4. 0. 1. 1. 5. 5. 1. // H CHAM830107 D A parameter of charge transfer capability (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 0. 1. 1. 0. 0. 1. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. // H CHAM830108 D A parameter of charge transfer donor capability (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 1. 1. 0. 1. 1. 0. 0. 1. 0. 0. 1. 1. 1. 0. 0. 0. 1. 1. 0. // H CHOC750101 D Average volume of buried residue (Chothia, 1975) R PMID:1118010 A Chothia, C. T Structural invariants in protein folding J Nature 254, 304-308 (1975) * (Arg missing) C TSAJ990102 0.996 TSAJ990101 0.995 FAUJ880103 0.990 BIGC670101 0.990 GOLD730102 0.989 CHAM820101 0.982 KRIW790103 0.982 CHOC760101 0.981 GRAR740103 0.973 FASG760101 0.956 LEVM760105 0.939 LEVM760102 0.933 ROSG850101 0.908 CHAM830106 0.906 DAWD720101 0.901 FAUJ880106 0.888 RADA880106 0.867 LEVM760107 0.858 LEVM760106 0.841 MCMT640101 0.822 HUTJ700102 0.802 RADA880103 -0.892 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 91.5 202.0 135.2 124.5 117.7 161.1 155.1 66.4 167.3 168.8 167.9 171.3 170.8 203.4 129.3 99.1 122.1 237.6 203.6 141.7 // H CHOC760101 D Residue accessible surface area in tripeptide (Chothia, 1976) R LIT:2004094b PMID:994183 A Chothia, C. T The nature of the accessible and buried surfaces in proteins J J. Mol. Biol. 105, 1-14 (1976) C FAUJ880103 0.985 CHOC750101 0.981 FASG760101 0.978 LEVM760102 0.972 TSAJ990102 0.972 LEVM760105 0.968 TSAJ990101 0.968 CHAM820101 0.966 GOLD730102 0.960 BIGC670101 0.960 KRIW790103 0.948 GRAR740103 0.945 CHAM830106 0.937 DAWD720101 0.901 FAUJ880106 0.898 RADA880106 0.875 WOLS870102 0.845 ROSG850101 0.842 FAUJ880104 0.835 CHAM830105 0.833 OOBM770102 0.824 HUTJ700102 0.819 MCMT640101 0.809 LEVM760107 0.807 RADA880103 -0.924 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 115. 225. 160. 150. 135. 180. 190. 75. 195. 175. 170. 200. 185. 210. 145. 115. 140. 255. 230. 155. // H CHOC760102 D Residue accessible surface area in folded protein (Chothia, 1976) R LIT:2004094b PMID:994183 A Chothia, C. T The nature of the accessible and buried surfaces in proteins J J. Mol. Biol. 105, 1-14 (1976) C JANJ780101 0.973 JANJ780103 0.959 OOBM770101 0.925 FAUJ880109 0.872 ROSM880102 0.845 MEIH800102 0.839 PRAM900101 0.826 RACS770102 0.809 GUYH850101 0.807 MEIH800103 -0.802 EISD860103 -0.802 NADH010104 -0.809 JANJ790101 -0.809 RADA880101 -0.814 ROSG850102 -0.819 DESM900102 -0.823 RADA880104 -0.830 KYTJ820101 -0.838 WOLR810101 -0.840 NADH010103 -0.840 CHOC760104 -0.845 WARP780101 -0.849 JURD980101 -0.851 EISD840101 -0.892 NADH010102 -0.893 CHOC760103 -0.912 RADA880107 -0.925 JANJ780102 -0.935 JANJ790102 -0.969 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 25. 90. 63. 50. 19. 71. 49. 23. 43. 18. 23. 97. 31. 24. 50. 44. 47. 32. 60. 18. // H CHOC760103 D Proportion of residues 95% buried (Chothia, 1976) R LIT:2004094b PMID:994183 A Chothia, C. T The nature of the accessible and buried surfaces in proteins J J. Mol. Biol. 105, 1-14 (1976) C JURD980101 0.967 KYTJ820101 0.964 JANJ780102 0.950 NADH010102 0.910 CHOC760104 0.907 JANJ790102 0.905 EISD860103 0.892 JANJ790101 0.887 EISD840101 0.885 NADH010101 0.881 DESM900102 0.877 NADH010103 0.875 WOLR810101 0.873 RADA880107 0.870 MEIH800103 0.865 MANP780101 0.859 RADA880101 0.853 ROSG850102 0.851 NADH010104 0.848 PONP800103 0.837 PONP800102 0.836 PONP800101 0.830 RADA880108 0.830 WARP780101 0.824 NAKH920108 0.824 BIOV880101 0.823 RADA880104 0.821 PONP930101 0.816 PONP800107 0.813 MIYS850101 0.810 LIFS790102 0.810 PONP800108 0.809 FAUJ880109 -0.806 PRAM900101 -0.814 ROSM880101 -0.819 GUYH850101 -0.856 KUHL950101 -0.865 ROSM880102 -0.869 RACS770102 -0.875 JANJ780103 -0.888 JANJ780101 -0.892 MEIH800102 -0.894 OOBM770101 -0.902 CHOC760102 -0.912 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.38 0.01 0.12 0.15 0.45 0.07 0.18 0.36 0.17 0.60 0.45 0.03 0.40 0.50 0.18 0.22 0.23 0.27 0.15 0.54 // H CHOC760104 D Proportion of residues 100% buried (Chothia, 1976) R LIT:2004094b PMID:994183 A Chothia, C. T The nature of the accessible and buried surfaces in proteins J J. Mol. Biol. 105, 1-14 (1976) * (normalized by the total number) C CHOC760103 0.907 JANJ780102 0.903 KYTJ820101 0.889 JANJ790101 0.886 JURD980101 0.870 WOLR810101 0.868 PONP800104 0.844 JANJ790102 0.835 DESM900102 0.824 NADH010102 0.817 WARP780101 0.815 NADH010101 0.804 CHOC760102 -0.845 JANJ780103 -0.851 JANJ780101 -0.854 OOBM770101 -0.857 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.20 0.00 0.03 0.04 0.22 0.01 0.03 0.18 0.02 0.19 0.16 0.00 0.11 0.14 0.04 0.08 0.08 0.04 0.03 0.18 // H CHOP780101 D Normalized frequency of beta-turn (Chou-Fasman, 1978a) R LIT:2004003a PMID:354496 A Chou, P.Y. and Fasman, G.D. T Empirical predictions of protein conformation J Ann. Rev. Biochem. 47, 251-276 (1978) C PALJ810106 0.977 TANS770110 0.956 CHAM830101 0.946 CHOP780203 0.940 CHOP780216 0.929 CHOP780210 0.921 ROBB760113 0.907 GEIM800108 0.899 QIAN880133 0.897 QIAN880132 0.896 LEVM780103 0.893 PRAM900104 0.891 LEVM780106 0.890 ROBB760108 0.887 BEGF750103 0.885 ISOY800103 0.885 CRAJ730103 0.882 GEIM800111 0.878 PALJ810105 0.868 ROBB760110 0.863 NAGK730103 0.827 QIAN880131 0.824 AURR980114 -0.803 BEGF750101 -0.803 QIAN880107 -0.809 KANM800103 -0.824 AURR980109 -0.837 SUEM840101 -0.845 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.66 0.95 1.56 1.46 1.19 0.98 0.74 1.56 0.95 0.47 0.59 1.01 0.60 0.60 1.52 1.43 0.96 0.96 1.14 0.50 // H CHOP780201 D Normalized frequency of alpha-helix (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C PALJ810102 0.981 ROBB760101 0.969 ISOY800101 0.959 MAXF760101 0.956 KANM800101 0.956 TANS770101 0.947 BURA740101 0.917 GEIM800101 0.912 KANM800103 0.912 NAGK730101 0.886 LEVM780104 0.886 PALJ810101 0.881 QIAN880106 0.874 PRAM900102 0.873 LEVM780101 0.873 GEIM800104 0.868 RACS820108 0.868 AURR980108 0.867 AURR980109 0.859 AURR980112 0.856 CRAJ730101 0.851 QIAN880107 0.843 BEGF750101 0.841 QIAN880105 0.835 AURR980114 0.828 AURR980115 0.816 AURR980110 0.814 PALJ810109 0.814 AURR980111 0.813 ROBB760103 0.806 MUNV940101 -0.802 CRAJ730103 -0.808 ROBB760113 -0.811 MUNV940102 -0.812 CHAM830101 -0.828 NAGK730103 -0.837 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.42 0.98 0.67 1.01 0.70 1.11 1.51 0.57 1.00 1.08 1.21 1.16 1.45 1.13 0.57 0.77 0.83 1.08 0.69 1.06 // H CHOP780202 D Normalized frequency of beta-sheet (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C PALJ810104 0.970 LIFS790101 0.947 KANM800102 0.945 PALJ810103 0.937 ROBB760106 0.931 LEVM780105 0.930 GEIM800107 0.929 QIAN880120 0.915 PTIO830102 0.913 QIAN880121 0.911 LIFS790103 0.908 GEIM800105 0.890 ROBB760105 0.885 PONP930101 0.867 NAGK730102 0.858 QIAN880119 0.855 CHOP780208 0.851 KANM800104 0.839 GEIM800106 0.839 PRAM900103 0.833 LEVM780102 0.833 NISK860101 0.832 SWER830101 0.823 CHOP780209 0.822 PALJ810112 0.815 PONP800108 0.809 PALJ810110 0.808 MANP780101 0.805 VENT840101 0.805 VINM940102 -0.810 OOBM770103 -0.820 GEIM800110 -0.824 VINM940101 -0.831 MUNV940103 -0.892 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.83 0.93 0.89 0.54 1.19 1.10 0.37 0.75 0.87 1.60 1.30 0.74 1.05 1.38 0.55 0.75 1.19 1.37 1.47 1.70 // H CHOP780203 D Normalized frequency of beta-turn (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C CHOP780216 0.979 CHOP780101 0.940 TANS770110 0.940 LEVM780106 0.935 GEIM800111 0.933 ISOY800103 0.933 CHAM830101 0.931 PRAM900104 0.928 QIAN880132 0.928 LEVM780103 0.927 GEIM800108 0.925 CHOP780210 0.918 QIAN880133 0.915 PALJ810106 0.907 PALJ810105 0.878 QIAN880131 0.861 QIAN880134 0.838 RACS770101 0.827 QIAN880135 0.811 QIAN880119 -0.814 PONP800107 -0.818 SUEM840101 -0.892 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.74 1.01 1.46 1.52 0.96 0.96 0.95 1.56 0.95 0.47 0.50 1.19 0.60 0.66 1.56 1.43 0.98 0.60 1.14 0.59 // H CHOP780204 D Normalized frequency of N-terminal helix (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C ROBB760102 0.911 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.29 0.44 0.81 2.02 0.66 1.22 2.44 0.76 0.73 0.67 0.58 0.66 0.71 0.61 2.01 0.74 1.08 1.47 0.68 0.61 // H CHOP780205 D Normalized frequency of C-terminal helix (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C ROBB760104 0.841 QIAN880109 0.806 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.20 1.25 0.59 0.61 1.11 1.22 1.24 0.42 1.77 0.98 1.13 1.83 1.57 1.10 0.00 0.96 0.75 0.40 0.73 1.25 // H CHOP780206 D Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.70 0.34 1.42 0.98 0.65 0.75 1.04 1.41 1.22 0.78 0.85 1.01 0.83 0.93 1.10 1.55 1.09 0.62 0.99 0.75 // H CHOP780207 D Normalized frequency of C-terminal non helical region (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.52 1.24 1.64 1.06 0.94 0.70 0.59 1.64 1.86 0.87 0.84 1.49 0.52 1.04 1.58 0.93 0.86 0.16 0.96 0.32 // H CHOP780208 D Normalized frequency of N-terminal beta-sheet (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C NAGK730102 0.860 CHOP780202 0.851 ROBB760106 0.846 LIFS790101 0.820 QIAN880119 0.807 KANM800102 0.804 QIAN880120 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.86 0.90 0.66 0.38 0.87 1.65 0.35 0.63 0.54 1.94 1.30 1.00 1.43 1.50 0.66 0.63 1.17 1.49 1.07 1.69 // H CHOP780209 D Normalized frequency of C-terminal beta-sheet (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C PALJ810104 0.849 CHOP780202 0.822 VENT840101 0.817 PTIO830102 0.814 QIAN880121 0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.75 0.90 1.21 0.85 1.11 0.65 0.55 0.74 0.90 1.35 1.27 0.74 0.95 1.50 0.40 0.79 0.75 1.19 1.96 1.79 // H CHOP780210 D Normalized frequency of N-terminal non beta region (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C CHOP780101 0.921 CHOP780203 0.918 PALJ810106 0.905 CHAM830101 0.905 CHOP780216 0.896 GEIM800108 0.896 GEIM800111 0.867 TANS770110 0.858 QIAN880132 0.852 LEVM780103 0.852 PRAM900104 0.850 ISOY800103 0.829 QIAN880131 0.826 QIAN880133 0.820 NAGK730103 0.814 LEVM780106 0.812 PALJ810105 0.803 RICJ880111 -0.804 BEGF750101 -0.804 RICJ880107 -0.818 PONP800107 -0.820 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.67 0.89 1.86 1.39 1.34 1.09 0.92 1.46 0.78 0.59 0.46 1.09 0.52 0.30 1.58 1.41 1.09 0.48 1.23 0.42 // H CHOP780211 D Normalized frequency of C-terminal non beta region (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C ROBB760112 0.841 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.74 1.05 1.13 1.32 0.53 0.77 0.85 1.68 0.96 0.53 0.59 0.82 0.85 0.44 1.69 1.49 1.16 1.59 1.01 0.59 // H CHOP780212 D Frequency of the 1st residue in turn (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C PALJ810106 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.060 0.070 0.161 0.147 0.149 0.074 0.056 0.102 0.140 0.043 0.061 0.055 0.068 0.059 0.102 0.120 0.086 0.077 0.082 0.062 // H CHOP780213 D Frequency of the 2nd residue in turn (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C TANS770104 0.954 ISOY800104 0.916 QIAN880134 0.870 QIAN880135 0.851 MUNV940104 0.836 FINA910102 0.832 MUNV940105 0.826 BUNA790101 -0.822 BLAM930101 -0.824 PTIO830101 -0.835 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.076 0.106 0.083 0.110 0.053 0.098 0.060 0.085 0.047 0.034 0.025 0.115 0.082 0.041 0.301 0.139 0.108 0.013 0.065 0.048 // H CHOP780214 D Frequency of the 3rd residue in turn (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C ISOY800105 0.923 TANS770105 0.862 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.035 0.099 0.191 0.179 0.117 0.037 0.077 0.190 0.093 0.013 0.036 0.072 0.014 0.065 0.034 0.125 0.065 0.064 0.114 0.028 // H CHOP780215 D Frequency of the 4th residue in turn (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C ROBB760111 0.825 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.058 0.085 0.091 0.081 0.128 0.098 0.064 0.152 0.054 0.056 0.070 0.095 0.055 0.065 0.068 0.106 0.079 0.167 0.125 0.053 // H CHOP780216 D Normalized frequency of the 2nd and 3rd residues in turn (Chou-Fasman, 1978b) R PMID:364941 A Chou, P.Y. and Fasman, G.D. T Prediction of the secondary structure of proteins from their amino acid sequence J Adv. Enzymol. 47, 45-148 (1978) C CHOP780203 0.979 GEIM800111 0.955 LEVM780106 0.953 LEVM780103 0.952 PRAM900104 0.951 CHAM830101 0.942 GEIM800108 0.942 QIAN880133 0.939 QIAN880132 0.931 TANS770110 0.930 CHOP780101 0.929 ISOY800103 0.921 PALJ810106 0.904 QIAN880134 0.900 CHOP780210 0.896 QIAN880135 0.884 PALJ810105 0.881 QIAN880131 0.873 NAGK730103 0.819 QIAN880120 -0.800 FAUJ880102 -0.807 KANM800103 -0.808 QIAN880107 -0.808 ROBB760103 -0.841 PTIO830101 -0.855 SUEM840101 -0.874 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.64 1.05 1.56 1.61 0.92 0.84 0.80 1.63 0.77 0.29 0.36 1.13 0.51 0.62 2.04 1.52 0.98 0.48 1.08 0.43 // H CIDH920101 D Normalized hydrophobicity scales for alpha-proteins (Cid et al., 1992) R LIT:1817105b PMID:1518784 A Cid, H., Bunster, M., Canales, M. and Gazitua, F. T Hydrophobicity and structural classes in proteins J Protein Engineering 5, 373-375 (1992) C CIDH920102 0.921 CIDH920105 0.921 NISK860101 0.882 WERD780101 0.878 CIDH920103 0.872 RADA880108 0.858 SWER830101 0.853 BIOV880101 0.847 ROBB790101 0.846 MIYS850101 0.843 PLIV810101 0.843 CIDH920104 0.833 ROSG850101 0.831 LEVM760106 0.826 BIOV880102 0.819 PONP800101 0.805 VINM940103 -0.814 OOBM770103 -0.818 KARP850102 -0.828 RACS770101 -0.837 VINM940101 -0.854 FUKS010103 -0.854 MEIH800101 -0.863 KARP850101 -0.864 PARJ860101 -0.871 PARS000101 -0.877 VINM940102 -0.885 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.45 -0.24 -0.20 -1.52 0.79 -0.99 -0.80 -1.00 1.07 0.76 1.29 -0.36 1.37 1.48 -0.12 -0.98 -0.70 1.38 1.49 1.26 // H CIDH920102 D Normalized hydrophobicity scales for beta-proteins (Cid et al., 1992) R LIT:1817105b PMID:1518784 A Cid, H., Bunster, M., Canales, M. and Gazitua, F. T Hydrophobicity and structural classes in proteins J Protein Engineering 5, 373-375 (1992) C CIDH920105 0.969 CIDH920101 0.921 CIDH920103 0.911 CIDH920104 0.904 NISK860101 0.897 ROBB790101 0.896 NOZY710101 0.889 MEEJ810101 0.887 PLIV810101 0.877 LEVM760106 0.873 MIYS850101 0.873 WERD780101 0.871 SWER830101 0.870 ROSG850101 0.866 BIOV880101 0.864 RADA880102 0.862 ARGP820101 0.862 JOND750101 0.861 TAKK010101 0.859 MEEJ800102 0.856 FAUJ830101 0.856 MEEJ810102 0.843 BIOV880102 0.837 WIMW960101 0.837 RADA880108 0.833 SIMZ760101 0.832 GUOD860101 0.831 GOLD730101 0.829 PONP930101 0.820 EISD860101 0.819 ZASB820101 0.809 LIFS790101 0.808 RACS770101 -0.825 VINM940103 -0.826 FUKS010103 -0.826 GRAR740102 -0.842 BULH740101 -0.851 MEIH800101 -0.867 WOLS870101 -0.869 PARS000101 -0.871 VINM940101 -0.872 KARP850101 -0.873 OOBM770103 -0.877 VINM940102 -0.925 PARJ860101 -0.930 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.08 -0.09 -0.70 -0.71 0.76 -0.40 -1.31 -0.84 0.43 1.39 1.24 -0.09 1.27 1.53 -0.01 -0.93 -0.59 2.25 1.53 1.09 // H CIDH920103 D Normalized hydrophobicity scales for alpha+beta-proteins (Cid et al., 1992) R LIT:1817105b PMID:1518784 A Cid, H., Bunster, M., Canales, M. and Gazitua, F. T Hydrophobicity and structural classes in proteins J Protein Engineering 5, 373-375 (1992) C CIDH920105 0.973 CIDH920104 0.955 CIDH920102 0.911 NISK860101 0.909 MIYS850101 0.906 MANP780101 0.905 PLIV810101 0.899 PONP930101 0.899 RADA880108 0.891 BIOV880101 0.887 ROBB790101 0.884 WERD780101 0.881 PONP800101 0.876 CIDH920101 0.872 FAUJ830101 0.868 SWER830101 0.865 BIOV880102 0.860 NISK800101 0.855 PONP800102 0.849 ROSG850102 0.846 GUOD860101 0.845 PONP800108 0.841 MEEJ810101 0.837 PONP800107 0.833 ARGP820101 0.827 JOND750101 0.826 PONP800103 0.823 EISD860101 0.821 RADA880102 0.819 LIFS790101 0.815 PTIO830102 0.807 MEIH800103 0.802 FUKS010103 -0.804 KRIW790101 -0.819 PARS000101 -0.821 MEIH800102 -0.825 RACS770102 -0.834 VINM940101 -0.837 BULH740101 -0.848 KARP850102 -0.852 VINM940102 -0.855 OOBM770103 -0.863 GRAR740102 -0.871 WOLS870101 -0.879 RACS770101 -0.881 MEIH800101 -0.905 PARJ860101 -0.916 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.36 -0.52 -0.90 -1.09 0.70 -1.05 -0.83 -0.82 0.16 2.17 1.18 -0.56 1.21 1.01 -0.06 -0.60 -1.20 1.31 1.05 1.21 // H CIDH920104 D Normalized hydrophobicity scales for alpha/beta-proteins (Cid et al., 1992) R LIT:1817105b PMID:1518784 A Cid, H., Bunster, M., Canales, M. and Gazitua, F. T Hydrophobicity and structural classes in proteins J Protein Engineering 5, 373-375 (1992) C CIDH920105 0.970 CIDH920103 0.955 NISK860101 0.944 BIOV880101 0.933 PONP930101 0.930 FAUJ830101 0.922 MANP780101 0.918 MIYS850101 0.915 RADA880108 0.914 PONP800108 0.909 CIDH920102 0.904 ROBB790101 0.903 NISK800101 0.900 ROSG850102 0.896 WERD780101 0.896 PLIV810101 0.893 BIOV880102 0.890 PONP800101 0.888 NADH010104 0.888 NADH010103 0.885 PONP800102 0.880 MEEJ810101 0.878 NADH010105 0.869 NADH010101 0.865 PONP800103 0.863 SWER830101 0.862 GUOD860101 0.860 NADH010102 0.856 MEIH800103 0.853 PTIO830102 0.842 MEEJ810102 0.837 EISD860103 0.834 CIDH920101 0.833 PONP800107 0.832 JURD980101 0.832 LIFS790101 0.832 KYTJ820101 0.824 ARGP820101 0.819 JOND750101 0.818 RADA880102 0.817 EISD860101 0.812 JANJ780102 0.803 DESM900102 0.802 KARP850101 -0.801 GUYH850101 -0.821 KUHL950101 -0.822 WOEC730101 -0.823 ROSM880101 -0.828 BULH740101 -0.829 ROSM880102 -0.831 KARP850102 -0.833 VINM940103 -0.835 RACS770102 -0.854 RACS770101 -0.864 KRIW790101 -0.867 MEIH800102 -0.868 VINM940101 -0.883 VINM940102 -0.884 WOLS870101 -0.891 OOBM770103 -0.912 PARJ860101 -0.913 GRAR740102 -0.915 MEIH800101 -0.917 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.17 -0.70 -0.90 -1.05 1.24 -1.20 -1.19 -0.57 -0.25 2.06 0.96 -0.62 0.60 1.29 -0.21 -0.83 -0.62 1.51 0.66 1.21 // H CIDH920105 D Normalized average hydrophobicity scales (Cid et al., 1992) R LIT:1817105b PMID:1518784 A Cid, H., Bunster, M., Canales, M. and Gazitua, F. T Hydrophobicity and structural classes in proteins J Protein Engineering 5, 373-375 (1992) C CIDH920103 0.973 CIDH920104 0.970 CIDH920102 0.969 NISK860101 0.938 ROBB790101 0.921 CIDH920101 0.921 MIYS850101 0.916 PLIV810101 0.914 BIOV880101 0.912 WERD780101 0.905 RADA880108 0.898 FAUJ830101 0.893 MEEJ810101 0.892 PONP930101 0.891 SWER830101 0.890 BIOV880102 0.882 MANP780101 0.879 ARGP820101 0.867 JOND750101 0.866 RADA880102 0.861 GUOD860101 0.858 ROSG850102 0.858 NOZY710101 0.857 PONP800101 0.856 NISK800101 0.854 MEEJ810102 0.844 PONP800108 0.843 MEEJ800102 0.840 TAKK010101 0.840 EISD860101 0.839 SIMZ760101 0.837 PONP800102 0.831 LIFS790101 0.828 LEVM760106 0.828 GOLD730101 0.820 PONP800107 0.818 NADH010104 0.817 PTIO830102 0.813 VENT840101 0.813 NADH010103 0.810 PONP800103 0.807 MEIH800103 0.804 NADH010105 0.800 WOEC730101 -0.800 KRIW790101 -0.816 FUKS010103 -0.821 MEIH800102 -0.826 RACS770102 -0.830 VINM940103 -0.832 KARP850102 -0.839 PARS000101 -0.860 KARP850101 -0.866 BULH740101 -0.871 GRAR740102 -0.884 VINM940101 -0.885 RACS770101 -0.887 WOLS870101 -0.899 OOBM770103 -0.904 VINM940102 -0.910 MEIH800101 -0.923 PARJ860101 -0.948 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.02 -0.42 -0.77 -1.04 0.77 -1.10 -1.14 -0.80 0.26 1.81 1.14 -0.41 1.00 1.35 -0.09 -0.97 -0.77 1.71 1.11 1.13 // H COHE430101 D Partial specific volume (Cohn-Edsall, 1943) R A Cohn, E.J. and Edsall, J.T. T J "Protein, Amino Acid, and Peptides", Reinhold, New York (1943) C BULH740102 0.923 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.75 0.70 0.61 0.60 0.61 0.67 0.66 0.64 0.67 0.90 0.90 0.82 0.75 0.77 0.76 0.68 0.70 0.74 0.71 0.86 // H CRAJ730101 D Normalized frequency of middle helix (Crawford et al., 1973) R PMID:4510294 A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G. T The reverse turn as a polypeptide conformation in globular proteins J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) * Reported values normalized by the total percentage C NAGK730101 0.925 BURA740101 0.900 PALJ810101 0.891 PRAM900102 0.887 LEVM780101 0.887 ROBB760101 0.875 PALJ810102 0.872 GEIM800101 0.870 LEVM780104 0.869 CHOP780201 0.851 TANS770101 0.843 KANM800101 0.842 ISOY800101 0.840 RACS820108 0.839 GEIM800104 0.838 MAXF760101 0.826 PALJ810109 0.811 NAGK730103 -0.850 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.33 0.79 0.72 0.97 0.93 1.42 1.66 0.58 1.49 0.99 1.29 1.03 1.40 1.15 0.49 0.83 0.94 1.33 0.49 0.96 // H CRAJ730102 D Normalized frequency of beta-sheet (Crawford et al., 1973) R PMID:4510294 A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G. T The reverse turn as a polypeptide conformation in globular proteins J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) * Reported values normalized by the total percentage C ROBB760106 0.865 PTIO830102 0.820 PALJ810104 0.817 NAGK730102 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.00 0.74 0.75 0.89 0.99 0.87 0.37 0.56 0.36 1.75 1.53 1.18 1.40 1.26 0.36 0.65 1.15 0.84 1.41 1.61 // H CRAJ730103 D Normalized frequency of turn (Crawford et al., 1973) R PMID:4510294 A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G. T The reverse turn as a polypeptide conformation in globular proteins J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) * Reported values normalized by the total percentage C ROBB760113 0.916 ROBB760108 0.912 ROBB760110 0.887 PALJ810106 0.884 CHOP780101 0.882 BEGF750103 0.874 TANS770110 0.859 CHAM830101 0.821 CHOP780201 -0.808 PALJ810102 -0.809 BEGF750101 -0.812 QIAN880107 -0.840 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.60 0.79 1.42 1.24 1.29 0.92 0.64 1.38 0.95 0.67 0.70 1.10 0.67 1.05 1.47 1.26 1.05 1.23 1.35 0.48 // H DAWD720101 D Size (Dawson, 1972) R A Dawson, D.M. T J In "The Biochemical Genetics of Man" (Brock, D.J.H. and Mayo, O., eds.), Academic Press, New York, pp.1-38 (1972) C TSAJ990102 0.905 GOLD730102 0.904 TSAJ990101 0.903 BIGC670101 0.903 CHOC750101 0.901 CHOC760101 0.901 LEVM760105 0.898 KRIW790103 0.893 FAUJ880103 0.880 LEVM760102 0.873 CHAM820101 0.865 FAUJ880106 0.853 GRAR740103 0.853 FASG760101 0.833 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.5 7.5 5.0 2.5 3.0 6.0 5.0 0.5 6.0 5.5 5.5 7.0 6.0 6.5 5.5 3.0 5.0 7.0 7.0 5.0 // H DAYM780101 D Amino acid composition (Dayhoff et al., 1978a) R A Dayhoff, M.O., Hunt, L.T. and Hurst-Calderone, S. T Composition of proteins J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., ed.), National Biomedical Research Foundation, Washington, D.C., p.363 (1978) C JUNJ780101 0.986 JUKT750101 0.975 CEDJ970101 0.970 JOND920101 0.954 CEDJ970104 0.952 CEDJ970102 0.945 NAKH900101 0.940 KUMS000102 0.925 FUKS010110 0.897 NAKH900102 0.883 FUKS010111 0.882 NAKH920101 0.882 KUMS000101 0.866 NAKH920107 0.861 FUKS010112 0.856 NAKH920106 0.856 NAKH920103 0.851 CEDJ970105 0.839 NAKH920104 0.819 CEDJ970103 0.807 NAKH920102 0.802 FUKS010109 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.6 4.9 4.3 5.5 2.9 3.9 6.0 8.4 2.0 4.5 7.4 6.6 1.7 3.6 5.2 7.0 6.1 1.3 3.4 6.6 // H DAYM780201 D Relative mutability (Dayhoff et al., 1978b) R A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. T A model of evolutionary change in proteins J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., ed.), National Biomedical Research Foundation, Washington, D.C. pp. 345-352 (1978) C JOND920102 0.889 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 100. 65. 134. 106. 20. 93. 102. 49. 66. 96. 40. 56. 94. 41. 56. 120. 97. 18. 41. 74. // H DESM900101 D Membrane preference for cytochrome b: MPH89 (Degli Esposti et al., 1990) R LIT:1612111b PMID:2364947 A Degli Esposti, M., Crimi, M. and Venturoli, G. T A critical evaluation of the hydropathy profile of membrane proteins J Eur. J. Biochem. 190, 207-219 (1990) C DESM900102 0.955 PONP800103 0.887 NADH010102 0.885 PONP800102 0.871 NADH010103 0.866 ROSG850102 0.866 WARP780101 0.864 JANJ780102 0.853 MEIH800103 0.853 PONP800101 0.847 NADH010104 0.843 KYTJ820101 0.837 NISK800101 0.837 JURD980101 0.829 NADH010101 0.825 BIOV880102 0.821 JANJ790102 0.818 RADA880108 0.812 BIOV880101 0.807 PONP930101 0.807 RACS770102 -0.801 VINM940101 -0.806 KRIW710101 -0.807 MEIH800102 -0.822 KARP850102 -0.829 GUYH850101 -0.831 KRIW790102 -0.835 RACS770103 -0.837 JANJ780103 -0.838 KRIW790101 -0.847 MONM990101 -0.848 OOBM770101 -0.894 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.56 0.59 0.51 0.23 1.80 0.39 0.19 1.03 1. 1.27 1.38 0.15 1.93 1.42 0.27 0.96 1.11 0.91 1.10 1.58 // H DESM900102 D Average membrane preference: AMP07 (Degli Esposti et al., 1990) R LIT:1612111b PMID:2364947 A Degli Esposti, M., Crimi, M. and Venturoli, G. T A critical evaluation of the hydropathy profile of membrane proteins J Eur. J. Biochem. 190, 207-219 (1990) C DESM900101 0.955 JANJ780102 0.935 NADH010102 0.933 MEIH800103 0.924 ROSG850102 0.914 NADH010103 0.910 NADH010101 0.905 JURD980101 0.900 KYTJ820101 0.898 JANJ790102 0.897 PONP800103 0.896 NADH010104 0.886 WARP780101 0.882 RADA880108 0.881 PONP800102 0.880 BIOV880101 0.878 CHOC760103 0.877 BIOV880102 0.876 PONP800101 0.858 JANJ790101 0.855 NISK800101 0.852 EISD860103 0.848 NISK860101 0.843 PONP930101 0.834 PONP800108 0.833 MIYS850101 0.831 RADA880101 0.828 EISD840101 0.828 CHOC760104 0.824 MANP780101 0.816 NADH010105 0.816 FAUJ830101 0.816 WERD780101 0.814 CIDH920104 0.802 VINM940104 -0.803 MEIH800101 -0.804 ROSM880101 -0.812 KARP850102 -0.815 ROSM880102 -0.816 CHOC760102 -0.823 VINM940103 -0.824 VINM940101 -0.829 WOEC730101 -0.847 MONM990101 -0.850 KRIW790102 -0.852 KRIW790101 -0.859 GRAR740102 -0.862 KUHL950101 -0.863 RACS770102 -0.867 RACS770103 -0.868 JANJ780101 -0.878 PRAM900101 -0.890 GUYH850101 -0.895 MEIH800102 -0.898 JANJ780103 -0.908 OOBM770101 -0.950 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.26 0.38 0.59 0.27 1.60 0.39 0.23 1.08 1. 1.44 1.36 0.33 1.52 1.46 0.54 0.98 1.01 1.06 0.89 1.33 // H EISD840101 D Consensus normalized hydrophobicity scale (Eisenberg, 1984) R LIT:2004004a PMID:6383201 A Eisenberg, D. T Three-dimensional structure of membrane and surface proteins J Ann. Rev. Biochem. 53, 595-623 (1984) * Original references: * Eisenberg, D., Weiss, R.M., Terwilliger, T.C. and Wilcox, W. * Faraday Symp. Chem. Soc. 17, 109-120 (1982) * Eisenberg, D., Weiss, R.M. and Terwilliger, T.C. * The hydrophobic moment detects periodicity in protein hydrophobicity * Proc. Natl. Acad. Sci. USA 81, 140-144 (1984) C RADA880101 0.968 RADA880107 0.927 WOLR810101 0.914 RADA880104 0.908 JANJ790102 0.900 JURD980101 0.895 NADH010102 0.887 CHOC760103 0.885 EISD860101 0.884 KYTJ820101 0.878 FAUJ830101 0.875 JANJ780102 0.874 NADH010101 0.861 NADH010103 0.840 NAKH900110 0.838 EISD860103 0.837 DESM900102 0.828 RADA880108 0.817 BIOV880102 0.814 BIOV880101 0.811 YUTK870101 0.809 NADH010104 0.809 ROSG850102 0.806 WOLS870101 -0.820 GRAR740102 -0.823 MEIH800102 -0.829 HOPT810101 -0.846 GUYH850101 -0.849 LEVM760101 -0.859 OOBM770101 -0.878 JANJ780103 -0.881 FAUJ880109 -0.890 CHOC760102 -0.892 JANJ780101 -0.907 KUHL950101 -0.907 VHEG790101 -0.924 ROSM880102 -0.925 PRAM900101 -0.936 ROSM880101 -0.947 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.25 -1.76 -0.64 -0.72 0.04 -0.69 -0.62 0.16 -0.40 0.73 0.53 -1.10 0.26 0.61 -0.07 -0.26 -0.18 0.37 0.02 0.54 // H EISD860101 D Solvation free energy (Eisenberg-McLachlan, 1986) R LIT:2004121b PMID: 3945310 A Eisenberg, D. and McLachlan, A.D. T Solvation energy in protein folding and binding J Nature 319, 199-203 (1986) C FAUJ830101 0.919 RADA880102 0.912 PLIV810101 0.904 ZIMJ680105 0.900 RADA880101 0.891 MEEJ800102 0.890 EISD840101 0.884 RADA880108 0.844 MIYS850101 0.842 GUOD860101 0.839 CIDH920105 0.839 BIOV880102 0.832 BIOV880101 0.828 SWER830101 0.824 NOZY710101 0.822 CIDH920103 0.821 NAKH900110 0.820 CIDH920102 0.819 CIDH920104 0.812 NAKH900104 0.812 NAKH900106 0.812 MEEJ810102 0.808 MEEJ810101 0.805 GUYH850101 -0.823 BULH740101 -0.833 KUHL950101 -0.835 WOEC730101 -0.838 PRAM900101 -0.862 VHEG790101 -0.862 ROSM880102 -0.868 GRAR740102 -0.871 PARJ860101 -0.876 HOPT810101 -0.905 ROSM880101 -0.917 WOLS870101 -0.918 LEVM760101 -0.921 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.67 -2.1 -0.6 -1.2 0.38 -0.22 -0.76 0. 0.64 1.9 1.9 -0.57 2.4 2.3 1.2 0.01 0.52 2.6 1.6 1.5 // H EISD860102 D Atom-based hydrophobic moment (Eisenberg-McLachlan, 1986) R LIT:2004121b PMID: 3945310 A Eisenberg, D. and McLachlan, A.D. T Solvation energy in protein folding and binding J Nature 319, 199-203 (1986) C FAUJ880109 0.841 HUTJ700103 0.841 RADA880107 -0.837 YUTK870103 -0.839 YUTK870104 -0.840 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 10. 1.3 1.9 0.17 1.9 3. 0. 0.99 1.2 1.0 5.7 1.9 1.1 0.18 0.73 1.5 1.6 1.8 0.48 // H EISD860103 D Direction of hydrophobic moment (Eisenberg-McLachlan, 1986) R LIT:2004121b PMID: 3945310 A Eisenberg, D. and McLachlan, A.D. T Solvation energy in protein folding and binding J Nature 319, 199-203 (1986) * (Gly Ala missing) C JURD980101 0.901 KYTJ820101 0.897 CHOC760103 0.892 JANJ780102 0.883 FAUJ830101 0.876 RADA880108 0.873 NADH010102 0.872 MEIH800103 0.870 NADH010101 0.868 BIOV880101 0.864 MIYS850101 0.858 NADH010103 0.855 PLIV810101 0.852 RADA880101 0.850 DESM900102 0.848 ROSG850102 0.846 BIOV880102 0.845 PONP800103 0.842 NADH010104 0.840 JANJ790102 0.838 EISD840101 0.837 CIDH920104 0.834 JANJ790101 0.829 MANP780101 0.826 WARP780101 0.820 PONP800102 0.814 RADA880107 0.812 NISK860101 0.811 ARGP820103 0.810 PONP800108 0.809 CHOC760102 -0.802 WOEC730101 -0.803 JANJ780101 -0.808 MEIH800101 -0.810 FAUJ880110 -0.815 JANJ780103 -0.819 PRAM900101 -0.831 GUYH850101 -0.832 WOLS870101 -0.841 RACS770102 -0.858 ROSM880101 -0.871 GRAR740102 -0.871 OOBM770101 -0.880 MEIH800102 -0.882 KUHL950101 -0.894 ROSM880102 -0.943 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. -0.96 -0.86 -0.98 0.76 -1.0 -0.89 0. -0.75 0.99 0.89 -0.99 0.94 0.92 0.22 -0.67 0.09 0.67 -0.93 0.84 // H FASG760101 D Molecular weight (Fasman, 1976) R A Fasman, G.D., ed. T J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume 1, CRC Press, Cleveland (1976) C FAUJ880103 0.979 CHOC760101 0.978 LEVM760102 0.966 CHAM820101 0.962 CHOC750101 0.956 LEVM760105 0.951 CHAM830106 0.943 TSAJ990102 0.940 TSAJ990101 0.935 BIGC670101 0.919 GOLD730102 0.918 KRIW790103 0.910 GRAR740103 0.908 FAUJ880106 0.899 RADA880106 0.870 WOLS870102 0.866 MCMT640101 0.845 CHAM830105 0.839 ROSG850101 0.838 DAWD720101 0.833 FAUJ880104 0.825 OOBM770102 0.821 LEVM760107 0.815 RADA880103 -0.954 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 89.09 174.20 132.12 133.10 121.15 146.15 147.13 75.07 155.16 131.17 131.17 146.19 149.21 165.19 115.13 105.09 119.12 204.24 181.19 117.15 // H FASG760102 D Melting point (Fasman, 1976) R A Fasman, G.D., ed. T J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume 1, CRC Press, Cleveland (1976) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 297. 238. 236. 270. 178. 185. 249. 290. 277. 284. 337. 224. 283. 284. 222. 228. 253. 282. 344. 293. // H FASG760103 D Optical rotation (Fasman, 1976) R A Fasman, G.D., ed. T J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume 1, CRC Press, Cleveland (1976) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.80 12.50 -5.60 5.05 -16.50 6.30 12.00 0.00 -38.50 12.40 -11.00 14.60 -10.00 -34.50 -86.20 -7.50 -28.00 -33.70 -10.00 5.63 // H FASG760104 D pK-N (Fasman, 1976) R A Fasman, G.D., ed. T J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume 1, CRC Press, Cleveland (1976) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.69 8.99 8.80 9.60 8.35 9.13 9.67 9.78 9.17 9.68 9.60 9.18 9.21 9.18 10.64 9.21 9.10 9.44 9.11 9.62 // H FASG760105 D pK-C (Fasman, 1976) R A Fasman, G.D., ed. T J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume 1, CRC Press, Cleveland (1976) C JOND750102 0.833 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.34 1.82 2.02 1.88 1.92 2.17 2.10 2.35 1.82 2.36 2.36 2.16 2.28 2.16 1.95 2.19 2.09 2.43 2.20 2.32 // H FAUJ830101 D Hydrophobic parameter pi (Fauchere-Pliska, 1983) R LIT:0912085 A Fauchere, J.L. and Pliska, V. T Hydrophobic parameters pi of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides J Eur. J. Med. Chem. 18, 369-375 (1983) C BIOV880101 0.942 RADA880108 0.932 PLIV810101 0.931 CIDH920104 0.922 EISD860101 0.919 MIYS850101 0.914 BIOV880102 0.911 NISK860101 0.906 ROSG850102 0.904 MEEJ810101 0.902 GUOD860101 0.900 NADH010103 0.899 NADH010104 0.894 CIDH920105 0.893 NADH010102 0.891 MEEJ810102 0.890 EISD860103 0.876 EISD840101 0.875 PONP800108 0.875 RADA880101 0.873 ROBB790101 0.868 CIDH920103 0.868 PONP800103 0.863 WERD780101 0.862 MEEJ800102 0.858 CIDH920102 0.856 NISK800101 0.849 MEIH800103 0.849 RADA880102 0.846 MANP780101 0.843 PONP930101 0.843 PONP800102 0.841 NADH010101 0.837 SWER830101 0.833 JURD980101 0.833 JANJ790102 0.826 JANJ780102 0.825 NADH010105 0.822 PONP800101 0.822 ZIMJ680105 0.816 DESM900102 0.816 KYTJ820101 0.811 NOZY710101 0.803 VINM940103 -0.804 FUKS010102 -0.805 BULH740101 -0.830 OOBM770101 -0.832 FUKS010104 -0.832 RACS770102 -0.843 VINM940102 -0.844 PRAM900101 -0.853 GUYH850101 -0.863 MEIH800101 -0.863 KUHL950101 -0.863 KRIW790101 -0.865 VINM940101 -0.871 MEIH800102 -0.875 WOEC730101 -0.880 OOBM770103 -0.899 PARJ860101 -0.907 ROSM880101 -0.907 HOPT810101 -0.909 LEVM760101 -0.919 ROSM880102 -0.927 WOLS870101 -0.928 GRAR740102 -0.948 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.31 -1.01 -0.60 -0.77 1.54 -0.22 -0.64 0.00 0.13 1.80 1.70 -0.99 1.23 1.79 0.72 -0.04 0.26 2.25 0.96 1.22 // H FAUJ880101 D Graph shape index (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * Original reference: * Kier, L.B. * Quant. Struct. Act. Relat. 6, 117-122 (1987) C ZIMJ680102 0.888 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.28 2.34 1.60 1.60 1.77 1.56 1.56 0.00 2.99 4.19 2.59 1.89 2.35 2.94 2.67 1.31 3.03 3.21 2.94 3.67 // H FAUJ880102 D Smoothed upsilon steric parameter (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * (Pro missing) * Original reference of these two data: * Fauchere, L.J. * In "QSAR in Design of Bioactive Compounds", (Kuchar, M., ed.), * Prous, Barcelona pp.135-144 (1984) C AVBF000102 0.881 CHAM810101 0.881 PTIO830101 0.832 CHOP780216 -0.807 CHAM830101 -0.809 GEIM800108 -0.819 MUNV940104 -0.824 PRAM900104 -0.844 LEVM780103 -0.846 QIAN880132 -0.849 QIAN880133 -0.851 QIAN880134 -0.852 LEVM780106 -0.865 GEIM800111 -0.873 KIMC930101 -0.886 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.53 0.69 0.58 0.59 0.66 0.71 0.72 0.00 0.64 0.96 0.92 0.78 0.77 0.71 0. 0.55 0.63 0.84 0.71 0.89 // H FAUJ880103 D Normalized van der Waals volume (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * (Pro !) * Original reference of these two data: * Fauchere, L.J. * In "QSAR in Design of Bioactive Compounds", (Kuchar, M., ed.), * Prous, Barcelona pp.135-144 (1984) C CHAM820101 0.992 CHOC750101 0.990 CHOC760101 0.985 TSAJ990102 0.985 TSAJ990101 0.983 FASG760101 0.979 BIGC670101 0.972 GOLD730102 0.972 KRIW790103 0.965 GRAR740103 0.959 LEVM760102 0.947 LEVM760105 0.945 CHAM830106 0.927 FAUJ880106 0.908 ROSG850101 0.892 DAWD720101 0.880 LEVM760107 0.875 RADA880106 0.869 MCMT640101 0.847 WOLS870102 0.814 CHAM830105 0.813 HUTJ700102 0.807 FAUJ880104 0.804 OOBM770102 0.801 RADA880103 -0.923 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.00 6.13 2.95 2.78 2.43 3.95 3.78 0.00 4.66 4.00 4.00 4.77 4.43 5.89 2.72 1.60 2.60 8.08 6.47 3.00 // H FAUJ880104 D STERIMOL length of the side chain (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * (Pro !) * Original reference of these three data: * Verloop, A. * In "IUPAC, Pesticide Chemistry", Vol.1 * (Miyamoto, J. and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983) C LEVM760105 0.896 LEVM760102 0.867 HUTJ700103 0.839 CHOC760101 0.835 HUTJ700102 0.835 FASG760101 0.825 CHAM830106 0.817 FAUJ880103 0.804 RADA880103 -0.806 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.87 7.82 4.58 4.74 4.47 6.11 5.97 2.06 5.23 4.92 4.92 6.89 6.36 4.62 4.11 3.97 4.11 7.68 4.73 4.11 // H FAUJ880105 D STERIMOL minimum width of the side chain (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * (Pro !) * Original reference of these three data: * Verloop, A. * In "IUPAC, Pesticide Chemistry", Vol.1 * (Miyamoto, J. and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983) C AVBF000102 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.52 1.52 1.52 1.52 1.52 1.52 1.52 1.00 1.52 1.90 1.52 1.52 1.52 1.52 1.52 1.52 1.73 1.52 1.52 1.90 // H FAUJ880106 D STERIMOL maximum width of the side chain (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * Original reference of these three data: * Verloop, A. * In "IUPAC, Pesticide Chemistry", Vol.1 * (Miyamoto, J. and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983) C FAUJ880103 0.908 CHAM820101 0.902 LEVM760102 0.900 FASG760101 0.899 CHOC760101 0.898 LEVM760105 0.889 CHOC750101 0.888 TSAJ990102 0.882 TSAJ990101 0.879 WOLS870102 0.866 BIGC670101 0.860 GOLD730102 0.857 DAWD720101 0.853 KRIW790103 0.845 CHAM830106 0.845 GRAR740103 0.819 HUTJ700102 0.806 RADA880103 -0.823 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.04 6.24 4.37 3.78 3.41 3.53 3.31 1.00 5.66 3.49 4.45 4.87 4.80 6.02 4.31 2.70 3.17 5.90 6.72 3.17 // H FAUJ880107 D N.m.r. chemical shift of alpha-carbon (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * Original reference: * Fauchere, J.L. and Lauterwein, J. * Quant. Struct. Act. Rel. 4, 11-13 (1985) C AVBF000105 0.931 AVBF000107 0.884 AVBF000103 0.873 AVBF000106 0.853 AVBF000108 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.3 11.1 8.0 9.2 14.4 10.6 11.4 0.0 10.2 16.1 10.1 10.9 10.4 13.9 17.8 13.1 16.7 13.2 13.9 17.2 // H FAUJ880108 D Localized electrical effect (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * (Pro missing) * Original reference: * Charton, M. and Charton, B.I. * J. Theor. Biol. 102, 121-134 (1983) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.01 0.04 0.06 0.15 0.12 0.05 0.07 0.00 0.08 -0.01 -0.01 0.00 0.04 0.03 0. 0.11 0.04 0.00 0.03 0.01 // H FAUJ880109 D Number of hydrogen bond donors (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * Original reference of these two data: * IUPAC-IUB Joint Commission on Biochemical Nomenclature * Eur. J. Biochem. 138, 9-37 (1984) C CHOC760102 0.872 JANJ780101 0.850 ROSM880101 0.846 EISD860102 0.841 KUHL950101 0.827 ROSM880102 0.824 PRAM900101 0.815 CHOC760103 -0.806 JANJ790102 -0.822 RADA880101 -0.873 RADA880105 -0.889 EISD840101 -0.890 WOLR810101 -0.904 RADA880104 -0.926 RADA880107 -0.957 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 4. 2. 1. 0. 2. 1. 0. 1. 0. 0. 2. 0. 0. 0. 1. 1. 1. 1. 0. // H FAUJ880110 D Number of full nonbonding orbitals (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * Original reference of these two data: * IUPAC-IUB Joint Commission on Biochemical Nomenclature * Eur. J. Biochem. 138, 9-37 (1984) C KUHL950101 0.922 ROSM880101 0.888 WOEC730101 0.812 SNEP660102 -0.804 NADH010101 -0.813 EISD860103 -0.815 RADA880101 -0.838 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 3. 3. 4. 0. 3. 4. 0. 1. 0. 0. 1. 0. 0. 0. 2. 2. 0. 2. 0. // H FAUJ880111 D Positive charge (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) C ZIMJ680104 0.813 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 1. 0. 0. 0. 0. 0. 0. 1. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. // H FAUJ880112 D Negative charge (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) C RICJ880106 0.849 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 0. 0. 1. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. // H FAUJ880113 D pK-a(RCOOH) (Fauchere et al., 1988) R LIT:1414114 PMID:3209351 A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. T Amino acid side chain parameters for correlation studies in biology and pharmacology J Int. J. Peptide Protein Res. 32, 269-278 (1988) * (Pro missing) C BLAM930101 0.839 ONEK900101 0.820 BUNA790101 0.818 ROBB760103 0.802 MUNV940102 -0.826 MUNV940101 -0.836 ONEK900102 -0.839 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.76 4.30 3.64 5.69 3.67 4.54 5.48 3.77 2.84 4.81 4.79 4.27 4.25 4.31 0. 3.83 3.87 4.75 4.30 4.86 // H FINA770101 D Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977) R LIT:2004052b PMID:843599 A Finkelstein, A.V. and Ptitsyn, O.B. T Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments J Biopolymers 16, 497-524 (1977) * (Pro 0.096) C SUEM840101 0.883 AURR980114 0.875 AURR980113 0.849 PTIO830101 0.826 KANM800103 0.823 QIAN880107 0.814 QIAN880106 0.810 MAXF760101 0.810 AURR980109 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.08 1.05 0.85 0.85 0.95 0.95 1.15 0.55 1.00 1.05 1.25 1.15 1.15 1.10 0.71 0.75 0.75 1.10 1.10 0.95 // H FINA910101 D Helix initiation parameter at posision i-1 (Finkelstein et al., 1991) R LIT:1716158b PMID:1946339 A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. T Physical reasons for secondary structure stability: alpha-helices in short peptides J PROTEINS 10, 287-299 (1991) * In these four data, each of Arg, Asp, Glu, His and Lys has two value. * See comment lines. * Arg pH < 12 ( 1 when pH > 12 ) * Asp pH > 4 ( 1.7 when pH < 4 ) * Glu pH > 4.3 ( 1 when pH < 4.3 ) * His pH > 6.3 ( 0.7 when pH < 6.3 ) * Lys pH < 10.5 ( 1 when pH > 10.5 ) C MONM990201 0.812 AURR980104 0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1. 0.70 1.70 3.20 1. 1. 1.70 1. 1. 0.60 1. 0.70 1. 1. 1. 1.70 1.70 1. 1. 0.60 // H FINA910102 D Helix initiation parameter at posision i,i+1,i+2 (Finkelstein et al., 1991) R LIT:1716158b PMID:1946339 A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. T Physical reasons for secondary structure stability: alpha-helices in short peptides J PROTEINS 10, 287-299 (1991) * In these four data, each of Arg, Asp, Glu, His and Lys has two value. * See comment lines. * Arg pH < 12 ( 1 when pH > 12 ) * Asp pH > 4 ( 1 when pH < 4 ) * Glu pH > 4.3 ( 1 when pH < 4.3 ) * His pH > 6.3 ( 0.7 when pH < 6.3 ) * Lys pH < 10.5 ( 1 when pH > 10.5 ) * (Pro !) C ONEK900102 0.964 MUNV940105 0.911 AVBF000104 0.901 MUNV940104 0.896 TANS770104 0.876 ISOY800104 0.844 CHOP780213 0.832 ROBB760104 -0.844 ONEK900101 -0.920 BLAM930101 -0.961 BUNA790101 -0.992 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1. 0.70 1. 1.70 1. 1. 1.70 1.30 1. 1. 1. 0.70 1. 1. 13. 1. 1. 1. 1. 1. // H FINA910103 D Helix termination parameter at posision j-2,j-1,j (Finkelstein et al., 1991) R LIT:1716158b PMID:1946339 A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. T Physical reasons for secondary structure stability: alpha-helices in short peptides J PROTEINS 10, 287-299 (1991) * In these four data, each of Arg, Asp, Glu, His and Lys has two value. * See comment lines. * Arg pH < 12 ( 1 when pH > 12 ) * Asp pH > 4 ( 1 when pH < 4 ) * Glu pH > 4.3 ( 1 when pH < 4.3 ) * His pH > 6.3 ( 1.7 when pH < 6.3 ) * Lys pH < 10.5 ( 1 when pH > 10.5 ) C ZIMJ680104 0.805 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.20 1.70 1.20 0.70 1. 1. 0.70 0.80 1.20 0.80 1. 1.70 1. 1. 1. 1.50 1. 1. 1. 0.80 // H FINA910104 D Helix termination parameter at posision j+1 (Finkelstein et al., 1991) R LIT:1716158b PMID:1946339 A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B. T Physical reasons for secondary structure stability: alpha-helices in short peptides J PROTEINS 10, 287-299 (1991) * In these four data, each of Arg, Asp, Glu, His and Lys has two value. * See comment lines. * Arg pH < 12 ( 1 when pH > 12 ) * Asp pH > 4 ( 1 when pH < 4 ) * Glu pH > 4.3 ( 1 when pH < 4.3 ) * His pH > 6.3 ( 1.7 when pH < 6.3 ) * Lys pH < 10.5 ( 1 when pH > 10.5 ) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1. 1.70 1. 0.70 1. 1. 0.70 1.50 1. 1. 1. 1.70 1. 1. 0.10 1. 1. 1. 1. 1. // H GARJ730101 D Partition coefficient (Garel et al., 1973) R LIT:2004092b PMID:4700470 A Garel, J.P., Filliol, D. and Mandel, P. T Coefficients de partage d'aminoacides, nucleobases, nucleosides et nucleotides dans un systeme solvant salin J J. Chromatogr. 78, 381-391 (1973) C LEVM760107 0.860 NOZY710101 0.821 OOBM850102 -0.877 WEBA780101 -0.924 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.28 0.10 0.25 0.21 0.28 0.35 0.33 0.17 0.21 0.82 1.00 0.09 0.74 2.18 0.39 0.12 0.21 5.70 1.26 0.60 // H GEIM800101 D Alpha-helix indices (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C PALJ810101 0.951 LEVM780104 0.950 KANM800101 0.942 TANS770101 0.918 CHOP780201 0.912 NAGK730101 0.912 PRAM900102 0.912 LEVM780101 0.912 PALJ810102 0.910 GEIM800104 0.903 ISOY800101 0.903 ROBB760101 0.897 MAXF760101 0.895 KANM800103 0.881 RACS820108 0.880 CRAJ730101 0.870 BURA740101 0.858 PALJ810109 0.816 AURR980115 0.804 AURR980112 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.29 1. 0.81 1.10 0.79 1.07 1.49 0.63 1.33 1.05 1.31 1.33 1.54 1.13 0.63 0.78 0.77 1.18 0.71 0.81 // H GEIM800102 D Alpha-helix indices for alpha-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C PALJ810107 0.919 GEIM800109 -0.993 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.13 1.09 1.06 0.94 1.32 0.93 1.20 0.83 1.09 1.05 1.13 1.08 1.23 1.01 0.82 1.01 1.17 1.32 0.88 1.13 // H GEIM800103 D Alpha-helix indices for beta-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.55 0.20 1.20 1.55 1.44 1.13 1.67 0.59 1.21 1.27 1.25 1.20 1.37 0.40 0.21 1.01 0.55 1.86 1.08 0.64 // H GEIM800104 D Alpha-helix indices for alpha/beta-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C PALJ810109 0.937 KANM800101 0.916 LEVM780101 0.907 PRAM900102 0.907 GEIM800101 0.903 MAXF760101 0.897 ISOY800101 0.891 PALJ810102 0.886 LEVM780104 0.872 CHOP780201 0.868 ROBB760101 0.855 RACS820108 0.851 PALJ810101 0.841 TANS770101 0.841 CRAJ730101 0.838 NAGK730101 0.828 BURA740101 0.819 AURR980112 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.19 1. 0.94 1.07 0.95 1.32 1.64 0.60 1.03 1.12 1.18 1.27 1.49 1.02 0.68 0.81 0.85 1.18 0.77 0.74 // H GEIM800105 D Beta-strand indices (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C PALJ810103 0.945 LEVM780105 0.926 KANM800102 0.916 GEIM800107 0.901 CHOP780202 0.890 ROBB760105 0.877 KANM800104 0.861 PALJ810104 0.856 ROBB760106 0.856 LIFS790101 0.855 TANS770103 0.850 ISOY800102 0.843 LIFS790103 0.832 PALJ810112 0.830 QIAN880119 0.829 QIAN880120 0.822 MAXF760102 0.819 QIAN880121 0.811 PTIO830102 0.810 QIAN880118 0.810 MUNV940103 -0.841 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.84 1.04 0.66 0.59 1.27 1.02 0.57 0.94 0.81 1.29 1.10 0.86 0.88 1.15 0.80 1.05 1.20 1.15 1.39 1.56 // H GEIM800106 D Beta-strand indices for beta-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C GEIM800107 0.878 PALJ810110 0.851 CHOP780202 0.839 ROBB760106 0.838 QIAN880120 0.825 KANM800102 0.821 LIFS790103 0.814 MUNV940103 -0.800 GEIM800110 -0.929 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.86 1.15 0.60 0.66 0.91 1.11 0.37 0.86 1.07 1.17 1.28 1.01 1.15 1.34 0.61 0.91 1.14 1.13 1.37 1.31 // H GEIM800107 D Beta-strand indices for alpha/beta-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C KANM800102 0.955 CHOP780202 0.929 PALJ810104 0.928 PALJ810112 0.905 GEIM800105 0.901 ROBB760106 0.899 PALJ810103 0.890 LIFS790101 0.888 LEVM780105 0.884 GEIM800106 0.878 KANM800104 0.876 QIAN880121 0.875 PTIO830102 0.850 QIAN880120 0.843 PRAM900103 0.842 LEVM780102 0.842 PONP930101 0.838 ROBB760105 0.836 NAGK730102 0.830 PALJ810110 0.826 LIFS790103 0.823 PONP800108 0.817 NISK860101 0.813 QIAN880119 0.807 GEIM800110 -0.815 VINM940101 -0.819 MUNV940103 -0.869 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.91 0.99 0.72 0.74 1.12 0.90 0.41 0.91 1.01 1.29 1.23 0.86 0.96 1.26 0.65 0.93 1.05 1.15 1.21 1.58 // H GEIM800108 D Aperiodic indices (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C GEIM800111 0.967 CHOP780216 0.942 LEVM780106 0.932 PRAM900104 0.931 LEVM780103 0.931 QIAN880133 0.930 ISOY800103 0.930 CHOP780203 0.925 CHAM830101 0.916 QIAN880132 0.906 CHOP780101 0.899 CHOP780210 0.896 TANS770110 0.886 QIAN880134 0.884 QIAN880135 0.877 PALJ810105 0.873 GEIM800110 0.870 PALJ810106 0.862 QIAN880131 0.860 MUNV940103 0.806 ROBB760103 -0.802 QIAN880120 -0.804 QIAN880119 -0.810 FAUJ880102 -0.819 PTIO830101 -0.840 SUEM840101 -0.875 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.91 1. 1.64 1.40 0.93 0.94 0.97 1.51 0.90 0.65 0.59 0.82 0.58 0.72 1.66 1.23 1.04 0.67 0.92 0.60 // H GEIM800109 D Aperiodic indices for alpha-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C PALJ810107 -0.909 GEIM800102 -0.993 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.80 0.96 1.10 1.60 0. 1.60 0.40 2. 0.96 0.85 0.80 0.94 0.39 1.20 2.10 1.30 0.60 0. 1.80 0.80 // H GEIM800110 D Aperiodic indices for beta-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C MUNV940103 0.880 GEIM800108 0.870 GEIM800111 0.857 QIAN880134 0.853 QIAN880135 0.842 PARS000101 0.831 QIAN880133 0.822 LEVM780106 0.809 QIAN880121 -0.806 KANM800102 -0.814 GEIM800107 -0.815 ROBB760106 -0.819 CHOP780202 -0.824 AVBF000101 -0.825 PALJ810110 -0.840 QIAN880119 -0.853 LIFS790101 -0.862 LIFS790103 -0.889 QIAN880120 -0.898 GEIM800106 -0.929 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.10 0.93 1.57 1.41 1.05 0.81 1.40 1.30 0.85 0.67 0.52 0.94 0.69 0.60 1.77 1.13 0.88 0.62 0.41 0.58 // H GEIM800111 D Aperiodic indices for alpha/beta-proteins (Geisow-Roberts, 1980) R LIT:0701087b A Geisow, M.J. and Roberts, R.D.B. T Amino acid preferences for secondary structure vary with protein class J Int. J. Biol. Macromol. 2, 387-389 (1980) C GEIM800108 0.967 CHOP780216 0.955 PRAM900104 0.954 LEVM780103 0.952 LEVM780106 0.951 QIAN880133 0.943 CHAM830101 0.938 CHOP780203 0.933 ISOY800103 0.929 QIAN880132 0.929 QIAN880134 0.919 QIAN880135 0.895 TANS770110 0.883 CHOP780101 0.878 CHOP780210 0.867 QIAN880131 0.857 GEIM800110 0.857 PALJ810105 0.855 PALJ810106 0.844 LIFS790101 -0.801 AVBF000101 -0.806 KANM800103 -0.812 AURR980109 -0.814 QIAN880120 -0.816 ROBB760103 -0.843 FAUJ880102 -0.873 PTIO830101 -0.876 SUEM840101 -0.885 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.93 1.01 1.36 1.22 0.92 0.83 1.05 1.45 0.96 0.58 0.59 0.91 0.60 0.71 1.67 1.25 1.08 0.68 0.98 0.62 // H GOLD730101 D Hydrophobicity factor (Goldsack-Chalifoux, 1973) R LIT:2004110b PMID:4354159 A Goldsack, D.E. and Chalifoux, R.C. T Contribution of the free energy of mixing of hydrophobic side chains to the stability of the tertiary structure J J. Theor. Biol. 39, 645-651 (1973) * (Asn Gln !) C SIMZ760101 0.939 ARGP820101 0.936 JOND750101 0.935 TAKK010101 0.872 MEEJ800102 0.866 LAWE840101 0.829 CIDH920102 0.829 LEVM760106 0.827 BULH740102 0.825 MEEJ810101 0.824 ZIMJ680105 0.820 CIDH920105 0.820 ZIMJ680102 0.818 MEEJ800101 0.808 MEEJ810102 0.806 VENT840101 0.802 PARJ860101 -0.827 WOLS870101 -0.854 BULH740101 -0.874 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.75 0.75 0.69 0.00 1.00 0.59 0.00 0.00 0.00 2.95 2.40 1.50 1.30 2.65 2.60 0.00 0.45 3.00 2.85 1.70 // H GOLD730102 D Residue volume (Goldsack-Chalifoux, 1973) R LIT:2004110b PMID:4354159 A Goldsack, D.E. and Chalifoux, R.C. T Contribution of the free energy of mixing of hydrophobic side chains to the stability of the tertiary structure J J. Theor. Biol. 39, 645-651 (1973) * (Asn Gln 8.8) C BIGC670101 1.000 KRIW790103 0.994 TSAJ990101 0.993 TSAJ990102 0.991 CHOC750101 0.989 GRAR740103 0.984 FAUJ880103 0.972 CHAM820101 0.967 CHOC760101 0.960 FASG760101 0.918 LEVM760105 0.911 ROSG850101 0.909 DAWD720101 0.904 LEVM760102 0.893 LEVM760106 0.875 CHAM830106 0.869 LEVM760107 0.865 FAUJ880106 0.857 RADA880106 0.854 MCMT640101 0.814 RADA880103 -0.864 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 88.3 181.2 125.1 110.8 112.4 148.7 140.5 60.0 152.6 168.5 168.5 175.6 162.2 189.0 122.2 88.7 118.2 227.0 193.0 141.4 // H GRAR740101 D Composition (Grantham, 1974) R LIT:2004143b PMID:4843792 A Grantham, R. T Amino acid difference formula to help explain protein evolution J Science 185, 862-864 (1974) * (Atomic weight ratio of noncarbons to carbons in the side chain) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 0.00 0.00 0.33 0.00 0.00 0.39 1.42 0.71 0.13 0.20 0.00 // H GRAR740102 D Polarity (Grantham, 1974) R LIT:2004143b PMID:4843792 A Grantham, R. T Amino acid difference formula to help explain protein evolution J Science 185, 862-864 (1974) C WOEC730101 0.960 WOLS870101 0.910 OOBM770103 0.896 PARJ860101 0.891 ROSM880101 0.887 HOPT810101 0.874 ROSM880102 0.870 VINM940101 0.869 LEVM760101 0.865 KUHL950101 0.865 PRAM900101 0.855 KRIW790101 0.847 OOBM770101 0.841 VINM940102 0.837 MEIH800102 0.836 MONM990101 0.831 MEIH800101 0.824 BULH740101 0.822 GUYH850101 0.818 WIMW960101 -0.804 JANJ780102 -0.809 MEEJ810102 -0.811 NADH010105 -0.812 EISD840101 -0.823 WERD780101 -0.826 ROBB790101 -0.832 MEEJ810101 -0.839 CIDH920102 -0.842 PONP800101 -0.849 GUOD860101 -0.855 KYTJ820101 -0.859 NADH010101 -0.859 RADA880101 -0.861 DESM900102 -0.862 JURD980101 -0.864 MEIH800103 -0.866 NADH010104 -0.868 MANP780101 -0.868 PONP800102 -0.871 EISD860101 -0.871 EISD860103 -0.871 CIDH920103 -0.871 PONP930101 -0.872 NISK800101 -0.879 ROSG850102 -0.880 BIOV880102 -0.881 NADH010103 -0.881 NADH010102 -0.881 CIDH920105 -0.884 PLIV810101 -0.888 MIYS850101 -0.895 SWER830101 -0.896 PONP800103 -0.897 RADA880108 -0.899 NISK860101 -0.900 PONP800108 -0.907 BIOV880101 -0.910 CIDH920104 -0.915 FAUJ830101 -0.948 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9 // H GRAR740103 D Volume (Grantham, 1974) R LIT:2004143b PMID:4843792 A Grantham, R. T Amino acid difference formula to help explain protein evolution J Science 185, 862-864 (1974) C KRIW790103 0.989 BIGC670101 0.984 GOLD730102 0.984 TSAJ990101 0.979 TSAJ990102 0.978 CHOC750101 0.973 FAUJ880103 0.959 CHAM820101 0.951 CHOC760101 0.945 ROSG850101 0.922 RADA880106 0.920 FASG760101 0.908 LEVM760105 0.900 CHAM830106 0.890 LEVM760102 0.885 DAWD720101 0.853 LEVM760106 0.846 LEVM760107 0.841 FAUJ880106 0.819 MCMT640101 0.817 RADA880103 -0.881 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 31. 124. 56. 54. 55. 85. 83. 3. 96. 111. 111. 119. 105. 132. 32.5 32. 61. 170. 136. 84. // H GUYH850101 D Partition energy (Guy, 1985) R LIT:2004051b PMID:3978191 A Guy, H.R. T Amino acid side-chain partition energies and distribution of residues in soluble proteins J Biophys. J. 47, 61-70 (1985) C MEIH800102 0.934 RACS770102 0.934 MEIH800101 0.893 KRIW790101 0.885 VINM940103 0.865 KRIW790102 0.864 RACS770101 0.853 OOBM770101 0.848 KARP850102 0.840 ROSM880102 0.837 KRIW710101 0.831 VINM940101 0.829 JANJ780103 0.829 KUHL950101 0.827 JANJ780101 0.821 PRAM900101 0.820 GRAR740102 0.818 RACS770103 0.816 CHOC760102 0.807 ROSM880101 0.803 HOPT810101 0.802 NISK800101 -0.811 YUTK870101 -0.813 RADA880101 -0.815 PONP930101 -0.817 CIDH920104 -0.821 EISD860101 -0.823 PONP800106 -0.826 DESM900101 -0.831 EISD860103 -0.832 PLIV810101 -0.836 MANP780101 -0.838 KYTJ820101 -0.843 EISD840101 -0.849 NADH010105 -0.855 CHOC760103 -0.856 NADH010101 -0.862 FAUJ830101 -0.863 JURD980101 -0.864 JANJ790102 -0.865 WERD780101 -0.871 JANJ780102 -0.872 PONP800101 -0.877 NISK860101 -0.877 MEIH800103 -0.880 PONP800102 -0.883 BIOV880102 -0.885 PONP800103 -0.887 DESM900102 -0.895 MIYS850101 -0.909 NADH010104 -0.910 NADH010102 -0.910 NADH010103 -0.916 BIOV880101 -0.929 ROSG850102 -0.929 RADA880108 -0.948 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.10 1.91 0.48 0.78 -1.42 0.95 0.83 0.33 -0.50 -1.13 -1.18 1.40 -1.59 -2.12 0.73 0.52 0.07 -0.51 -0.21 -1.27 // H HOPA770101 D Hydration number (Hopfinger, 1971), Cited by Charton-Charton (1982) R A Hopfinger, A.J. T J "Intermolecular Interactions and Biomolecular Organizations", Wiley, New York (1977) * Cited by Charton-Charton (1982) * (Cys !) C WOEC730101 0.876 ZIMJ680103 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.0 2.3 2.2 6.5 0.1 2.1 6.2 1.1 2.8 0.8 0.8 5.3 0.7 1.4 0.9 1.7 1.5 1.9 2.1 0.9 // H HOPT810101 D Hydrophilicity value (Hopp-Woods, 1981) R LIT:0707598 PMID:6167991 A Hopp, T.P. and Woods, K.R. T Prediction of protein antigenic determinants from amino acid sequecces J Proc. Natl. Acad. Sci. USA 78, 3824-3828 (1981) C LEVM760101 0.985 WOEC730101 0.886 FUKS010104 0.884 PRAM900101 0.881 GRAR740102 0.874 VINM940101 0.859 FUKS010102 0.854 VHEG790101 0.849 ROSM880101 0.848 OOBM770103 0.833 WOLS870101 0.830 PARJ860101 0.819 GUYH850101 0.802 MIYS850101 -0.800 NADH010103 -0.805 NAKH900110 -0.812 ZIMJ680105 -0.816 NADH010102 -0.820 NISK860101 -0.822 ROSG850102 -0.825 MEEJ800102 -0.826 RADA880101 -0.829 RADA880108 -0.831 EISD840101 -0.846 BIOV880101 -0.848 WIMW960101 -0.855 RADA880102 -0.859 BIOV880102 -0.864 EISD860101 -0.905 FAUJ830101 -0.909 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.5 3.0 0.2 3.0 -1.0 0.2 3.0 0.0 -0.5 -1.8 -1.8 3.0 -1.3 -2.5 0.0 0.3 -0.4 -3.4 -2.3 -1.5 // H HUTJ700101 D Heat capacity (Hutchens, 1970) R A Hutchens, J.O. T Heat capacities, absolute entropies, and entropies of formation of amino acids and related compounds J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber Co., Cleveland, Ohio, pp. B60-B61 (1970) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 29.22 26.37 38.30 37.09 50.70 44.02 41.84 23.71 59.64 45.00 48.03 57.10 69.32 48.52 36.13 32.40 35.20 56.92 51.73 40.35 // H HUTJ700102 D Absolute entropy (Hutchens, 1970) R A Hutchens, J.O. T Heat capacities, absolute entropies, and entropies of formation of amino acids and related compounds J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber Co., Cleveland, Ohio, pp. B60-B61 (1970) C HUTJ700103 0.867 LEVM760105 0.864 LEVM760102 0.835 FAUJ880104 0.835 CHOC760101 0.819 CHAM820101 0.815 FAUJ880103 0.807 FAUJ880106 0.806 CHOC750101 0.802 RADA880103 -0.812 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 30.88 68.43 41.70 40.66 53.83 46.62 44.98 24.74 65.99 49.71 50.62 63.21 55.32 51.06 39.21 35.65 36.50 60.00 51.15 42.75 // H HUTJ700103 D Entropy of formation (Hutchens, 1970) R A Hutchens, J.O. T Heat capacities, absolute entropies, and entropies of formation of amino acids and related compounds J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber Co., Cleveland, Ohio, pp. B60-B61 (1970) C HUTJ700102 0.867 EISD860102 0.841 FAUJ880104 0.839 LEVM760105 0.834 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 154.33 341.01 207.90 194.91 219.79 235.51 223.16 127.90 242.54 233.21 232.30 300.46 202.65 204.74 179.93 174.06 205.80 237.01 229.15 207.60 // H ISOY800101 D Normalized relative frequency of alpha-helix (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C MAXF760101 0.982 PALJ810102 0.965 KANM800101 0.963 CHOP780201 0.959 ROBB760101 0.957 KANM800103 0.931 LEVM780101 0.929 PRAM900102 0.929 TANS770101 0.906 LEVM780104 0.904 RACS820108 0.904 QIAN880106 0.903 GEIM800101 0.903 AURR980109 0.894 GEIM800104 0.891 QIAN880107 0.887 PALJ810101 0.882 PALJ810109 0.874 AURR980112 0.870 NAGK730101 0.862 AURR980114 0.857 AURR980108 0.856 AURR980110 0.855 AURR980115 0.844 ROBB760103 0.841 CRAJ730101 0.840 BURA740101 0.839 QIAN880105 0.828 AURR980113 0.815 AURR980111 0.801 CHAM830101 -0.815 NAGK730103 -0.821 MUNV940101 -0.875 MUNV940102 -0.877 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.53 1.17 0.60 1.00 0.89 1.27 1.63 0.44 1.03 1.07 1.32 1.26 1.66 1.22 0.25 0.65 0.86 1.05 0.70 0.93 // H ISOY800102 D Normalized relative frequency of extended structure (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C MAXF760102 0.931 TANS770103 0.929 ROBB760105 0.847 GEIM800105 0.843 PALJ810103 0.807 WOEC730101 -0.803 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.86 0.98 0.74 0.69 1.39 0.89 0.66 0.70 1.06 1.31 1.01 0.77 1.06 1.16 1.16 1.09 1.24 1.17 1.28 1.40 // H ISOY800103 D Normalized relative frequency of bend (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C LEVM780106 0.941 PRAM900104 0.934 CHOP780203 0.933 LEVM780103 0.932 GEIM800108 0.930 GEIM800111 0.929 PALJ810105 0.928 CHOP780216 0.921 QIAN880133 0.908 TANS770110 0.897 QIAN880132 0.892 CHOP780101 0.885 CHAM830101 0.881 CHOP780210 0.829 QIAN880134 0.828 PALJ810116 0.814 PALJ810114 0.809 PALJ810106 0.807 ROBB760112 0.807 AVBF000102 -0.821 SUEM840101 -0.850 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.78 1.06 1.56 1.50 0.60 0.78 0.97 1.73 0.83 0.40 0.57 1.01 0.30 0.67 1.55 1.19 1.09 0.74 1.14 0.44 // H ISOY800104 D Normalized relative frequency of bend R (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C TANS770104 0.918 CHOP780213 0.916 QIAN880134 0.893 MUNV940104 0.866 FINA910102 0.844 MUNV940105 0.844 QIAN880135 0.837 ONEK900102 0.828 ROBB760104 -0.817 ROBB760103 -0.830 PTIO830101 -0.832 BUNA790101 -0.842 QIAN880108 -0.847 BLAM930101 -0.860 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.09 0.97 1.14 0.77 0.50 0.83 0.92 1.25 0.67 0.66 0.44 1.25 0.45 0.50 2.96 1.21 1.33 0.62 0.94 0.56 // H ISOY800105 D Normalized relative frequency of bend S (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C CHOP780214 0.923 TANS770105 0.836 ISOY800108 0.812 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.35 0.75 2.12 2.16 0.50 0.73 0.65 2.40 1.19 0.12 0.58 0.83 0.22 0.89 0.43 1.24 0.85 0.62 1.44 0.43 // H ISOY800106 D Normalized relative frequency of helix end (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C MAXF760106 0.849 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.09 1.07 0.88 1.24 1.04 1.09 1.14 0.27 1.07 0.97 1.30 1.20 0.55 0.80 1.78 1.20 0.99 1.03 0.69 0.77 // H ISOY800107 D Normalized relative frequency of double bend (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.34 2.78 0.92 1.77 1.44 0.79 2.54 0.95 0.00 0.52 1.05 0.79 0.00 0.43 0.37 0.87 1.14 1.79 0.73 0.00 // H ISOY800108 D Normalized relative frequency of coil (Isogai et al., 1980) R LIT:2004053b PMID:7378550 A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A T Characterization of multiple bends in proteins J Biopolymers 19, 1183-1210 (1980) * Recalculated by Kidera using a different set of proteins C MAXF760104 0.945 RICJ880115 0.889 RACS820109 0.848 RACS820106 0.831 TANS770107 0.827 AURR980117 0.822 TANS770109 0.816 ISOY800105 0.812 MAXF760105 0.810 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.47 0.52 2.16 1.15 0.41 0.95 0.64 3.03 0.89 0.62 0.53 0.98 0.68 0.61 0.63 1.03 0.39 0.63 0.83 0.76 // H JANJ780101 D Average accessible surface area (Janin et al., 1978) R LIT:0502087 PMID:731698 A Janin, J., Wodak, S., Levitt, M. and Maigret, B. T Conformation of amino acid side-chains in proteins J J. Mol. Biol. 125, 357-386 (1978) C JANJ780103 0.985 CHOC760102 0.973 OOBM770101 0.953 PRAM900101 0.901 ROSM880102 0.853 FAUJ880109 0.850 MEIH800102 0.843 KUHL950101 0.839 ROSM880101 0.822 GUYH850101 0.821 EISD860103 -0.808 BIOV880102 -0.809 MEIH800103 -0.811 JANJ790101 -0.824 RADA880104 -0.825 NADH010104 -0.832 ROSG850102 -0.836 RADA880101 -0.844 KYTJ820101 -0.852 CHOC760104 -0.854 JURD980101 -0.862 WOLR810101 -0.864 NADH010103 -0.868 WARP780101 -0.869 DESM900102 -0.878 CHOC760103 -0.892 EISD840101 -0.907 RADA880107 -0.917 NADH010102 -0.924 JANJ780102 -0.949 JANJ790102 -0.989 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 27.8 94.7 60.1 60.6 15.5 68.7 68.2 24.5 50.7 22.8 27.6 103.0 33.5 25.5 51.5 42.0 45.0 34.7 55.2 23.7 // H JANJ780102 D Percentage of buried residues (Janin et al., 1978) R LIT:0502087 PMID:731698 A Janin, J., Wodak, S., Levitt, M. and Maigret, B. T Conformation of amino acid side-chains in proteins J J. Mol. Biol. 125, 357-386 (1978) C JANJ790102 0.966 CHOC760103 0.950 NADH010102 0.949 JANJ790101 0.941 DESM900102 0.935 JURD980101 0.928 NADH010103 0.923 KYTJ820101 0.922 ROSG850102 0.909 CHOC760104 0.903 NADH010104 0.898 MEIH800103 0.897 NADH010101 0.892 EISD860103 0.883 PONP800103 0.882 WARP780101 0.878 PONP800102 0.875 BIOV880101 0.875 EISD840101 0.874 RADA880108 0.869 PONP800108 0.863 BIOV880102 0.862 RADA880107 0.856 RADA880101 0.855 DESM900101 0.853 NISK800101 0.853 PONP800101 0.851 WOLR810101 0.851 MANP780101 0.842 PONP930101 0.825 FAUJ830101 0.825 NADH010105 0.814 NISK860101 0.813 MIYS850101 0.806 CIDH920104 0.803 GRAR740102 -0.809 KRIW790102 -0.818 RACS770103 -0.828 ROSM880101 -0.835 KRIW790101 -0.837 PRAM900101 -0.860 RACS770102 -0.869 ROSM880102 -0.870 GUYH850101 -0.872 KUHL950101 -0.890 MEIH800102 -0.907 CHOC760102 -0.935 JANJ780101 -0.949 JANJ780103 -0.957 OOBM770101 -0.968 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 51. 5. 22. 19. 74. 16. 16. 52. 34. 66. 60. 3. 52. 58. 25. 35. 30. 49. 24. 64. // H JANJ780103 D Percentage of exposed residues (Janin et al., 1978) R LIT:0502087 PMID:731698 A Janin, J., Wodak, S., Levitt, M. and Maigret, B. T Conformation of amino acid side-chains in proteins J J. Mol. Biol. 125, 357-386 (1978) C JANJ780101 0.985 OOBM770101 0.965 CHOC760102 0.959 PRAM900101 0.884 MEIH800102 0.873 KRIW790102 0.848 RACS770103 0.847 ROSM880102 0.838 GUYH850101 0.829 KUHL950101 0.826 RACS770102 0.823 VINM940104 0.811 ROSM880101 0.810 KRIW790101 0.805 NADH010101 -0.804 RADA880108 -0.805 PONP800103 -0.812 RADA880101 -0.817 EISD860103 -0.819 WOLR810101 -0.822 BIOV880101 -0.829 JANJ790101 -0.832 DESM900101 -0.838 KYTJ820101 -0.845 CHOC760104 -0.851 JURD980101 -0.853 RADA880107 -0.856 BIOV880102 -0.860 NADH010104 -0.860 MEIH800103 -0.866 ROSG850102 -0.879 EISD840101 -0.881 CHOC760103 -0.888 WARP780101 -0.890 NADH010103 -0.892 DESM900102 -0.908 NADH010102 -0.938 JANJ780102 -0.957 JANJ790102 -0.980 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 15. 67. 49. 50. 5. 56. 55. 10. 34. 13. 16. 85. 20. 10. 45. 32. 32. 17. 41. 14. // H JANJ790101 D Ratio of buried and accessible molar fractions (Janin, 1979) R LIT:2004120b PMID:763335 A Janin, J. T Surface and inside volumes in globular proteins J Nature 277, 491-492 (1979) C JANJ780102 0.941 PONP800102 0.897 CHOC760103 0.887 CHOC760104 0.886 PONP800103 0.886 PONP800108 0.881 NADH010103 0.879 NISK800101 0.875 NADH010102 0.872 NADH010104 0.871 JURD980101 0.868 KYTJ820101 0.867 PONP800101 0.866 JANJ790102 0.860 ROSG850102 0.857 DESM900102 0.855 NADH010101 0.847 NADH010105 0.843 MANP780101 0.842 MEIH800103 0.838 EISD860103 0.829 BIOV880101 0.827 RADA880108 0.824 PONP930101 0.816 CHOC760102 -0.809 KRIW790101 -0.810 KUHL950101 -0.811 KRIW710101 -0.815 MEIH800102 -0.821 JANJ780101 -0.824 JANJ780103 -0.832 OOBM770101 -0.871 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.7 0.1 0.4 0.4 4.6 0.3 0.3 1.8 0.8 3.1 2.4 0.05 1.9 2.2 0.6 0.8 0.7 1.6 0.5 2.9 // H JANJ790102 D Transfer free energy (Janin, 1979) R LIT:2004120b PMID:763335 A Janin, J. T Surface and inside volumes in globular proteins J Nature 277, 491-492 (1979) C JANJ780102 0.966 NADH010102 0.945 RADA880107 0.906 CHOC760103 0.905 EISD840101 0.900 NADH010103 0.899 DESM900102 0.897 ROSG850102 0.892 JURD980101 0.879 WARP780101 0.877 NADH010104 0.868 KYTJ820101 0.866 JANJ790101 0.860 BIOV880102 0.856 RADA880108 0.853 MEIH800103 0.853 BIOV880101 0.848 PONP800103 0.844 RADA880101 0.839 EISD860103 0.838 CHOC760104 0.835 WOLR810101 0.828 FAUJ830101 0.826 PONP800102 0.822 DESM900101 0.818 NADH010101 0.808 PONP800108 0.802 FAUJ880109 -0.822 ROSM880101 -0.824 KRIW790101 -0.825 RACS770103 -0.834 KUHL950101 -0.844 KRIW790102 -0.847 RACS770102 -0.851 GUYH850101 -0.865 ROSM880102 -0.866 PRAM900101 -0.890 MEIH800102 -0.894 OOBM770101 -0.963 CHOC760102 -0.969 JANJ780103 -0.980 JANJ780101 -0.989 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.3 -1.4 -0.5 -0.6 0.9 -0.7 -0.7 0.3 -0.1 0.7 0.5 -1.8 0.4 0.5 -0.3 -0.1 -0.2 0.3 -0.4 0.6 // H JOND750101 D Hydrophobicity (Jones, 1975) R PMID:1127956 A Jones, D.D. T Amino acid properties and side-chain orientation in proteins: A cross correlation approach J J. Theor. Biol. 50, 167-183 (1975) C ARGP820101 1.000 SIMZ760101 0.966 GOLD730101 0.935 TAKK010101 0.906 MEEJ810101 0.891 CIDH920105 0.866 LEVM760106 0.864 CIDH920102 0.861 MEEJ800102 0.855 MEEJ810102 0.852 CIDH920103 0.826 PLIV810101 0.819 CIDH920104 0.818 LEVM760107 0.806 PARJ860101 -0.834 WOLS870101 -0.837 BULH740101 -0.853 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.87 0.85 0.09 0.66 1.52 0.00 0.67 0.10 0.87 3.15 2.17 1.64 1.67 2.87 2.77 0.07 0.07 3.77 2.67 1.87 // H JOND750102 D pK (-COOH) (Jones, 1975) R PMID:1127956 A Jones, D.D. T Amino acid properties and side-chain orientation in proteins: A cross correlation approach J J. Theor. Biol. 50, 167-183 (1975) * Original reference of this data: * McMeekin, T.L., Groves, M.L. and Hipp, N.J. * In "Amino Acids and Serum Proteins" (Stekol, J.A., ed.), American * Chemical Society, Washington, D.C., p. 54 (1964) C FASG760105 0.833 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.34 1.18 2.02 2.01 1.65 2.17 2.19 2.34 1.82 2.36 2.36 2.18 2.28 1.83 1.99 2.21 2.10 2.38 2.20 2.32 // H JOND920101 D Relative frequency of occurrence (Jones et al., 1992) R LIT:1814076 PMID:1633570 A Jones, D.T., Taylor, W.R. and Thornton, J.M. T The rapid generation of mutation data matrices from protein sequences J CABIOS 8, 275-282 (1992) C CEDJ970102 0.995 NAKH900101 0.993 CEDJ970104 0.983 CEDJ970101 0.968 DAYM780101 0.954 JUKT750101 0.953 FUKS010110 0.944 FUKS010112 0.943 JUNJ780101 0.932 CEDJ970103 0.911 KUMS000102 0.909 NAKH920101 0.900 NAKH920107 0.893 NAKH920106 0.889 NAKH920104 0.887 NAKH920103 0.881 NAKH900109 0.878 KUMS000101 0.863 FUKS010109 0.861 NAKH900102 0.846 CEDJ970105 0.834 FUKS010111 0.832 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.077 0.051 0.043 0.052 0.020 0.041 0.062 0.074 0.023 0.053 0.091 0.059 0.024 0.040 0.051 0.069 0.059 0.014 0.032 0.066 // H JOND920102 D Relative mutability (Jones et al., 1992) R LIT:1814076 PMID:1633570 A Jones, D.T., Taylor, W.R. and Thornton, J.M. T The rapid generation of mutation data matrices from protein sequences J CABIOS 8, 275-282 (1992) C DAYM780201 0.889 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 100. 83. 104. 86. 44. 84. 77. 50. 91. 103. 54. 72. 93. 51. 58. 117. 107. 25. 50. 98. // H JUKT750101 D Amino acid distribution (Jukes et al., 1975) R PMID:237322 A Jukes, T.H., Holmquist, R. and Moise, H. T Amino acid composition of proteins: Selection against the genetic code J Science 189, 50-51 (1975) C JUNJ780101 0.980 DAYM780101 0.975 CEDJ970101 0.973 JOND920101 0.953 KUMS000102 0.948 CEDJ970104 0.942 CEDJ970102 0.942 NAKH900101 0.941 FUKS010111 0.927 FUKS010110 0.908 KUMS000101 0.879 FUKS010112 0.875 NAKH920107 0.862 NAKH920101 0.849 NAKH920103 0.837 CEDJ970103 0.835 NAKH920106 0.831 NAKH920104 0.827 NAKH900109 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.3 2.6 3.0 3.6 1.3 2.4 3.3 4.8 1.4 3.1 4.7 4.1 1.1 2.3 2.5 4.5 3.7 0.8 2.3 4.2 // H JUNJ780101 D Sequence frequency (Jungck, 1978) R LIT:2004107b PMID:691072 A Jungck, J.R. T The genetic code as a periodic table J J. Mol. Evol. 11, 211-224 (1978) C DAYM780101 0.986 JUKT750101 0.980 CEDJ970101 0.968 JOND920101 0.932 KUMS000102 0.927 CEDJ970104 0.921 CEDJ970102 0.920 NAKH900101 0.918 FUKS010111 0.906 FUKS010110 0.868 NAKH920107 0.856 KUMS000101 0.854 NAKH900102 0.853 FUKS010112 0.836 NAKH920106 0.829 NAKH920101 0.826 NAKH920103 0.820 NAKH920104 0.807 CEDJ970103 0.806 CEDJ970105 0.803 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 685. 382. 397. 400. 241. 313. 427. 707. 155. 394. 581. 575. 132. 303. 366. 593. 490. 99. 292. 553. // H KANM800101 D Average relative probability of helix (Kanehisa-Tsong, 1980) R LIT:0611060 PMID:7426680 A Kanehisa, M.I. and Tsong, T.Y. T Local hydrophobicity stabilizes secondary structures in proteins J Biopolymers 19, 1617-1628 (1980) C ISOY800101 0.963 PALJ810102 0.962 LEVM780104 0.958 CHOP780201 0.956 MAXF760101 0.950 ROBB760101 0.945 GEIM800101 0.942 LEVM780101 0.942 PRAM900102 0.942 PALJ810101 0.928 TANS770101 0.927 GEIM800104 0.916 RACS820108 0.914 KANM800103 0.912 NAGK730101 0.883 AURR980115 0.858 BURA740101 0.855 QIAN880106 0.854 QIAN880107 0.854 AURR980109 0.852 AURR980114 0.852 PALJ810109 0.849 AURR980112 0.847 CRAJ730101 0.842 AURR980110 0.830 QIAN880105 0.827 MUNV940102 -0.843 MUNV940101 -0.846 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.36 1.00 0.89 1.04 0.82 1.14 1.48 0.63 1.11 1.08 1.21 1.22 1.45 1.05 0.52 0.74 0.81 0.97 0.79 0.94 // H KANM800102 D Average relative probability of beta-sheet (Kanehisa-Tsong, 1980) R LIT:0611060 PMID:7426680 A Kanehisa, M.I. and Tsong, T.Y. T Local hydrophobicity stabilizes secondary structures in proteins J Biopolymers 19, 1617-1628 (1980) C GEIM800107 0.955 PALJ810104 0.948 CHOP780202 0.945 LIFS790101 0.940 LEVM780105 0.938 ROBB760106 0.938 PALJ810103 0.932 KANM800104 0.928 PTIO830102 0.917 GEIM800105 0.916 QIAN880121 0.900 ROBB760105 0.898 QIAN880120 0.896 QIAN880119 0.888 NAGK730102 0.878 PALJ810112 0.869 PONP930101 0.866 LIFS790103 0.863 AVBF000101 0.859 LEVM780102 0.856 PRAM900103 0.856 PONP800108 0.849 PALJ810110 0.836 MANP780101 0.833 PONP800101 0.829 GEIM800106 0.821 NISK860101 0.819 PONP800102 0.815 NISK800101 0.809 CHOP780208 0.804 PONP800103 0.803 LIFS790102 0.801 QIAN880118 0.801 OOBM770103 -0.812 GEIM800110 -0.814 MUNV940103 -0.916 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.81 0.85 0.62 0.71 1.17 0.98 0.53 0.88 0.92 1.48 1.24 0.77 1.05 1.20 0.61 0.92 1.18 1.18 1.23 1.66 // H KANM800103 D Average relative probability of inner helix (Kanehisa-Tsong, 1980) R LIT:0611060 PMID:7426680 A Kanehisa, M.I. and Tsong, T.Y. T Local hydrophobicity stabilizes secondary structures in proteins J Biopolymers 19, 1617-1628 (1980) C AURR980109 0.944 ISOY800101 0.931 PALJ810102 0.916 AURR980114 0.916 KANM800101 0.912 CHOP780201 0.912 QIAN880107 0.908 AURR980113 0.905 MAXF760101 0.901 BEGF750101 0.893 QIAN880106 0.889 ROBB760103 0.887 ROBB760101 0.886 GEIM800101 0.881 AURR980112 0.871 LEVM780104 0.859 RACS820108 0.858 AURR980108 0.857 PRAM900102 0.850 LEVM780101 0.850 TANS770101 0.843 PALJ810101 0.836 RICJ880109 0.829 QIAN880108 0.829 QIAN880109 0.824 FINA770101 0.823 QIAN880110 0.820 SUEM840101 0.820 QIAN880105 0.820 BURA740101 0.810 CHOP780216 -0.808 GEIM800111 -0.812 PRAM900104 -0.814 LEVM780103 -0.816 MUNV940102 -0.823 CHOP780101 -0.824 MUNV940101 -0.826 PALJ810106 -0.840 NAGK730103 -0.847 CHAM830101 -0.889 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.45 1.15 0.64 0.91 0.70 1.14 1.29 0.53 1.13 1.23 1.56 1.27 1.83 1.20 0.21 0.48 0.77 1.17 0.74 1.10 // H KANM800104 D Average relative probability of inner beta-sheet (Kanehisa-Tsong, 1980) R LIT:0611060 PMID:7426680 A Kanehisa, M.I. and Tsong, T.Y. T Local hydrophobicity stabilizes secondary structures in proteins J Biopolymers 19, 1617-1628 (1980) C KANM800102 0.928 ROBB760105 0.885 ROBB760106 0.877 GEIM800107 0.876 GEIM800105 0.861 PTIO830102 0.858 PALJ810104 0.851 PONP800108 0.849 LEVM780105 0.841 QIAN880119 0.841 CHOP780202 0.839 LIFS790101 0.834 PONP930101 0.833 QIAN880121 0.829 MANP780101 0.827 JURD980101 0.826 KYTJ820101 0.824 PALJ810103 0.823 PONP800101 0.823 PALJ810112 0.813 PONP800102 0.813 LIFS790102 0.809 QIAN880120 0.803 MUNV940103 -0.857 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.75 0.79 0.33 0.31 1.46 0.75 0.46 0.83 0.83 1.87 1.56 0.66 0.86 1.37 0.52 0.82 1.36 0.79 1.08 2.00 // H KARP850101 D Flexibility parameter for no rigid neighbors (Karplus-Schulz, 1985) R LIT:1110994 A Karplus, P.A. and Schulz, G.E. T Prediction of chain flexibility in proteins J Naturwiss. 72, 212-213 (1985) C VINM940102 0.874 VINM940103 0.837 RACS770101 0.837 FUKS010103 0.834 MEIH800101 0.832 VINM940101 0.821 PARS000101 0.816 CIDH920104 -0.801 BIOV880102 -0.804 RADA880108 -0.804 ROSG850101 -0.807 MIYS850101 -0.811 MEEJ810101 -0.818 BIOV880101 -0.825 NISK860101 -0.828 WERD780101 -0.842 CIDH920101 -0.864 CIDH920105 -0.866 CIDH920102 -0.873 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.041 1.038 1.117 1.033 0.960 1.165 1.094 1.142 0.982 1.002 0.967 1.093 0.947 0.930 1.055 1.169 1.073 0.925 0.961 0.982 // H KARP850102 D Flexibility parameter for one rigid neighbor (Karplus-Schulz, 1985) R LIT:1110994 A Karplus, P.A. and Schulz, G.E. T Prediction of chain flexibility in proteins J Naturwiss. 72, 212-213 (1985) C KRIW790101 0.917 VINM940101 0.885 MEIH800101 0.884 RACS770101 0.869 VINM940103 0.863 KRIW710101 0.855 PARS000101 0.852 RACS770102 0.852 KRIW790102 0.843 GUYH850101 0.840 MEIH800102 0.837 FUKS010103 0.835 VINM940102 0.834 FUKS010104 0.822 OOBM770103 0.820 BHAR880101 0.806 NADH010102 -0.807 DESM900102 -0.815 PONP800106 -0.820 CIDH920101 -0.828 DESM900101 -0.829 CIDH920104 -0.833 NADH010103 -0.834 NADH010104 -0.835 CIDH920105 -0.839 CIDH920103 -0.852 BIOV880102 -0.859 MANP780101 -0.863 PONP800103 -0.870 MIYS850101 -0.878 RADA880108 -0.879 BIOV880101 -0.880 NISK800101 -0.885 PONP800102 -0.887 PONP800101 -0.889 PONP930101 -0.893 ROSG850102 -0.897 NISK860101 -0.901 WERD780101 -0.909 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.946 1.028 1.006 1.089 0.878 1.025 1.036 1.042 0.952 0.892 0.961 1.082 0.862 0.912 1.085 1.048 1.051 0.917 0.930 0.927 // H KARP850103 D Flexibility parameter for two rigid neighbors (Karplus-Schulz, 1985) R LIT:1110994 A Karplus, P.A. and Schulz, G.E. T Prediction of chain flexibility in proteins J Naturwiss. 72, 212-213 (1985) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.892 0.901 0.930 0.932 0.925 0.885 0.933 0.923 0.894 0.872 0.921 1.057 0.804 0.914 0.932 0.923 0.934 0.803 0.837 0.913 // H KHAG800101 D The Kerr-constant increments (Khanarian-Moore, 1980) R LIT:0611050b A Khanarian, G. and Moore, W.J. T The Kerr effect of amino acids in water J Aust. J. Chem. 33, 1727-1741 (1980) * (Cys Lys Tyr !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 49.1 133. -3.6 0. 0. 20. 0. 64.6 75.7 18.9 15.6 0. 6.8 54.7 43.8 44.4 31.0 70.5 0. 29.5 // H KLEP840101 D Net charge (Klein et al., 1984) R LIT:1008055 PMID:6547351 A Klein, P., Kanehisa, M. and DeLisi, C. T Prediction of protein function from sequence properties: Discriminant analysis of a data base J Biochim. Biophys. Acta 787, 221-226 (1984) C ZIMJ680104 0.941 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 1. 0. -1. 0. 0. -1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. 0. 0. 0. // H KRIW710101 D Side chain interaction parameter (Krigbaum-Rubin, 1971) R LIT:2004046b PMID:5553983 A Krigbaum, W.R. and Rubin, B.H. T Local interactions as structure determinant for globular proteins J Biochim. Biophys. Acta 229, 368-383 (1971) C KRIW790101 0.908 KARP850102 0.855 KRIW790102 0.839 GUYH850101 0.831 DESM900101 -0.807 BIOV880101 -0.813 JANJ790101 -0.815 WERD780101 -0.819 NADH010102 -0.825 NISK800101 -0.831 PONP800106 -0.841 NADH010105 -0.842 NADH010106 -0.846 RADA880108 -0.847 PONP800101 -0.850 ROSG850102 -0.852 NADH010103 -0.860 NADH010104 -0.874 PONP800102 -0.887 PONP800103 -0.890 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.60 6.50 5.90 5.70 -1.00 6.10 5.60 7.60 4.50 2.60 3.25 7.90 1.40 3.20 7.00 5.25 4.80 4.00 4.35 3.40 // H KRIW790101 D Side chain interaction parameter (Krigbaum-Komoriya, 1979) R LIT:0502056 PMID:760806 A Krigbaum, W.R. and Komoriya, A. T Local interactions as a structure determinant for protein molecules: II J Biochim. Biophys. Acta 576, 204-228 (1979) C KARP850102 0.917 KRIW790102 0.914 KRIW710101 0.908 VINM940101 0.890 GUYH850101 0.885 MEIH800102 0.876 VINM940103 0.875 RACS770102 0.871 MEIH800101 0.869 OOBM770103 0.865 GRAR740102 0.847 VINM940102 0.834 MONM990101 0.830 RACS770101 0.828 FUKS010104 0.828 OOBM770101 0.816 JANJ780103 0.805 PARS000101 0.804 PTIO830102 -0.801 QIAN880121 -0.803 KYTJ820101 -0.805 JANJ790101 -0.810 CIDH920105 -0.816 CIDH920103 -0.819 JURD980101 -0.824 JANJ790102 -0.825 NADH010101 -0.827 JANJ780102 -0.837 DESM900101 -0.847 MEIH800103 -0.850 DESM900102 -0.859 PONP800108 -0.860 NADH010106 -0.861 FAUJ830101 -0.865 CIDH920104 -0.867 MANP780101 -0.870 BIOV880102 -0.876 PONP800101 -0.888 NISK800101 -0.896 RADA880108 -0.897 NADH010105 -0.898 WERD780101 -0.899 NISK860101 -0.907 PONP930101 -0.909 MIYS850101 -0.910 BIOV880101 -0.910 PONP800102 -0.915 NADH010102 -0.929 PONP800103 -0.930 ROSG850102 -0.935 NADH010103 -0.954 NADH010104 -0.958 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.32 6.55 6.24 6.04 1.73 6.13 6.17 6.09 5.66 2.31 3.93 7.92 2.44 2.59 7.19 5.37 5.16 2.78 3.58 3.31 // H KRIW790102 D Fraction of site occupied by water (Krigbaum-Komoriya, 1979) R LIT:0502056 PMID:760806 A Krigbaum, W.R. and Komoriya, A. T Local interactions as a structure determinant for protein molecules: II J Biochim. Biophys. Acta 576, 204-228 (1979) C KRIW790101 0.914 MEIH800102 0.898 RACS770102 0.895 RACS770103 0.889 GUYH850101 0.864 FUKS010104 0.853 VINM940101 0.853 JANJ780103 0.848 KARP850102 0.843 KRIW710101 0.839 VINM940103 0.836 MEIH800101 0.835 OOBM770103 0.824 OOBM770101 0.822 RACS770101 0.814 PONP800101 -0.804 JANJ780102 -0.818 PONP930101 -0.821 PONP800102 -0.830 DESM900101 -0.835 JANJ790102 -0.847 DESM900102 -0.852 PONP800103 -0.853 NISK860101 -0.855 RADA880108 -0.856 BIOV880101 -0.869 MIYS850101 -0.869 WERD780101 -0.875 BIOV880102 -0.878 NADH010104 -0.882 MEIH800103 -0.885 NADH010103 -0.887 NADH010102 -0.890 ROSG850102 -0.922 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.28 0.34 0.31 0.33 0.11 0.39 0.37 0.28 0.23 0.12 0.16 0.59 0.08 0.10 0.46 0.27 0.26 0.15 0.25 0.22 // H KRIW790103 D Side chain volume (Krigbaum-Komoriya, 1979) R LIT:0502056 PMID:760806 A Krigbaum, W.R. and Komoriya, A. T Local interactions as a structure determinant for protein molecules: II J Biochim. Biophys. Acta 576, 204-228 (1979) * (Gly Pro 7.8) C GOLD730102 0.994 BIGC670101 0.993 GRAR740103 0.989 TSAJ990101 0.988 TSAJ990102 0.987 CHOC750101 0.982 FAUJ880103 0.965 CHAM820101 0.963 CHOC760101 0.948 ROSG850101 0.920 FASG760101 0.910 LEVM760105 0.900 DAWD720101 0.893 LEVM760102 0.884 RADA880106 0.883 CHAM830106 0.876 LEVM760106 0.862 LEVM760107 0.860 FAUJ880106 0.845 MCMT640101 0.810 RADA880103 -0.871 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 27.5 105.0 58.7 40.0 44.6 80.7 62.0 0.0 79.0 93.5 93.5 100.0 94.1 115.5 41.9 29.3 51.3 145.5 117.3 71.5 // H KYTJ820101 D Hydropathy index (Kyte-Doolittle, 1982) R LIT:0807099 PMID:7108955 A Kyte, J. and Doolittle, R.F. T A simple method for displaying the hydropathic character of a protein J J. Mol. Biol. 157, 105-132 (1982) C JURD980101 0.996 CHOC760103 0.964 JANJ780102 0.922 NADH010102 0.920 NADH010101 0.918 DESM900102 0.898 EISD860103 0.897 CHOC760104 0.889 NADH010103 0.885 WOLR810101 0.885 RADA880101 0.884 MANP780101 0.881 EISD840101 0.878 PONP800103 0.870 NAKH920108 0.868 JANJ790101 0.867 JANJ790102 0.866 PONP800102 0.861 MEIH800103 0.856 NADH010104 0.856 PONP800101 0.851 PONP800108 0.850 WARP780101 0.845 PONP930101 0.844 RADA880108 0.842 ROSG850102 0.841 DESM900101 0.837 BIOV880101 0.829 RADA880107 0.828 KANM800104 0.824 LIFS790102 0.824 CIDH920104 0.824 MIYS850101 0.821 RADA880104 0.819 NAKH900111 0.817 NISK800101 0.812 FAUJ830101 0.811 ARGP820103 0.806 NADH010105 0.804 NAKH920105 0.803 ARGP820102 0.803 KRIW790101 -0.805 CHOC760102 -0.838 MONM990101 -0.842 GUYH850101 -0.843 RACS770102 -0.844 ROSM880101 -0.845 JANJ780103 -0.845 PRAM900101 -0.850 JANJ780101 -0.852 GRAR740102 -0.859 MEIH800102 -0.871 ROSM880102 -0.878 KUHL950101 -0.883 OOBM770101 -0.899 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5 3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2 // H LAWE840101 D Transfer free energy, CHP/water (Lawson et al., 1984) R LIT:1004126 PMID:6699000 A Lawson, E.Q., Sadler, A.J., Harmatz, D., Brandau, D.T., Micanovic, R. MacElroy, R.D. and Middaught, C.R. T A simple experimental model for hydrophobic interactions in proteins J J. Biol. Chem. 259, 2910-2912 (1984) C GOLD730101 0.829 SIMZ760101 0.815 ZIMJ680105 0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.48 -0.06 -0.87 -0.75 -0.32 -0.32 -0.71 0.00 -0.51 0.81 1.02 -0.09 0.81 1.03 2.03 0.05 -0.35 0.66 1.24 0.56 // H LEVM760101 D Hydrophobic parameter (Levitt, 1976) R LIT:2004093b PMID:957439 A Levitt, M. T A simplified representation of protein conformations for rapid simulation of protein folfing J J. Mol. Biol. 104, 59-107 (1976) C HOPT810101 0.985 PRAM900101 0.881 ROSM880101 0.876 WOEC730101 0.872 FUKS010104 0.869 GRAR740102 0.865 WOLS870101 0.845 FUKS010102 0.837 VHEG790101 0.825 ROSM880102 0.823 VINM940101 0.815 KUHL950101 0.807 PARJ860101 0.806 OOBM770103 0.805 PLIV810101 -0.801 WIMW960101 -0.812 RADA880108 -0.824 BIOV880101 -0.831 RADA880101 -0.838 RADA880102 -0.838 ZIMJ680105 -0.844 BIOV880102 -0.847 MEEJ800102 -0.855 EISD840101 -0.859 FAUJ830101 -0.919 EISD860101 -0.921 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.5 3.0 0.2 2.5 -1.0 0.2 2.5 0.0 -0.5 -1.8 -1.8 3.0 -1.3 -2.5 -1.4 0.3 -0.4 -3.4 -2.3 -1.5 // H LEVM760102 D Distance between C-alpha and centroid of side chain (Levitt, 1976) R LIT:2004093b PMID:957439 A Levitt, M. T A simplified representation of protein conformations for rapid simulation of protein folfing J J. Mol. Biol. 104, 59-107 (1976) C LEVM760105 0.987 CHOC760101 0.972 FASG760101 0.966 CHAM830106 0.962 FAUJ880103 0.947 CHOC750101 0.933 TSAJ990102 0.918 CHAM820101 0.915 TSAJ990101 0.910 FAUJ880106 0.900 BIGC670101 0.896 GOLD730102 0.893 GRAR740103 0.885 KRIW790103 0.884 WOLS870102 0.881 DAWD720101 0.873 RADA880106 0.871 OOBM770102 0.869 FAUJ880104 0.867 CHAM830105 0.843 HUTJ700102 0.835 RADA880103 -0.913 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.77 3.72 1.98 1.99 1.38 2.58 2.63 0.00 2.76 1.83 2.08 2.94 2.34 2.97 1.42 1.28 1.43 3.58 3.36 1.49 // H LEVM760103 D Side chain angle theta(AAR) (Levitt, 1976) R LIT:2004093b PMID:957439 A Levitt, M. T A simplified representation of protein conformations for rapid simulation of protein folfing J J. Mol. Biol. 104, 59-107 (1976) * (Gly missing) C AVBF000102 0.816 RICJ880115 -0.829 LEVM760104 -0.840 KIMC930101 -0.861 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 121.9 121.4 117.5 121.2 113.7 118.0 118.2 0. 118.2 118.9 118.1 122.0 113.1 118.2 81.9 117.9 117.1 118.4 110.0 121.7 // H LEVM760104 D Side chain torsion angle phi(AAAR) (Levitt, 1976) R LIT:2004093b PMID:957439 A Levitt, M. T A simplified representation of protein conformations for rapid simulation of protein folfing J J. Mol. Biol. 104, 59-107 (1976) C KIMC930101 0.842 PRAM820102 0.812 CHAM810101 -0.818 LEVM760103 -0.840 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 243.2 206.6 207.1 215.0 209.4 205.4 213.6 300.0 219.9 217.9 205.6 210.9 204.0 203.7 237.4 232.0 226.7 203.7 195.6 220.3 // H LEVM760105 D Radius of gyration of side chain (Levitt, 1976) R LIT:2004093b PMID:957439 A Levitt, M. T A simplified representation of protein conformations for rapid simulation of protein folfing J J. Mol. Biol. 104, 59-107 (1976) * (Gly 0.089) C LEVM760102 0.987 CHOC760101 0.968 CHAM830106 0.958 FASG760101 0.951 FAUJ880103 0.945 CHOC750101 0.939 TSAJ990102 0.928 TSAJ990101 0.922 CHAM820101 0.915 BIGC670101 0.913 GOLD730102 0.911 GRAR740103 0.900 KRIW790103 0.900 DAWD720101 0.898 FAUJ880104 0.896 FAUJ880106 0.889 RADA880106 0.871 OOBM770102 0.868 HUTJ700102 0.864 WOLS870102 0.836 HUTJ700103 0.834 CHAM830105 0.829 RADA880103 -0.893 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.77 2.38 1.45 1.43 1.22 1.75 1.77 0.58 1.78 1.56 1.54 2.08 1.80 1.90 1.25 1.08 1.24 2.21 2.13 1.29 // H LEVM760106 D van der Waals parameter R0 (Levitt, 1976) R LIT:2004093b PMID:957439 A Levitt, M. T A simplified representation of protein conformations for rapid simulation of protein folfing J J. Mol. Biol. 104, 59-107 (1976) C ROSG850101 0.896 BIGC670101 0.876 GOLD730102 0.875 ZIMJ680102 0.873 CIDH920102 0.873 ARGP820101 0.865 JOND750101 0.864 KRIW790103 0.862 TSAJ990101 0.849 SIMZ760101 0.848 GRAR740103 0.846 CHOC750101 0.841 TSAJ990102 0.841 TAKK010101 0.841 PLIV810101 0.830 CIDH920105 0.828 GOLD730101 0.827 MEEJ810101 0.827 CIDH920101 0.826 CHAM820101 0.818 ROBB790101 0.804 LEVM760107 0.804 BULH740101 -0.818 FUKS010103 -0.829 PARJ860101 -0.832 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.2 6.0 5.0 5.0 6.1 6.0 6.0 4.2 6.0 7.0 7.0 6.0 6.8 7.1 6.2 4.9 5.0 7.6 7.1 6.4 // H LEVM760107 D van der Waals parameter epsilon (Levitt, 1976) R LIT:2004093b PMID:957439 A Levitt, M. T A simplified representation of protein conformations for rapid simulation of protein folfing J J. Mol. Biol. 104, 59-107 (1976) C CHAM820101 0.891 FAUJ880103 0.875 TSAJ990101 0.866 GOLD730102 0.865 BIGC670101 0.863 TSAJ990102 0.861 GARJ730101 0.860 KRIW790103 0.860 CHOC750101 0.858 ROSG850101 0.852 NOZY710101 0.845 GRAR740103 0.841 TAKK010101 0.819 SNEP660103 0.818 FASG760101 0.815 CHOC760101 0.807 JOND750101 0.806 ARGP820101 0.806 LEVM760106 0.804 WEBA780101 -0.923 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.025 0.20 0.10 0.10 0.10 0.10 0.10 0.025 0.10 0.19 0.19 0.20 0.19 0.39 0.17 0.025 0.10 0.56 0.39 0.15 // H LEVM780101 D Normalized frequency of alpha-helix, with weights (Levitt, 1978) R LIT:0411042 PMID:708713 A Levitt, M. T Conformational preferences of amino acids in globular proteins J Biochemistry 17, 4277-4285 (1978) C PRAM900102 1.000 LEVM780104 0.964 PALJ810101 0.943 KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924 ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907 RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898 NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873 TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829 QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.29 0.96 0.90 1.04 1.11 1.27 1.44 0.56 1.22 0.97 1.30 1.23 1.47 1.07 0.52 0.82 0.82 0.99 0.72 0.91 // H LEVM780102 D Normalized frequency of beta-sheet, with weights (Levitt, 1978) R LIT:0411042 PMID:708713 A Levitt, M. T Conformational preferences of amino acids in globular proteins J Biochemistry 17, 4277-4285 (1978) C PRAM900103 1.000 PALJ810112 0.913 LEVM780105 0.899 PALJ810104 0.868 PTIO830102 0.865 LIFS790101 0.864 QIAN880120 0.858 KANM800102 0.856 PALJ810103 0.846 GEIM800107 0.842 BEGF750102 0.834 QIAN880119 0.834 CHOP780202 0.833 AVBF000101 0.815 QIAN880121 0.805 MUNV940103 -0.848 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.90 0.99 0.76 0.72 0.74 0.80 0.75 0.92 1.08 1.45 1.02 0.77 0.97 1.32 0.64 0.95 1.21 1.14 1.25 1.49 // H LEVM780103 D Normalized frequency of reverse turn, with weights (Levitt, 1978) R LIT:0411042 PMID:708713 A Levitt, M. T Conformational preferences of amino acids in globular proteins J Biochemistry 17, 4277-4285 (1978) C PRAM900104 1.000 LEVM780106 0.984 GEIM800111 0.952 CHOP780216 0.952 QIAN880133 0.948 QIAN880134 0.935 ISOY800103 0.932 QIAN880132 0.931 GEIM800108 0.931 CHOP780203 0.927 CHAM830101 0.909 PALJ810105 0.909 QIAN880135 0.906 CHOP780101 0.893 TANS770110 0.875 CHOP780210 0.852 PALJ810106 0.848 RACS770101 0.808 AURR980109 -0.814 KANM800103 -0.816 QIAN880108 -0.820 QIAN880107 -0.834 AVBF000102 -0.834 ROBB760103 -0.843 FAUJ880102 -0.846 QIAN880109 -0.848 PTIO830101 -0.860 SUEM840101 -0.864 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.77 0.88 1.28 1.41 0.81 0.98 0.99 1.64 0.68 0.51 0.58 0.96 0.41 0.59 1.91 1.32 1.04 0.76 1.05 0.47 // H LEVM780104 D Normalized frequency of alpha-helix, unweighted (Levitt, 1978) R LIT:0411042 PMID:708713 A Levitt, M. T Conformational preferences of amino acids in globular proteins J Biochemistry 17, 4277-4285 (1978) C PALJ810101 0.988 PRAM900102 0.964 LEVM780101 0.964 KANM800101 0.958 GEIM800101 0.950 NAGK730101 0.918 ROBB760101 0.911 TANS770101 0.908 PALJ810102 0.906 MAXF760101 0.904 ISOY800101 0.904 RACS820108 0.889 CHOP780201 0.886 GEIM800104 0.872 CRAJ730101 0.869 KANM800103 0.859 BURA740101 0.833 QIAN880107 0.822 PALJ810109 0.819 AURR980115 0.818 QIAN880106 0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.32 0.98 0.95 1.03 0.92 1.10 1.44 0.61 1.31 0.93 1.31 1.25 1.39 1.02 0.58 0.76 0.79 0.97 0.73 0.93 // H LEVM780105 D Normalized frequency of beta-sheet, unweighted (Levitt, 1978) R LIT:0411042 PMID:708713 A Levitt, M. T Conformational preferences of amino acids in globular proteins J Biochemistry 17, 4277-4285 (1978) C PALJ810103 0.980 KANM800102 0.938 CHOP780202 0.930 LIFS790101 0.928 GEIM800105 0.926 PALJ810104 0.921 QIAN880120 0.913 QIAN880119 0.903 PRAM900103 0.899 LEVM780102 0.899 LIFS790103 0.897 PTIO830102 0.894 GEIM800107 0.884 QIAN880121 0.876 PALJ810112 0.870 ROBB760106 0.869 ROBB760105 0.842 KANM800104 0.841 AVBF000101 0.824 QIAN880118 0.819 MUNV940103 -0.891 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.86 0.97 0.73 0.69 1.04 1.00 0.66 0.89 0.85 1.47 1.04 0.77 0.93 1.21 0.68 1.02 1.27 1.26 1.31 1.43 // H LEVM780106 D Normalized frequency of reverse turn, unweighted (Levitt, 1978) R LIT:0411042 PMID:708713 A Levitt, M. T Conformational preferences of amino acids in globular proteins J Biochemistry 17, 4277-4285 (1978) C LEVM780103 0.984 PRAM900104 0.983 QIAN880133 0.971 CHOP780216 0.953 GEIM800111 0.951 QIAN880132 0.943 ISOY800103 0.941 CHOP780203 0.935 QIAN880134 0.932 GEIM800108 0.932 QIAN880135 0.902 PALJ810105 0.902 CHAM830101 0.900 TANS770110 0.892 CHOP780101 0.890 PALJ810106 0.850 MUNV940103 0.815 CHOP780210 0.812 GEIM800110 0.809 AVBF000101 -0.805 LIFS790101 -0.806 QIAN880119 -0.810 QIAN880107 -0.813 QIAN880109 -0.815 QIAN880120 -0.831 PTIO830101 -0.854 AVBF000102 -0.860 FAUJ880102 -0.865 SUEM840101 -0.878 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.79 0.90 1.25 1.47 0.79 0.92 1.02 1.67 0.81 0.50 0.57 0.99 0.51 0.77 1.78 1.30 0.97 0.79 0.93 0.46 // H LEWP710101 D Frequency of occurrence in beta-bends (Lewis et al., 1971) R PMID:5289387 A Lewis, P. N., Momany, F.A. and Scheraga, H.A. T Folding of polypeptide chains in proteins: A proposed mechanism for folding J Proc. Natl. Acad. Sci. USA 68, 2293-2297 (1971) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.22 0.28 0.42 0.73 0.20 0.26 0.08 0.58 0.14 0.22 0.19 0.27 0.38 0.08 0.46 0.55 0.49 0.43 0.46 0.08 // H LIFS790101 D Conformational preference for all beta-strands (Lifson-Sander, 1979) R LIT:0512128 PMID:503185 A Lifson, S. and Sander, C. T Antiparallel and parallel beta-strands differ in amino acid residue preference J Nature 282, 109-111 (1979) C QIAN880120 0.969 CHOP780202 0.947 LIFS790103 0.944 PTIO830102 0.941 KANM800102 0.940 QIAN880121 0.930 PALJ810104 0.929 QIAN880119 0.929 LEVM780105 0.928 PALJ810103 0.912 PONP930101 0.908 ROBB760106 0.906 GEIM800107 0.888 ROBB760105 0.867 LEVM780102 0.864 PRAM900103 0.864 MANP780101 0.859 NISK860101 0.859 AVBF000101 0.857 GEIM800105 0.855 PALJ810112 0.845 KANM800104 0.834 CIDH920104 0.832 CIDH920105 0.828 PONP800108 0.828 NISK800101 0.827 PONP800101 0.823 CHOP780208 0.820 PALJ810110 0.817 SWER830101 0.815 CIDH920103 0.815 VENT840101 0.814 CIDH920102 0.808 BEGF750102 0.807 LIFS790102 0.803 PONP800107 0.801 GEIM800111 -0.801 QIAN880134 -0.804 LEVM780106 -0.806 QIAN880132 -0.806 MEIH800101 -0.809 VINM940101 -0.834 VINM940102 -0.843 PARS000101 -0.844 QIAN880133 -0.848 OOBM770103 -0.855 GEIM800110 -0.862 MUNV940103 -0.941 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.92 0.93 0.60 0.48 1.16 0.95 0.61 0.61 0.93 1.81 1.30 0.70 1.19 1.25 0.40 0.82 1.12 1.54 1.53 1.81 // H LIFS790102 D Conformational preference for parallel beta-strands (Lifson-Sander, 1979) R LIT:0512128 PMID:503185 A Lifson, S. and Sander, C. T Antiparallel and parallel beta-strands differ in amino acid residue preference J Nature 282, 109-111 (1979) C PTIO830102 0.874 MANP780101 0.870 PONP800107 0.849 PONP930101 0.833 JURD980101 0.824 KYTJ820101 0.824 CHOC760103 0.810 KANM800104 0.809 PONP800101 0.804 LIFS790101 0.803 KANM800102 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.00 0.68 0.54 0.50 0.91 0.28 0.59 0.79 0.38 2.60 1.42 0.59 1.49 1.30 0.35 0.70 0.59 0.89 1.08 2.63 // H LIFS790103 D Conformational preference for antiparallel beta-strands (Lifson-Sander, 1979) R LIT:0512128 PMID:503185 A Lifson, S. and Sander, C. T Antiparallel and parallel beta-strands differ in amino acid residue preference J Nature 282, 109-111 (1979) C LIFS790101 0.944 QIAN880120 0.939 CHOP780202 0.908 LEVM780105 0.897 QIAN880121 0.882 PALJ810103 0.877 QIAN880119 0.877 KANM800102 0.863 PALJ810104 0.860 GEIM800105 0.832 ROBB760106 0.827 GEIM800107 0.823 PTIO830102 0.822 GEIM800106 0.814 AVBF000101 0.814 OOBM770103 -0.807 VINM940101 -0.829 PARS000101 -0.861 VINM940102 -0.862 GEIM800110 -0.889 MUNV940103 -0.902 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.90 1.02 0.62 0.47 1.24 1.18 0.62 0.56 1.12 1.54 1.26 0.74 1.09 1.23 0.42 0.87 1.30 1.75 1.68 1.53 // H MANP780101 D Average surrounding hydrophobicity (Manavalan-Ponnuswamy, 1978) R LIT:0411088 PMID:703834 A Manavalan, P. and Ponnuswamy, P.K. T Hydrophobic character of amino acid residues in globular proteins J Nature 275, 673-674 (1978) C PONP930101 0.967 PONP800101 0.963 PONP800102 0.945 NISK800101 0.940 PONP800108 0.935 NISK860101 0.930 CIDH920104 0.918 PONP800103 0.913 MIYS850101 0.909 CIDH920103 0.905 ROSG850102 0.903 RADA880108 0.900 BIOV880101 0.899 JURD980101 0.887 KYTJ820101 0.881 CIDH920105 0.879 NADH010103 0.878 NADH010104 0.873 PONP800107 0.871 LIFS790102 0.870 NADH010102 0.863 PTIO830102 0.861 LIFS790101 0.859 CHOC760103 0.859 PLIV810101 0.856 WERD780101 0.853 BIOV880102 0.847 NADH010101 0.847 FAUJ830101 0.843 JANJ790101 0.842 NADH010105 0.842 JANJ780102 0.842 MEIH800103 0.839 ROBB790101 0.834 KANM800102 0.833 KANM800104 0.827 EISD860103 0.826 ROBB760106 0.824 SWER830101 0.821 DESM900102 0.816 GUOD860101 0.815 PONP800106 0.813 QIAN880120 0.806 PALJ810104 0.805 CHOP780202 0.805 ROBB760105 0.805 QIAN880121 0.802 OOBM770101 -0.806 WOLS870101 -0.809 MUNV940103 -0.815 VINM940102 -0.821 VINM940101 -0.836 GUYH850101 -0.838 PARJ860101 -0.841 OOBM770103 -0.859 KARP850102 -0.863 RACS770102 -0.865 MEIH800102 -0.865 GRAR740102 -0.868 KRIW790101 -0.870 RACS770101 -0.878 MEIH800101 -0.897 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 12.97 11.72 11.42 10.85 14.63 11.76 11.89 12.43 12.16 15.67 14.90 11.36 14.39 14.00 11.37 11.23 11.69 13.93 13.42 15.71 // H MAXF760101 D Normalized frequency of alpha-helix (Maxfield-Scheraga, 1976) R LIT:2004036b PMID:990270 A Maxfield, F.R. and Scheraga, H.A. T Status of empirical methods for the prediction of protein backbone topography J Biochemistry 15, 5138-5153 (1976) * Recalculated by Kidera using a different set of proteins * Reported values normalized by the total number C ISOY800101 0.982 PALJ810102 0.959 CHOP780201 0.956 ROBB760101 0.956 KANM800101 0.950 TANS770101 0.930 PRAM900102 0.924 LEVM780101 0.924 LEVM780104 0.904 KANM800103 0.901 GEIM800104 0.897 GEIM800101 0.895 PALJ810101 0.889 QIAN880107 0.885 QIAN880106 0.881 NAGK730101 0.877 PALJ810109 0.876 AURR980109 0.865 AURR980110 0.860 RACS820108 0.860 AURR980114 0.853 BURA740101 0.852 AURR980115 0.852 AURR980108 0.841 AURR980112 0.838 CRAJ730101 0.826 QIAN880105 0.811 AURR980111 0.811 FINA770101 0.810 NAGK730103 -0.801 MUNV940102 -0.829 MUNV940101 -0.833 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.43 1.18 0.64 0.92 0.94 1.22 1.67 0.46 0.98 1.04 1.36 1.27 1.53 1.19 0.49 0.70 0.78 1.01 0.69 0.98 // H MAXF760102 D Normalized frequency of extended structure (Maxfield-Scheraga, 1976) R LIT:2004036b PMID:990270 A Maxfield, F.R. and Scheraga, H.A. T Status of empirical methods for the prediction of protein backbone topography J Biochemistry 15, 5138-5153 (1976) * Recalculated by Kidera using a different set of proteins * Reported values normalized by the total number C ISOY800102 0.931 TANS770103 0.891 GEIM800105 0.819 RACS820111 0.815 WOEC730101 -0.842 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.86 0.94 0.74 0.72 1.17 0.89 0.62 0.97 1.06 1.24 0.98 0.79 1.08 1.16 1.22 1.04 1.18 1.07 1.25 1.33 // H MAXF760103 D Normalized frequency of zeta R (Maxfield-Scheraga, 1976) R LIT:2004036b PMID:990270 A Maxfield, F.R. and Scheraga, H.A. T Status of empirical methods for the prediction of protein backbone topography J Biochemistry 15, 5138-5153 (1976) * Recalculated by Kidera using a different set of proteins * Reported values normalized by the total number C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.64 0.62 3.14 1.92 0.32 0.80 1.01 0.63 2.05 0.92 0.37 0.89 1.07 0.86 0.50 1.01 0.92 1.00 1.31 0.87 // H MAXF760104 D Normalized frequency of left-handed alpha-helix (Maxfield-Scheraga, 1976) R LIT:2004036b PMID:990270 A Maxfield, F.R. and Scheraga, H.A. T Status of empirical methods for the prediction of protein backbone topography J Biochemistry 15, 5138-5153 (1976) * Recalculated by Kidera using a different set of proteins * Reported values normalized by the total number C ISOY800108 0.945 RICJ880115 0.919 TANS770107 0.913 MAXF760105 0.850 AURR980117 0.849 RACS820109 0.844 TANS770109 0.821 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.17 0.76 2.62 1.08 0.95 0.91 0.28 5.02 0.57 0.26 0.21 1.17 0.00 0.28 0.12 0.57 0.23 0.00 0.97 0.24 // H MAXF760105 D Normalized frequency of zeta L (Maxfield-Scheraga, 1976) R LIT:2004036b PMID:990270 A Maxfield, F.R. and Scheraga, H.A. T Status of empirical methods for the prediction of protein backbone topography J Biochemistry 15, 5138-5153 (1976) * Recalculated by Kidera using a different set of proteins * Reported values normalized by the total number C TANS770109 0.878 MAXF760104 0.850 ISOY800108 0.810 RICJ880115 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.13 0.48 1.11 1.18 0.38 0.41 1.02 3.84 0.30 0.40 0.65 1.13 0.00 0.45 0.00 0.81 0.71 0.93 0.38 0.48 // H MAXF760106 D Normalized frequency of alpha region (Maxfield-Scheraga, 1976) R LIT:2004036b PMID:990270 A Maxfield, F.R. and Scheraga, H.A. T Status of empirical methods for the prediction of protein backbone topography J Biochemistry 15, 5138-5153 (1976) * Recalculated by Kidera using a different set of proteins * Reported values normalized by the total number C ISOY800106 0.849 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.00 1.18 0.87 1.39 1.09 1.13 1.04 0.46 0.71 0.68 1.01 1.05 0.36 0.65 1.95 1.56 1.23 1.10 0.87 0.58 // H MCMT640101 D Refractivity (McMeekin et al., 1964), Cited by Jones (1975) R A McMeekin, T.L., Groves, M.L. and Hipp, N.J. T J In "Amino Acids and Serum Proteins" (Stekol, J.A., ed.), American Chemical Society, Washington, D.C., p. 54 (1964) C CHAM820101 0.871 ROSG850101 0.857 FAUJ880103 0.847 FASG760101 0.845 CHOC750101 0.822 GRAR740103 0.817 BIGC670101 0.814 GOLD730102 0.814 KRIW790103 0.810 CHOC760101 0.809 FUKS010111 -0.806 RADA880103 -0.833 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.34 26.66 13.28 12.00 35.77 17.56 17.26 0.00 21.81 19.06 18.78 21.29 21.64 29.40 10.93 6.35 11.01 42.53 31.53 13.92 // H MEEJ800101 D Retention coefficient in HPLC, pH7.4 (Meek, 1980) R LIT:0604247 PMID:6929513 A Meek, J.L. T Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition J Proc. Natl. Acad. Sci. USA 77, 1632-1636 (1980) C MEEJ800102 0.886 ZIMJ680105 0.842 BROC820102 0.840 WIMW960101 0.838 GOLD730101 0.808 PARJ860101 -0.806 WOLS870101 -0.823 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.5 0.8 0.8 -8.2 -6.8 -4.8 -16.9 0.0 -3.5 13.9 8.8 0.1 4.8 13.2 6.1 1.2 2.7 14.9 6.1 2.7 // H MEEJ800102 D Retention coefficient in HPLC, pH2.1 (Meek, 1980) R LIT:0604247 PMID:6929513 A Meek, J.L. T Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition J Proc. Natl. Acad. Sci. USA 77, 1632-1636 (1980) C ZIMJ680105 0.921 RADA880102 0.900 NOZY710101 0.895 TAKK010101 0.891 EISD860101 0.890 MEEJ800101 0.886 MEEJ810102 0.881 BROC820101 0.877 MEEJ810101 0.871 PLIV810101 0.867 GOLD730101 0.866 GUOD860101 0.866 SIMZ760101 0.861 FAUJ830101 0.858 BROC820102 0.857 CIDH920102 0.856 ARGP820101 0.855 JOND750101 0.855 CIDH920105 0.840 WIMW960101 0.821 ROBB790101 0.807 WEBA780101 -0.808 HOPT810101 -0.826 LEVM760101 -0.855 BULH740101 -0.875 PARJ860101 -0.902 WOLS870101 -0.925 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.1 -4.5 -1.6 -2.8 -2.2 -2.5 -7.5 -0.5 0.8 11.8 10.0 -3.2 7.1 13.9 8.0 -3.7 1.5 18.1 8.2 3.3 // H MEEJ810101 D Retention coefficient in NaClO4 (Meek-Rossetti, 1981) R LIT:0708201 A Meek, J.L. and Rossetti, Z.L. T Factors affecting retention and resolution of peptides in high-performance liquid chromatography J J. Chromatogr. 211, 15-28 (1981) C MEEJ810102 0.987 GUOD860101 0.931 PLIV810101 0.914 FAUJ830101 0.902 CIDH920105 0.892 ARGP820101 0.891 JOND750101 0.891 CIDH920102 0.887 NOZY710101 0.882 CIDH920104 0.878 MEEJ800102 0.871 MIYS850101 0.863 ROBB790101 0.861 BIOV880101 0.855 NISK860101 0.848 CIDH920103 0.837 SIMZ760101 0.836 TAKK010101 0.836 LEVM760106 0.827 WERD780101 0.825 GOLD730101 0.824 BIOV880102 0.822 VENT840101 0.813 SWER830101 0.806 EISD860101 0.805 RADA880108 0.804 MEIH800101 -0.809 KARP850101 -0.818 WEBA780101 -0.831 GRAR740102 -0.839 VINM940102 -0.839 OOBM770103 -0.861 BULH740101 -0.876 WOLS870101 -0.906 PARJ860101 -0.920 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.1 -0.4 -4.2 -1.6 7.1 -2.9 0.7 -0.2 -0.7 8.5 11.0 -1.9 5.4 13.4 4.4 -3.2 -1.7 17.1 7.4 5.9 // H MEEJ810102 D Retention coefficient in NaH2PO4 (Meek-Rossetti, 1981) R LIT:0708201 A Meek, J.L. and Rossetti, Z.L. T Factors affecting retention and resolution of peptides in high-performance liquid chromatography J J. Chromatogr. 211, 15-28 (1981) C MEEJ810101 0.987 GUOD860101 0.949 NOZY710101 0.899 PLIV810101 0.898 FAUJ830101 0.890 MEEJ800102 0.881 ARGP820101 0.853 JOND750101 0.852 WILM950101 0.849 MIYS850101 0.844 CIDH920105 0.844 CIDH920102 0.843 CIDH920104 0.837 VENT840101 0.831 BIOV880101 0.824 ROBB790101 0.821 BROC820101 0.820 TAKK010101 0.819 RADA880102 0.813 NISK860101 0.810 WILM950102 0.809 EISD860101 0.808 SIMZ760101 0.808 GOLD730101 0.806 GRAR740102 -0.811 OOBM770103 -0.831 WEBA780101 -0.854 BULH740101 -0.880 PARJ860101 -0.897 WOLS870101 -0.905 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.0 -2.0 -3.0 -0.5 4.6 -2.0 1.1 0.2 -2.2 7.0 9.6 -3.0 4.0 12.6 3.1 -2.9 -0.6 15.1 6.7 4.6 // H MEIH800101 D Average reduced distance for C-alpha (Meirovitch et al., 1980) R LIT:0702089 A Meirovitch, H., Rackovsky, S. and Scheraga, H.A. T Empirical studies of hydrophobicity. 1. Effect of protein size on the hydrophobic behavior of amino acids J Macromolecules 13, 1398-1405 (1980) * Database taken from group C C RACS770101 0.973 RACS770102 0.963 MEIH800102 0.952 PARJ860101 0.905 VINM940101 0.900 OOBM770103 0.897 GUYH850101 0.893 KARP850102 0.884 VINM940103 0.875 KRIW790101 0.869 WOLS870101 0.852 RACS770103 0.837 KRIW790102 0.835 VINM940102 0.833 KARP850101 0.832 FUKS010103 0.832 GRAR740102 0.824 PARS000101 0.813 RICJ880111 -0.802 DESM900102 -0.804 NADH010105 -0.806 LIFS790101 -0.809 MEEJ810101 -0.809 EISD860103 -0.810 RADA880102 -0.816 PONP800108 -0.825 PTIO830102 -0.828 SWER830101 -0.830 BEGF750102 -0.832 GUOD860101 -0.833 NADH010102 -0.847 NISK800101 -0.852 PONP800103 -0.856 CIDH920101 -0.863 FAUJ830101 -0.863 NADH010104 -0.867 CIDH920102 -0.867 NADH010103 -0.868 ROBB790101 -0.868 PONP800102 -0.870 MEIH800103 -0.875 PONP800101 -0.888 PLIV810101 -0.896 MANP780101 -0.897 CIDH920103 -0.905 PONP800107 -0.909 PONP930101 -0.916 CIDH920104 -0.917 CIDH920105 -0.923 ROSG850102 -0.930 BIOV880102 -0.937 RADA880108 -0.940 WERD780101 -0.943 BIOV880101 -0.949 MIYS850101 -0.957 NISK860101 -0.960 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.93 0.98 0.98 1.01 0.88 1.02 1.02 1.01 0.89 0.79 0.85 1.05 0.84 0.78 1.00 1.02 0.99 0.83 0.93 0.81 // H MEIH800102 D Average reduced distance for side chain (Meirovitch et al., 1980) R LIT:0702089 A Meirovitch, H., Rackovsky, S. and Scheraga, H.A. T Empirical studies of hydrophobicity. 1. Effect of protein size on the hydrophobic behavior of amino acids J Macromolecules 13, 1398-1405 (1980) * Database taken from group C * (Gly 0.067) C RACS770102 0.987 MEIH800101 0.952 GUYH850101 0.934 RACS770101 0.905 RACS770103 0.903 KRIW790102 0.898 OOBM770101 0.881 KRIW790101 0.876 JANJ780103 0.873 VINM940101 0.872 ROSM880102 0.859 OOBM770103 0.859 JANJ780101 0.843 VINM940103 0.841 CHOC760102 0.839 KARP850102 0.837 GRAR740102 0.836 PARJ860101 0.831 KUHL950101 0.822 FUKS010104 0.822 WOLS870101 0.813 VINM940104 0.808 NAKH900110 -0.802 NADH010101 -0.818 JANJ790101 -0.821 DESM900101 -0.822 CIDH920103 -0.825 WARP780101 -0.826 CIDH920105 -0.826 EISD840101 -0.829 PONP800108 -0.836 NISK800101 -0.844 PLIV810101 -0.849 PONP800107 -0.858 MANP780101 -0.865 CIDH920104 -0.868 KYTJ820101 -0.871 FAUJ830101 -0.875 PONP800101 -0.877 JURD980101 -0.879 PONP930101 -0.881 EISD860103 -0.882 PONP800102 -0.883 PONP800103 -0.891 CHOC760103 -0.894 JANJ790102 -0.894 DESM900102 -0.898 NADH010104 -0.900 WERD780101 -0.903 JANJ780102 -0.907 NADH010103 -0.916 NISK860101 -0.920 NADH010102 -0.928 MIYS850101 -0.934 MEIH800103 -0.941 BIOV880102 -0.951 RADA880108 -0.953 BIOV880101 -0.956 ROSG850102 -0.959 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.94 1.09 1.04 1.08 0.84 1.11 1.12 1.01 0.92 0.76 0.82 1.23 0.83 0.73 1.04 1.04 1.02 0.87 1.03 0.81 // H MEIH800103 D Average side chain orientation angle (Meirovitch et al., 1980) R LIT:0702089 A Meirovitch, H., Rackovsky, S. and Scheraga, H.A. T Empirical studies of hydrophobicity. 1. Effect of protein size on the hydrophobic behavior of amino acids J Macromolecules 13, 1398-1405 (1980) * Database taken from group C * (Gly 7.4) C ROSG850102 0.948 BIOV880101 0.934 DESM900102 0.924 RADA880108 0.916 BIOV880102 0.916 NISK860101 0.909 MIYS850101 0.908 NADH010102 0.907 NADH010103 0.901 JANJ780102 0.897 WERD780101 0.895 PONP800103 0.895 NADH010104 0.890 PONP800102 0.885 NISK800101 0.871 EISD860103 0.870 PONP800101 0.869 CHOC760103 0.865 PONP930101 0.863 PONP800108 0.862 JURD980101 0.861 KYTJ820101 0.856 CIDH920104 0.853 DESM900101 0.853 JANJ790102 0.853 FAUJ830101 0.849 MANP780101 0.839 JANJ790101 0.838 WARP780101 0.835 NADH010101 0.824 NADH010105 0.816 PLIV810101 0.811 CIDH920105 0.804 CIDH920103 0.802 ROBB790101 0.801 WOEC730101 -0.802 CHOC760102 -0.802 PARJ860101 -0.808 KUHL950101 -0.809 JANJ780101 -0.811 ROSM880102 -0.829 VINM940103 -0.830 RACS770101 -0.845 KRIW790101 -0.850 VINM940101 -0.861 GRAR740102 -0.866 OOBM770103 -0.866 JANJ780103 -0.866 MEIH800101 -0.875 GUYH850101 -0.880 KRIW790102 -0.885 OOBM770101 -0.896 RACS770102 -0.918 RACS770103 -0.919 MEIH800102 -0.941 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 87. 81. 70. 71. 104. 66. 72. 90. 90. 105. 104. 65. 100. 108. 78. 83. 83. 94. 83. 94. // H MIYS850101 D Effective partition energy (Miyazawa-Jernigan, 1985) R LIT:2004114b A Miyazawa, S. and Jernigan, R.L. T Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation J Macromolecules 18, 534-552 (1985) C BIOV880101 0.960 NISK860101 0.960 RADA880108 0.950 PLIV810101 0.944 ROSG850102 0.937 WERD780101 0.934 BIOV880102 0.930 CIDH920105 0.916 CIDH920104 0.915 FAUJ830101 0.914 PONP930101 0.910 MANP780101 0.909 MEIH800103 0.908 GUOD860101 0.908 CIDH920103 0.906 PONP800103 0.898 NADH010104 0.897 NADH010103 0.896 ROBB790101 0.895 PONP800101 0.892 PONP800102 0.891 SWER830101 0.889 PONP800107 0.884 NADH010102 0.878 CIDH920102 0.873 NISK800101 0.864 MEEJ810101 0.863 EISD860103 0.858 PONP800108 0.847 MEEJ810102 0.844 NADH010105 0.844 CIDH920101 0.843 EISD860101 0.842 JURD980101 0.837 DESM900102 0.831 RADA880102 0.824 ARGP820103 0.822 KYTJ820101 0.821 NADH010101 0.815 PONP800106 0.812 CHOC760103 0.810 NOZY710101 0.810 PTIO830102 0.807 BEGF750102 0.806 JANJ780102 0.806 NAKH900110 0.804 HOPT810101 -0.800 KARP850101 -0.811 RACS770103 -0.818 PARS000101 -0.821 ROSM880102 -0.825 FUKS010103 -0.828 VINM940102 -0.832 BULH740101 -0.838 VINM940103 -0.849 KRIW790102 -0.869 KARP850102 -0.878 VINM940101 -0.883 GRAR740102 -0.895 WOLS870101 -0.899 GUYH850101 -0.909 OOBM770103 -0.910 KRIW790101 -0.910 PARJ860101 -0.929 MEIH800102 -0.934 RACS770101 -0.940 RACS770102 -0.943 MEIH800101 -0.957 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.36 1.92 1.70 1.67 3.36 1.75 1.74 2.06 2.41 4.17 3.93 1.23 4.22 4.37 1.89 1.81 2.04 3.82 2.91 3.49 // H NAGK730101 D Normalized frequency of alpha-helix (Nagano, 1973) R PMID:4728695 A Nagano, K. T Local analysis of the mechanism of protein folding. I. Prediction of helices, loops, and beta-structures from primary structure J J. Mol. Biol. 75, 401-420 (1973) C PALJ810101 0.953 CRAJ730101 0.925 TANS770101 0.925 LEVM780104 0.918 GEIM800101 0.912 ROBB760101 0.910 PRAM900102 0.894 LEVM780101 0.894 CHOP780201 0.886 KANM800101 0.883 BURA740101 0.883 MAXF760101 0.877 PALJ810102 0.876 ISOY800101 0.862 GEIM800104 0.828 RACS820108 0.820 NAGK730103 -0.870 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.29 0.83 0.77 1.00 0.94 1.10 1.54 0.72 1.29 0.94 1.23 1.23 1.23 1.23 0.70 0.78 0.87 1.06 0.63 0.97 // H NAGK730102 D Normalized frequency of bata-structure (Nagano, 1973) R PMID:4728695 A Nagano, K. T Local analysis of the mechanism of protein folding. I. Prediction of helices, loops, and beta-structures from primary structure J J. Mol. Biol. 75, 401-420 (1973) C ROBB760106 0.887 KANM800102 0.878 PALJ810104 0.867 CHOP780208 0.860 CHOP780202 0.858 BEGF750102 0.833 GEIM800107 0.830 ROBB760105 0.815 CRAJ730102 0.815 PTIO830102 0.811 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.96 0.67 0.72 0.90 1.13 1.18 0.33 0.90 0.87 1.54 1.26 0.81 1.29 1.37 0.75 0.77 1.23 1.13 1.07 1.41 // H NAGK730103 D Normalized frequency of coil (Nagano, 1973) R PMID:4728695 A Nagano, K. T Local analysis of the mechanism of protein folding. I. Prediction of helices, loops, and beta-structures from primary structure J J. Mol. Biol. 75, 401-420 (1973) C CHAM830101 0.857 CHOP780101 0.827 CHOP780216 0.819 CHOP780210 0.814 ROBB760113 0.811 PALJ810105 0.804 TANS770101 -0.800 MAXF760101 -0.801 PALJ810101 -0.808 LEVM780101 -0.809 PRAM900102 -0.809 PALJ810102 -0.818 ISOY800101 -0.821 BURA740101 -0.830 CHOP780201 -0.837 KANM800103 -0.847 CRAJ730101 -0.850 ROBB760101 -0.861 NAGK730101 -0.870 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.72 1.33 1.38 1.04 1.01 0.81 0.75 1.35 0.76 0.80 0.63 0.84 0.62 0.58 1.43 1.34 1.03 0.87 1.35 0.83 // H NAKH900101 D AA composition of total proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C JOND920101 0.993 CEDJ970102 0.988 CEDJ970104 0.978 CEDJ970101 0.954 FUKS010112 0.948 FUKS010110 0.946 JUKT750101 0.941 DAYM780101 0.940 JUNJ780101 0.918 CEDJ970103 0.908 NAKH920101 0.907 NAKH920106 0.900 KUMS000102 0.894 FUKS010109 0.868 NAKH900109 0.866 NAKH920107 0.863 CEDJ970105 0.860 NAKH900102 0.858 NAKH920104 0.857 KUMS000101 0.856 NAKH920103 0.854 FUKS010111 0.812 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.99 5.86 4.33 5.14 1.81 3.98 6.10 6.91 2.17 5.48 9.16 6.01 2.50 3.83 4.95 6.84 5.77 1.34 3.15 6.65 // H NAKH900102 D SD of AA composition of total proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C CEDJ970105 0.903 DAYM780101 0.883 NAKH920106 0.872 CEDJ970104 0.860 NAKH900101 0.858 NAKH920101 0.854 JUNJ780101 0.853 JOND920101 0.846 CEDJ970102 0.841 CEDJ970101 0.832 RACS820105 -0.839 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 3.73 3.34 2.33 2.23 2.30 2.36 3. 3.36 1.55 2.52 3.40 3.36 1.37 1.94 3.18 2.83 2.63 1.15 1.76 2.53 // H NAKH900103 D AA composition of mt-proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH900105 0.992 NAKH900112 0.966 NAKH900107 0.927 FUKS010108 0.864 NAKH900111 0.832 NAKH920105 0.829 NAKH920108 0.826 CEDJ970103 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.74 1.92 5.25 2.11 1.03 2.30 2.63 5.66 2.30 9.12 15.36 3.20 5.30 6.51 4.79 7.55 7.51 2.51 4.08 5.12 // H NAKH900104 D Normalized composition of mt-proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH900106 0.986 NAKH900108 0.849 EISD860101 0.812 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.60 -1.18 0.39 -1.36 -0.34 -0.71 -1.16 -0.37 0.08 1.44 1.82 -0.84 2.04 1.38 -0.05 0.25 0.66 1.02 0.53 -0.60 // H NAKH900105 D AA composition of mt-proteins from animal (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH900103 0.992 NAKH900112 0.974 NAKH900107 0.870 FUKS010108 0.846 NAKH900111 0.815 NAKH920105 0.806 NAKH920108 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.88 1.54 4.38 1.70 1.11 2.30 2.60 5.29 2.33 8.78 16.52 2.58 6.00 6.58 5.29 7.68 8.38 2.89 3.51 4.66 // H NAKH900106 D Normalized composition from animal (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH900104 0.986 EISD860101 0.812 ARGP820103 0.810 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.57 -1.29 0.02 -1.54 -0.30 -0.71 -1.17 -0.48 0.10 1.31 2.16 -1.02 2.55 1.42 0.11 0.30 0.99 1.35 0.20 -0.79 // H NAKH900107 D AA composition of mt-proteins from fungi and plant (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH900103 0.927 NAKH900105 0.870 NAKH900112 0.850 FUKS010108 0.830 CEDJ970103 0.820 NAKH920108 0.816 NAKH920105 0.814 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.39 2.81 7.31 3.07 0.86 2.31 2.70 6.52 2.23 9.94 12.64 4.67 3.68 6.34 3.62 7.24 5.44 1.64 5.42 6.18 // H NAKH900108 D Normalized composition from fungi and plant (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH900104 0.849 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.70 -0.91 1.28 -0.93 -0.41 -0.71 -1.13 -0.12 0.04 1.77 1.02 -0.40 0.86 1.29 -0.42 0.14 -0.13 0.26 1.29 -0.19 // H NAKH900109 D AA composition of membrane proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C CEDJ970103 0.970 FUKS010106 0.927 FUKS010107 0.903 FUKS010105 0.892 NAKH900111 0.890 JOND920101 0.878 FUKS010108 0.872 NAKH900101 0.866 CEDJ970102 0.865 CEDJ970101 0.861 FUKS010110 0.853 KUMS000102 0.837 NAKH920105 0.823 CEDJ970104 0.821 JUKT750101 0.815 NAKH920108 0.811 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.25 3.96 3.71 3.89 1.07 3.17 4.80 8.51 1.88 6.47 10.94 3.50 3.14 6.36 4.36 6.26 5.66 2.22 3.28 7.55 // H NAKH900110 D Normalized composition of membrane proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C EISD840101 0.838 BROC820101 0.830 BIOV880102 0.829 EISD860101 0.820 GUOD860101 0.805 MIYS850101 0.804 MEIH800102 -0.802 PARJ860101 -0.808 ROSM880101 -0.812 HOPT810101 -0.812 WOLS870101 -0.832 VHEG790101 -0.848 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.34 -0.57 -0.27 -0.56 -0.32 -0.34 -0.43 0.48 -0.19 0.39 0.52 -0.75 0.47 1.30 -0.19 -0.20 -0.04 0.77 0.07 0.36 // H NAKH900111 D Transmembrane regions of non-mt-proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH920108 0.975 NAKH920105 0.958 FUKS010108 0.954 FUKS010106 0.933 FUKS010105 0.911 NAKH900109 0.890 NAKH900112 0.878 FUKS010107 0.867 CEDJ970103 0.865 NAKH900103 0.832 KYTJ820101 0.817 NAKH900105 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 10.17 1.21 1.36 1.18 1.48 1.57 1.15 8.87 1.07 10.91 16.22 1.04 4.12 9.60 2.24 5.38 5.61 2.67 2.68 11.44 // H NAKH900112 D Transmembrane regions of mt-proteins (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C NAKH900105 0.974 NAKH900103 0.966 FUKS010108 0.896 NAKH920105 0.881 NAKH920108 0.879 NAKH900111 0.878 NAKH900107 0.850 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.61 0.41 1.84 0.59 0.83 1.20 1.63 4.88 1.14 12.91 21.66 1.15 7.17 7.76 3.51 6.84 8.89 2.11 2.57 6.30 // H NAKH900113 D Ratio of average and computed composition (Nakashima et al., 1990) R LIT:2004138b PMID:2235995 A Nakashima, H., Nishikawa, K. and Ooi, T. T Distinct character in hydrophobicity of amino acid composition of mitochondrial proteins J PROTEINS 8, 173-178 (1990) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.61 0.40 0.73 0.75 0.37 0.61 1.50 3.12 0.46 1.61 1.37 0.62 1.59 1.24 0.67 0.68 0.92 1.63 0.67 1.30 // H NAKH920101 D AA composition of CYT of single-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C CEDJ970105 0.942 NAKH920106 0.929 NAKH920102 0.929 CEDJ970104 0.920 NAKH900101 0.907 JOND920101 0.900 CEDJ970102 0.898 DAYM780101 0.882 FUKS010112 0.856 NAKH900102 0.854 CEDJ970101 0.850 JUKT750101 0.849 FUKS010110 0.833 JUNJ780101 0.826 NAKH920104 0.822 NAKH920103 0.811 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.63 6.75 4.18 6.24 1.03 4.76 7.82 6.80 2.70 3.48 8.44 6.25 2.14 2.73 6.28 8.53 4.43 0.80 2.54 5.44 // H NAKH920102 D AA composition of CYT2 of single-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C NAKH920101 0.929 CEDJ970105 0.843 CEDJ970104 0.834 NAKH920106 0.832 DAYM780101 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 10.88 6.01 5.75 6.13 0.69 4.68 9.34 7.72 2.15 1.80 8.03 6.11 3.79 2.93 7.21 7.25 3.51 0.47 1.01 4.57 // H NAKH920103 D AA composition of EXT of single-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C CEDJ970102 0.906 NAKH920104 0.904 NAKH920107 0.882 JOND920101 0.881 CEDJ970104 0.863 NAKH900101 0.854 DAYM780101 0.851 CEDJ970101 0.843 FUKS010112 0.842 JUKT750101 0.837 JUNJ780101 0.820 NAKH920101 0.811 NAKH920106 0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.15 4.38 4.81 5.75 3.24 4.45 7.05 6.38 2.69 4.40 8.11 5.25 1.60 3.52 5.65 8.04 7.41 1.68 3.42 7.00 // H NAKH920104 D AA composition of EXT2 of single-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C CEDJ970102 0.905 NAKH920103 0.904 NAKH920107 0.889 JOND920101 0.887 FUKS010112 0.882 CEDJ970104 0.865 CEDJ970101 0.859 NAKH900101 0.857 NAKH920106 0.829 JUKT750101 0.827 NAKH920101 0.822 DAYM780101 0.819 JUNJ780101 0.807 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.04 3.73 5.94 5.26 2.20 4.50 6.07 7.09 2.99 4.32 9.88 6.31 1.85 3.72 6.22 8.05 5.20 2.10 3.32 6.19 // H NAKH920105 D AA composition of MEM of single-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C FUKS010108 0.968 NAKH920108 0.959 NAKH900111 0.958 FUKS010106 0.931 FUKS010105 0.929 NAKH900112 0.881 CEDJ970103 0.836 FUKS010107 0.833 NAKH900103 0.829 NAKH900109 0.823 NAKH900107 0.814 NAKH900105 0.806 KYTJ820101 0.803 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.90 0.09 0.94 0.35 2.55 0.87 0.08 8.14 0.20 15.25 22.28 0.16 1.85 6.47 2.38 4.17 4.33 2.21 3.42 14.34 // H NAKH920106 D AA composition of CYT of multi-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C CEDJ970105 0.930 NAKH920101 0.929 CEDJ970104 0.923 FUKS010112 0.921 NAKH900101 0.900 JOND920101 0.889 CEDJ970102 0.886 NAKH900102 0.872 DAYM780101 0.856 NAKH920102 0.832 JUKT750101 0.831 NAKH920104 0.829 JUNJ780101 0.829 CEDJ970101 0.826 FUKS010110 0.824 FUKS010104 0.818 FUKS010109 0.814 NAKH920103 0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.69 6.65 4.49 4.97 1.70 5.39 7.76 6.32 2.11 4.51 8.23 8.36 2.46 3.59 5.20 7.40 5.18 1.06 2.75 5.27 // H NAKH920107 D AA composition of EXT of multi-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C JOND920101 0.893 CEDJ970102 0.891 NAKH920104 0.889 NAKH920103 0.882 NAKH900101 0.863 JUKT750101 0.862 DAYM780101 0.861 CEDJ970101 0.860 CEDJ970104 0.857 JUNJ780101 0.856 FUKS010111 0.841 KUMS000102 0.839 FUKS010112 0.824 FUKS010110 0.810 KUMS000101 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.08 4.75 5.75 5.96 2.95 4.24 6.04 8.20 2.10 4.95 8.03 4.93 2.61 4.36 4.84 6.41 5.87 2.31 4.55 6.07 // H NAKH920108 D AA composition of MEM of multi-spanning proteins (Nakashima-Nishikawa, 1992) R LIT:1811095b PMID:1607012 A Nakashima, H. and Nishikawa, K. T The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins J FEBS Lett. 303, 141-146 (1992) C NAKH900111 0.975 NAKH920105 0.959 FUKS010108 0.948 FUKS010106 0.898 FUKS010105 0.890 NAKH900112 0.879 KYTJ820101 0.868 JURD980101 0.858 NAKH900103 0.826 CHOC760103 0.824 FUKS010107 0.817 NAKH900107 0.816 NAKH900109 0.811 CEDJ970103 0.811 NAKH900105 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.36 0.27 2.31 0.94 2.56 1.14 0.94 6.17 0.47 13.73 16.64 0.58 3.93 10.99 1.96 5.58 4.68 2.20 3.13 12.43 // H NISK800101 D 8 A contact number (Nishikawa-Ooi, 1980) R LIT:2004068b PMID:7440060 A Nishikawa, K. and Ooi, T. T Prediction of the surface-interior diagram of globular proteins by an empirical method J Int. J. Peptide Protein Res. 16, 19-32 (1980) C PONP800108 0.976 PONP800102 0.965 PONP800101 0.960 PONP930101 0.956 NISK860101 0.943 ROSG850102 0.942 PONP800103 0.941 MANP780101 0.940 BIOV880101 0.920 NADH010104 0.909 NADH010103 0.908 RADA880108 0.902 CIDH920104 0.900 WERD780101 0.891 NADH010102 0.881 JANJ790101 0.875 BIOV880102 0.873 MEIH800103 0.871 MIYS850101 0.864 NADH010105 0.860 CIDH920103 0.855 CIDH920105 0.854 JANJ780102 0.853 DESM900102 0.852 FAUJ830101 0.849 DESM900101 0.837 ROBB790101 0.830 LIFS790101 0.827 QIAN880121 0.818 JURD980101 0.816 NADH010101 0.813 KYTJ820101 0.812 KANM800102 0.809 QIAN880122 0.808 RACS770101 -0.805 GUYH850101 -0.811 MUNV940103 -0.813 PARS000102 -0.814 RACS770102 -0.818 KRIW710101 -0.831 PARS000101 -0.832 VINM940103 -0.836 MEIH800102 -0.844 OOBM770101 -0.845 MEIH800101 -0.852 GRAR740102 -0.879 KARP850102 -0.885 OOBM770103 -0.894 KRIW790101 -0.896 VINM940102 -0.900 VINM940101 -0.922 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.23 -0.26 -0.94 -1.13 1.78 -0.57 -0.75 -0.07 0.11 1.19 1.03 -1.05 0.66 0.48 -0.76 -0.67 -0.36 0.90 0.59 1.24 // H NISK860101 D 14 A contact number (Nishikawa-Ooi, 1986) R LIT:1211490 PMID:3818558 A Nishikawa, K. and Ooi, T. T Radial locations of amino acid residues in a globular protein: Correlation with the sequence J J. Biochem. 100, 1043-1047 (1986) * Values supplied by the author C BIOV880101 0.972 WERD780101 0.966 ROSG850102 0.962 PONP930101 0.961 MIYS850101 0.960 RADA880108 0.950 CIDH920104 0.944 NISK800101 0.943 BIOV880102 0.939 CIDH920105 0.938 MANP780101 0.930 PONP800101 0.930 PONP800102 0.924 PONP800108 0.921 NADH010104 0.915 ROBB790101 0.912 PONP800103 0.910 NADH010103 0.910 MEIH800103 0.909 CIDH920103 0.909 FAUJ830101 0.906 CIDH920102 0.897 PLIV810101 0.892 CIDH920101 0.882 NADH010102 0.878 SWER830101 0.865 NADH010105 0.863 LIFS790101 0.859 MEEJ810101 0.848 PONP800107 0.847 DESM900102 0.843 GUOD860101 0.840 QIAN880120 0.837 CHOP780202 0.832 QIAN880121 0.829 PTIO830102 0.825 KANM800102 0.819 JANJ780102 0.813 GEIM800107 0.813 EISD860103 0.811 NADH010101 0.810 ROBB760106 0.810 MEEJ810102 0.810 PALJ810104 0.809 JURD980101 0.808 HOPT810101 -0.822 WOEC730101 -0.822 KARP850101 -0.828 FUKS010104 -0.832 RACS770103 -0.837 MUNV940103 -0.840 WOLS870101 -0.848 FUKS010103 -0.850 KRIW790102 -0.855 GUYH850101 -0.877 PARS000101 -0.884 GRAR740102 -0.900 KARP850102 -0.901 VINM940103 -0.903 KRIW790101 -0.907 RACS770102 -0.913 PARJ860101 -0.916 VINM940102 -0.919 MEIH800102 -0.920 RACS770101 -0.923 OOBM770103 -0.949 VINM940101 -0.959 MEIH800101 -0.960 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.22 -0.93 -2.65 -4.12 4.66 -2.76 -3.64 -1.62 1.28 5.58 5.01 -4.18 3.51 5.27 -3.03 -2.84 -1.20 5.20 2.15 4.45 // H NOZY710101 D Transfer energy, organic solvent/water (Nozaki-Tanford, 1971) R PMID:5555568 A Nozaki, Y. and Tanford, C. T The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions J J. Biol. Chem. 246, 2211-2217 (1971) * Missing values filled with zeros C RADA880102 0.917 MEEJ810102 0.899 VENT840101 0.897 MEEJ800102 0.895 CIDH920102 0.889 TAKK010101 0.884 GUOD860101 0.884 MEEJ810101 0.882 CIDH920105 0.857 LEVM760107 0.845 PLIV810101 0.839 ZIMJ680105 0.837 SWER830101 0.836 ROSG850101 0.834 BROC820101 0.829 EISD860101 0.822 GARJ730101 0.821 WIMW960101 0.818 MIYS850101 0.810 SIMZ760101 0.807 FAUJ830101 0.803 ARGP820101 0.800 OOBM770103 -0.828 PARS000101 -0.829 WOLS870101 -0.874 WEBA780101 -0.890 BULH740101 -0.892 PARJ860101 -0.900 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.8 1.8 0.0 1.3 2.5 0.0 0.0 0.4 3.4 2.3 1.5 // H OOBM770101 D Average non-bonded energy per atom (Oobatake-Ooi, 1977) R LIT:2004111b PMID:904331 A Oobatake, M. and Ooi, T. T An analysis of non-bonded energy of proteins J J. Theor. Biol. 67, 567-584 (1977) * Last two calcualted by Kidera; multiplied by the number of heavy atoms C JANJ780103 0.965 JANJ780101 0.953 CHOC760102 0.925 PRAM900101 0.907 MEIH800102 0.881 KUHL950101 0.876 RACS770103 0.871 ROSM880102 0.867 ROSM880101 0.854 GUYH850101 0.848 GRAR740102 0.841 RACS770102 0.838 KRIW790102 0.822 KRIW790101 0.816 WOEC730101 0.804 MANP780101 -0.806 FAUJ830101 -0.832 PONP800101 -0.835 NISK800101 -0.845 WOLR810101 -0.847 PONP800108 -0.851 RADA880107 -0.854 CHOC760104 -0.857 BIOV880101 -0.858 NADH010101 -0.861 PONP800102 -0.862 RADA880101 -0.863 RADA880108 -0.864 NADH010104 -0.871 JANJ790101 -0.871 BIOV880102 -0.877 EISD840101 -0.878 EISD860103 -0.880 PONP800103 -0.880 DESM900101 -0.894 MEIH800103 -0.896 KYTJ820101 -0.899 CHOC760103 -0.902 NADH010103 -0.902 JURD980101 -0.903 ROSG850102 -0.903 WARP780101 -0.937 NADH010102 -0.944 DESM900102 -0.950 JANJ790102 -0.963 JANJ780102 -0.968 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -1.895 -1.475 -1.560 -1.518 -2.035 -1.521 -1.535 -1.898 -1.755 -1.951 -1.966 -1.374 -1.963 -1.864 -1.699 -1.753 -1.767 -1.869 -1.686 -1.981 // H OOBM770102 D Short and medium range non-bonded energy per atom (Oobatake-Ooi, 1977) R LIT:2004111b PMID:904331 A Oobatake, M. and Ooi, T. T An analysis of non-bonded energy of proteins J J. Theor. Biol. 67, 567-584 (1977) * Last two calcualted by Kidera; multiplied by the number of heavy atoms C LEVM760102 0.869 LEVM760105 0.868 CHAM830106 0.858 CHOC760101 0.824 FASG760101 0.821 FAUJ880103 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -1.404 -0.921 -1.178 -1.162 -1.365 -1.116 -1.163 -1.364 -1.215 -1.189 -1.315 -1.074 -1.303 -1.135 -1.236 -1.297 -1.252 -1.030 -1.030 -1.254 // H OOBM770103 D Long range non-bonded energy per atom (Oobatake-Ooi, 1977) R LIT:2004111b PMID:904331 A Oobatake, M. and Ooi, T. T An analysis of non-bonded energy of proteins J J. Theor. Biol. 67, 567-584 (1977) * Last two calcualted by Kidera; multiplied by the number of heavy atoms C VINM940101 0.936 MEIH800101 0.897 GRAR740102 0.896 PARJ860101 0.891 VINM940102 0.891 KRIW790101 0.865 PARS000101 0.864 MEIH800102 0.859 WOLS870101 0.852 FUKS010104 0.849 VINM940103 0.845 WOEC730101 0.835 RACS770101 0.835 HOPT810101 0.833 RACS770102 0.828 KRIW790102 0.824 RACS770103 0.823 KARP850102 0.820 MUNV940103 0.805 LEVM760101 0.805 PTIO830102 -0.801 LIFS790103 -0.807 KANM800102 -0.812 WIMW960101 -0.814 CIDH920101 -0.818 PONP800107 -0.819 CHOP780202 -0.820 QIAN880120 -0.824 NOZY710101 -0.828 MEEJ810102 -0.831 SWER830101 -0.833 NADH010102 -0.838 GUOD860101 -0.838 PONP800101 -0.848 PLIV810101 -0.852 PONP800102 -0.854 LIFS790101 -0.855 MANP780101 -0.859 MEEJ810101 -0.861 NADH010103 -0.861 NADH010104 -0.863 CIDH920103 -0.863 PONP800103 -0.865 MEIH800103 -0.866 CIDH920102 -0.877 RADA880108 -0.878 NISK800101 -0.894 PONP800108 -0.896 FAUJ830101 -0.899 CIDH920105 -0.904 WERD780101 -0.906 ROBB790101 -0.909 MIYS850101 -0.910 CIDH920104 -0.912 PONP930101 -0.914 ROSG850102 -0.916 BIOV880101 -0.920 BIOV880102 -0.925 NISK860101 -0.949 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.491 -0.554 -0.382 -0.356 -0.670 -0.405 -0.371 -0.534 -0.540 -0.762 -0.650 -0.300 -0.659 -0.729 -0.463 -0.455 -0.515 -0.839 -0.656 -0.728 // H OOBM770104 D Average non-bonded energy per residue (Oobatake-Ooi, 1977) R LIT:2004111b PMID:904331 A Oobatake, M. and Ooi, T. T An analysis of non-bonded energy of proteins J J. Theor. Biol. 67, 567-584 (1977) * Last two calcualted by Kidera; multiplied by the number of heavy atoms C OOBM770105 0.980 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -9.475 -16.225 -12.480 -12.144 -12.210 -13.689 -13.815 -7.592 -17.550 -15.608 15.728 -12.366 -15.704 -20.504 -11.893 -10.518 -12.369 -26.166 -20.232 -13.867 // H OOBM770105 D Short and medium range non-bonded energy per residue (Oobatake-Ooi, 1977) R LIT:2004111b PMID:904331 A Oobatake, M. and Ooi, T. T An analysis of non-bonded energy of proteins J J. Theor. Biol. 67, 567-584 (1977) * Last two calcualted by Kidera; multiplied by the number of heavy atoms C OOBM770104 0.980 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -7.020 -10.131 -9.424 -9.296 -8.190 -10.044 -10.467 -5.456 -12.150 -9.512 10.520 -9.666 -10.424 -12.485 -8.652 -7.782 -8.764 -14.420 -12.360 -8.778 // H OOBM850101 D Optimized beta-structure-coil equilibrium constant (Oobatake et al., 1985) R LIT:1207075b A Oobatake, M., Kubota, Y. and Ooi, T. T Optimization of amino acid parameters for correspondence of sequence to tertiary structures of proteuins J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) C QIAN880119 0.825 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.01 0.84 0.03 -2.05 1.98 1.02 0.93 0.12 -0.14 3.70 2.73 2.55 1.75 2.68 0.41 1.47 2.39 2.49 2.23 3.50 // H OOBM850102 D Optimized propensity to form reverse turn (Oobatake et al., 1985) R LIT:1207075b A Oobatake, M., Kubota, Y. and Ooi, T. T Optimization of amino acid parameters for correspondence of sequence to tertiary structures of proteuins J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) C ZASB820101 -0.853 GARJ730101 -0.877 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.34 0.95 2.49 3.32 1.07 1.49 2.20 2.07 1.27 0.66 0.54 0.61 0.70 0.80 2.12 0.94 1.09 -4.65 -0.17 1.32 // H OOBM850103 D Optimized transfer energy parameter (Oobatake et al., 1985) R LIT:1207075b A Oobatake, M., Kubota, Y. and Ooi, T. T Optimization of amino acid parameters for correspondence of sequence to tertiary structures of proteuins J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.46 -1.54 1.31 -0.33 0.20 -1.12 0.48 0.64 -1.31 3.28 0.43 -1.71 0.15 0.52 -0.58 -0.83 -1.52 1.25 -2.21 0.54 // H OOBM850104 D Optimized average non-bonded energy per atom (Oobatake et al., 1985) R LIT:1207075b A Oobatake, M., Kubota, Y. and Ooi, T. T Optimization of amino acid parameters for correspondence of sequence to tertiary structures of proteuins J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -2.49 2.55 2.27 8.86 -3.13 1.79 4.04 -0.56 4.22 -10.87 -7.16 -9.97 -4.96 -6.64 5.19 -1.60 -4.75 -17.84 9.25 -3.97 // H OOBM850105 D Optimized side chain interaction parameter (Oobatake et al., 1985) R LIT:1207075b A Oobatake, M., Kubota, Y. and Ooi, T. T Optimization of amino acid parameters for correspondence of sequence to tertiary structures of proteuins J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985) C QIAN880127 -0.813 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.55 5.97 5.56 2.85 -0.78 4.15 5.16 9.14 4.48 2.10 3.24 10.68 2.18 4.37 5.14 6.78 8.60 1.97 2.40 3.81 // H PALJ810101 D Normalized frequency of alpha-helix from LG (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C LEVM780104 0.988 NAGK730101 0.953 GEIM800101 0.951 LEVM780101 0.943 PRAM900102 0.943 KANM800101 0.928 TANS770101 0.918 ROBB760101 0.914 CRAJ730101 0.891 PALJ810102 0.889 MAXF760101 0.889 ISOY800101 0.882 CHOP780201 0.881 RACS820108 0.872 BURA740101 0.850 GEIM800104 0.841 KANM800103 0.836 NAGK730103 -0.808 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.30 0.93 0.90 1.02 0.92 1.04 1.43 0.63 1.33 0.87 1.30 1.23 1.32 1.09 0.63 0.78 0.80 1.03 0.71 0.95 // H PALJ810102 D Normalized frequency of alpha-helix from CF (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C CHOP780201 0.981 ISOY800101 0.965 KANM800101 0.962 MAXF760101 0.959 ROBB760101 0.946 TANS770101 0.923 KANM800103 0.916 GEIM800101 0.910 LEVM780104 0.906 PRAM900102 0.902 LEVM780101 0.902 BURA740101 0.900 PALJ810101 0.889 AURR980112 0.888 GEIM800104 0.886 RACS820108 0.881 AURR980109 0.877 NAGK730101 0.876 CRAJ730101 0.872 AURR980108 0.871 QIAN880106 0.871 PALJ810109 0.864 QIAN880107 0.856 AURR980114 0.848 AURR980111 0.830 AURR980115 0.827 AURR980110 0.812 BEGF750101 0.811 CHAM830101 -0.808 CRAJ730103 -0.809 MUNV940101 -0.815 NAGK730103 -0.818 MUNV940102 -0.824 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.32 1.04 0.74 0.97 0.70 1.25 1.48 0.59 1.06 1.01 1.22 1.13 1.47 1.10 0.57 0.77 0.86 1.02 0.72 1.05 // H PALJ810103 D Normalized frequency of beta-sheet from LG (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C LEVM780105 0.980 GEIM800105 0.945 CHOP780202 0.937 KANM800102 0.932 LIFS790101 0.912 PALJ810104 0.907 GEIM800107 0.890 ROBB760106 0.886 QIAN880120 0.886 LIFS790103 0.877 QIAN880121 0.875 ROBB760105 0.869 PTIO830102 0.867 QIAN880119 0.861 PRAM900103 0.846 LEVM780102 0.846 QIAN880118 0.845 PALJ810112 0.841 TANS770103 0.824 KANM800104 0.823 ISOY800102 0.807 MUNV940103 -0.857 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.81 1.03 0.81 0.71 1.12 1.03 0.59 0.94 0.85 1.47 1.03 0.77 0.96 1.13 0.75 1.02 1.19 1.24 1.35 1.44 // H PALJ810104 D Normalized frequency of beta-sheet from CF (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C CHOP780202 0.970 KANM800102 0.948 PTIO830102 0.937 LIFS790101 0.929 GEIM800107 0.928 LEVM780105 0.921 QIAN880121 0.910 PALJ810103 0.907 ROBB760106 0.894 QIAN880120 0.886 PRAM900103 0.868 LEVM780102 0.868 NAGK730102 0.867 LIFS790103 0.860 PONP930101 0.857 GEIM800105 0.856 KANM800104 0.851 CHOP780209 0.849 PALJ810112 0.849 ROBB760105 0.835 VENT840101 0.831 QIAN880119 0.822 AVBF000101 0.818 CRAJ730102 0.817 SWER830101 0.809 NISK860101 0.809 MANP780101 0.805 BEGF750102 0.801 VINM940101 -0.801 MUNV940103 -0.888 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.90 0.75 0.82 0.75 1.12 0.95 0.44 0.83 0.86 1.59 1.24 0.75 0.94 1.41 0.46 0.70 1.20 1.28 1.45 1.73 // H PALJ810105 D Normalized frequency of turn from LG (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C ISOY800103 0.928 LEVM780103 0.909 PRAM900104 0.906 LEVM780106 0.902 PALJ810116 0.891 CHOP780216 0.881 CHOP780203 0.878 GEIM800108 0.873 CHOP780101 0.868 TANS770110 0.860 GEIM800111 0.855 QIAN880133 0.843 QIAN880132 0.830 CHAM830101 0.826 PALJ810106 0.809 NAGK730103 0.804 CHOP780210 0.803 AVBF000102 -0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.84 0.91 1.48 1.28 0.69 1. 0.78 1.76 0.53 0.55 0.49 0.95 0.52 0.88 1.47 1.29 1.05 0.88 1.28 0.51 // H PALJ810106 D Normalized frequency of turn from CF (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C CHOP780101 0.977 CHAM830101 0.939 TANS770110 0.925 CHOP780203 0.907 CHOP780210 0.905 CHOP780216 0.904 ROBB760113 0.895 CRAJ730103 0.884 ROBB760108 0.882 ROBB760110 0.864 GEIM800108 0.862 QIAN880133 0.860 BEGF750103 0.859 QIAN880132 0.859 LEVM780106 0.850 LEVM780103 0.848 GEIM800111 0.844 PRAM900104 0.844 QIAN880131 0.809 PALJ810105 0.809 ISOY800103 0.807 CHOP780212 0.801 QIAN880107 -0.821 SUEM840101 -0.832 KANM800103 -0.840 AURR980114 -0.842 AURR980109 -0.845 BEGF750101 -0.859 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.65 0.93 1.45 1.47 1.43 0.94 0.75 1.53 0.96 0.57 0.56 0.95 0.71 0.72 1.51 1.46 0.96 0.90 1.12 0.55 // H PALJ810107 D Normalized frequency of alpha-helix in all-alpha class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C GEIM800102 0.919 GEIM800109 -0.909 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.08 0.93 1.05 0.86 1.22 0.95 1.09 0.85 1.02 0.98 1.04 1.01 1.11 0.96 0.91 0.95 1.15 1.17 0.80 1.03 // H PALJ810108 D Normalized frequency of alpha-helix in alpha+beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.34 0.91 0.83 1.06 1.27 1.13 1.69 0.47 1.11 0.84 1.39 1.08 0.90 1.02 0.48 1.05 0.74 0.64 0.73 1.18 // H PALJ810109 D Normalized frequency of alpha-helix in alpha/beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C GEIM800104 0.937 PRAM900102 0.898 LEVM780101 0.898 MAXF760101 0.876 ISOY800101 0.874 PALJ810102 0.864 KANM800101 0.849 LEVM780104 0.819 AURR980112 0.817 GEIM800101 0.816 CHOP780201 0.814 CRAJ730101 0.811 ROBB760101 0.805 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.15 1.06 0.87 1. 1.03 1.43 1.37 0.64 0.95 0.99 1.22 1.20 1.45 0.92 0.72 0.84 0.97 1.11 0.72 0.82 // H PALJ810110 D Normalized frequency of beta-sheet in all-beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C GEIM800106 0.851 ROBB760106 0.836 KANM800102 0.836 BEGF750102 0.834 GEIM800107 0.826 QIAN880120 0.824 QIAN880119 0.824 LIFS790101 0.817 AVBF000101 0.816 CHOP780202 0.808 ROBB760105 0.804 GEIM800110 -0.840 MUNV940103 -0.845 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.89 1.06 0.67 0.71 1.04 1.06 0.72 0.87 1.04 1.14 1.02 1. 1.41 1.32 0.69 0.86 1.15 1.06 1.35 1.66 // H PALJ810111 D Normalized frequency of beta-sheet in alpha+beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.82 0.99 1.27 0.98 0.71 1.01 0.54 0.94 1.26 1.67 0.94 0.73 1.30 1.56 0.69 0.65 0.98 1.25 1.26 1.22 // H PALJ810112 D Normalized frequency of beta-sheet in alpha/beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C PRAM900103 0.913 LEVM780102 0.913 GEIM800107 0.905 LEVM780105 0.870 KANM800102 0.869 PALJ810104 0.849 LIFS790101 0.845 PALJ810103 0.841 GEIM800105 0.830 CHOP780202 0.815 KANM800104 0.813 QIAN880121 0.812 PTIO830102 0.811 MUNV940103 -0.830 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.98 1.03 0.66 0.74 1.01 0.63 0.59 0.90 1.17 1.38 1.05 0.83 0.82 1.23 0.73 0.98 1.20 1.26 1.23 1.62 // H PALJ810113 D Normalized frequency of turn in all-alpha class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. * (Arg Cys Leu Trp missing) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.69 0. 1.52 2.42 0. 1.44 0.63 2.64 0.22 0.43 0. 1.18 0.88 2.20 1.34 1.43 0.28 0. 1.53 0.14 // H PALJ810114 D Normalized frequency of turn in all-beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. * (Met missing) C ISOY800103 0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.87 1.30 1.36 1.24 0.83 1.06 0.91 1.69 0.91 0.27 0.67 0.66 0. 0.47 1.54 1.08 1.12 1.24 0.54 0.69 // H PALJ810115 D Normalized frequency of turn in alpha+beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C ROBB760112 0.885 QIAN880132 0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.91 0.77 1.32 0.90 0.50 1.06 0.53 1.61 1.08 0.36 0.77 1.27 0.76 0.37 1.62 1.34 0.87 1.10 1.24 0.52 // H PALJ810116 D Normalized frequency of turn in alpha/beta class (Palau et al., 1981) R LIT:0805095 PMID:7118409 A Palau, J., Argos, P. and Puigdomenech, P. T Protein secondary structure J Int. J. Peptide Protein Res. 19, 394-401 (1981) * LG :a set of protein samples formed by 44 proteins. * CF :a set of protein samples formed by 33 proteins. C PALJ810105 0.891 ISOY800103 0.814 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.92 0.90 1.57 1.22 0.62 0.66 0.92 1.61 0.39 0.79 0.50 0.86 0.50 0.96 1.30 1.40 1.11 0.57 1.78 0.50 // H PARJ860101 D HPLC parameter (Parker et al., 1986) R LIT:1211071 PMID:2430611 A Parker, J.M.R., Guo, D. and Hodges, R.S. T New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: Correlation of predicted surface residues with antigencity and x-ray-derived accessible sites J Biochemistry 25, 5425-5432 (1986) C WOLS870101 0.964 BULH740101 0.909 MEIH800101 0.905 GRAR740102 0.891 OOBM770103 0.891 RACS770101 0.871 VINM940101 0.837 RACS770102 0.834 VINM940102 0.833 MEIH800102 0.831 WOEC730101 0.821 HOPT810101 0.819 PARS000101 0.812 LEVM760101 0.806 ROSM880101 0.803 ROSM880102 0.801 WIMW960101 -0.804 MEEJ800101 -0.806 MEIH800103 -0.808 NAKH900110 -0.808 ROSG850102 -0.823 SIMZ760101 -0.825 GOLD730101 -0.827 LEVM760106 -0.832 JOND750101 -0.834 ARGP820101 -0.835 MANP780101 -0.841 PONP930101 -0.846 VENT840101 -0.846 BROC820101 -0.849 RADA880108 -0.865 PONP800107 -0.868 WERD780101 -0.869 TAKK010101 -0.870 CIDH920101 -0.871 BIOV880102 -0.875 EISD860101 -0.876 RADA880102 -0.883 ZIMJ680105 -0.886 BIOV880101 -0.889 SWER830101 -0.893 ROBB790101 -0.893 MEEJ810102 -0.897 NOZY710101 -0.900 MEEJ800102 -0.902 FAUJ830101 -0.907 CIDH920104 -0.913 NISK860101 -0.916 CIDH920103 -0.916 MEEJ810101 -0.920 GUOD860101 -0.925 MIYS850101 -0.929 CIDH920102 -0.930 CIDH920105 -0.948 PLIV810101 -0.958 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.1 4.2 7.0 10.0 1.4 6.0 7.8 5.7 2.1 -8.0 -9.2 5.7 -4.2 -9.2 2.1 6.5 5.2 -10.0 -1.9 -3.7 // H PLIV810101 D Partition coefficient (Pliska et al., 1981) R LIT:0712223 A Pliska, V., Schmidt, M. and Fauchere, J.L. T Partition coefficients of amino acids and hydrophobic parameters pi of their side-chains as measured by thin-layer chromatography J J. Chromatogr. 216, 79-92 (1981) * (Arg 0.25) C MIYS850101 0.944 GUOD860101 0.943 FAUJ830101 0.931 MEEJ810101 0.914 CIDH920105 0.914 RADA880108 0.906 EISD860101 0.904 CIDH920103 0.899 BIOV880101 0.899 MEEJ810102 0.898 CIDH920104 0.893 NISK860101 0.892 CIDH920102 0.877 SWER830101 0.875 ZIMJ680105 0.875 ROBB790101 0.875 MEEJ800102 0.867 PONP800107 0.866 BIOV880102 0.858 MANP780101 0.856 EISD860103 0.852 RADA880102 0.845 CIDH920101 0.843 WERD780101 0.841 ROSG850102 0.841 NOZY710101 0.839 LEVM760106 0.830 TAKK010101 0.822 ARGP820101 0.820 PONP930101 0.819 JOND750101 0.819 MEIH800103 0.811 PONP800101 0.806 NADH010104 0.806 SIMZ760101 0.805 NADH010103 0.804 PONP800103 0.802 LEVM760101 -0.801 FUKS010103 -0.805 VINM940102 -0.808 ROSM880101 -0.834 GUYH850101 -0.836 MEIH800102 -0.849 OOBM770103 -0.852 RACS770102 -0.859 ROSM880102 -0.864 RACS770101 -0.868 GRAR740102 -0.888 MEIH800101 -0.896 BULH740101 -0.912 PARJ860101 -0.958 WOLS870101 -0.963 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -2.89 -3.30 -3.41 -3.38 -2.49 -3.15 -2.94 -3.25 -2.84 -1.72 -1.61 -3.31 -1.84 -1.63 -2.50 -3.30 -2.91 -1.75 -2.42 -2.08 // H PONP800101 D Surrounding hydrophobicity in folded form (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C PONP800102 0.990 MANP780101 0.963 NISK800101 0.960 PONP800103 0.957 PONP930101 0.945 PONP800108 0.938 ROSG850102 0.938 RADA880108 0.934 NISK860101 0.930 BIOV880101 0.918 NADH010103 0.894 MIYS850101 0.892 NADH010104 0.892 CIDH920104 0.888 WERD780101 0.880 CIDH920103 0.876 NADH010102 0.875 PONP800106 0.871 MEIH800103 0.869 JANJ790101 0.866 BIOV880102 0.860 DESM900102 0.858 JURD980101 0.858 CIDH920105 0.856 NADH010105 0.853 KYTJ820101 0.851 JANJ780102 0.851 DESM900101 0.847 CHOC760103 0.830 ROBB760106 0.829 KANM800102 0.829 NADH010101 0.826 ROBB760105 0.823 KANM800104 0.823 LIFS790101 0.823 FAUJ830101 0.822 ROBB790101 0.822 PTIO830102 0.819 QIAN880121 0.815 PLIV810101 0.806 CIDH920101 0.805 LIFS790102 0.804 QIAN880122 0.801 FUKS010103 -0.801 KRIW790102 -0.804 VINM940103 -0.813 MUNV940103 -0.819 OOBM770101 -0.835 VINM940102 -0.845 OOBM770103 -0.848 GRAR740102 -0.849 KRIW710101 -0.850 RACS770101 -0.863 RACS770102 -0.870 MEIH800102 -0.877 GUYH850101 -0.877 VINM940101 -0.878 KRIW790101 -0.888 MEIH800101 -0.888 KARP850102 -0.889 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 12.28 11.49 11.00 10.97 14.93 11.28 11.19 12.01 12.84 14.77 14.10 10.80 14.33 13.43 11.19 11.26 11.65 12.95 13.29 15.07 // H PONP800102 D Average gain in surrounding hydrophobicity (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C PONP800101 0.990 PONP800103 0.986 NISK800101 0.965 ROSG850102 0.949 PONP800108 0.948 MANP780101 0.945 RADA880108 0.938 PONP930101 0.934 BIOV880101 0.926 NISK860101 0.924 NADH010103 0.919 NADH010104 0.917 NADH010102 0.901 JANJ790101 0.897 MIYS850101 0.891 MEIH800103 0.885 PONP800106 0.883 WERD780101 0.883 DESM900102 0.880 CIDH920104 0.880 JANJ780102 0.875 DESM900101 0.871 NADH010105 0.869 JURD980101 0.869 BIOV880102 0.867 KYTJ820101 0.861 CIDH920103 0.849 FAUJ830101 0.841 CHOC760103 0.836 NADH010101 0.832 CIDH920105 0.831 ROBB760105 0.828 JANJ790102 0.822 ROBB760106 0.822 KANM800102 0.815 EISD860103 0.814 KANM800104 0.813 ROBB790101 0.807 MUNV940103 -0.802 RACS770103 -0.809 VINM940103 -0.820 RACS770101 -0.827 KRIW790102 -0.830 VINM940102 -0.842 OOBM770103 -0.854 OOBM770101 -0.862 RACS770102 -0.864 MEIH800101 -0.870 GRAR740102 -0.871 GUYH850101 -0.883 MEIH800102 -0.883 VINM940101 -0.883 KARP850102 -0.887 KRIW710101 -0.887 KRIW790101 -0.915 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.62 6.81 6.17 6.18 10.93 6.67 6.38 7.31 7.85 9.99 9.37 5.72 9.83 8.99 6.64 6.93 7.08 8.41 8.53 10.38 // H PONP800103 D Average gain ratio in surrounding hydrophobicity (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C PONP800102 0.986 PONP800101 0.957 ROSG850102 0.947 NISK800101 0.941 RADA880108 0.934 NADH010103 0.932 PONP800108 0.931 BIOV880101 0.926 NADH010104 0.926 NADH010102 0.921 MANP780101 0.913 NISK860101 0.910 PONP930101 0.909 MIYS850101 0.898 DESM900102 0.896 MEIH800103 0.895 DESM900101 0.887 JANJ790101 0.886 PONP800106 0.883 JANJ780102 0.882 JURD980101 0.879 BIOV880102 0.879 WERD780101 0.876 KYTJ820101 0.870 NADH010105 0.866 FAUJ830101 0.863 CIDH920104 0.863 JANJ790102 0.844 EISD860103 0.842 CHOC760103 0.837 NADH010101 0.833 ROBB760105 0.823 CIDH920103 0.823 ROBB760106 0.812 CIDH920105 0.807 NADH010106 0.803 KANM800102 0.803 PLIV810101 0.802 JANJ780103 -0.812 VINM940103 -0.817 RACS770103 -0.819 VINM940102 -0.820 WOEC730101 -0.823 KRIW790102 -0.853 MEIH800101 -0.856 RACS770102 -0.860 OOBM770103 -0.865 KARP850102 -0.870 VINM940101 -0.878 OOBM770101 -0.880 GUYH850101 -0.887 KRIW710101 -0.890 MEIH800102 -0.891 GRAR740102 -0.897 KRIW790101 -0.930 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.63 2.45 2.27 2.29 3.36 2.45 2.31 2.55 2.57 3.08 2.98 2.12 3.18 3.02 2.46 2.60 2.55 2.85 2.79 3.21 // H PONP800104 D Surrounding hydrophobicity in alpha-helix (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C CHOC760104 0.844 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 13.65 11.28 12.24 10.98 14.49 11.30 12.55 15.36 11.59 14.63 14.01 11.96 13.40 14.08 11.51 11.26 13.00 12.06 12.64 12.88 // H PONP800105 D Surrounding hydrophobicity in beta-sheet (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 14.60 13.24 11.79 13.78 15.90 12.02 13.59 14.18 15.35 14.10 16.49 13.28 16.23 14.18 14.10 13.36 14.50 13.90 14.76 16.30 // H PONP800106 D Surrounding hydrophobicity in turn (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C PONP800102 0.883 PONP800103 0.883 PONP800101 0.871 RADA880108 0.835 MANP780101 0.813 MIYS850101 0.812 ROSG850102 0.807 KARP850102 -0.820 GUYH850101 -0.826 KRIW710101 -0.841 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 10.67 11.05 10.85 10.21 14.15 11.71 11.71 10.95 12.07 12.95 13.07 9.93 15.00 13.27 10.62 11.18 10.53 11.41 11.52 13.86 // H PONP800107 D Accessibility reduction ratio (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C MIYS850101 0.884 MANP780101 0.871 PLIV810101 0.866 GUOD860101 0.854 PONP930101 0.851 LIFS790102 0.849 NISK860101 0.847 PTIO830102 0.837 CIDH920103 0.833 CIDH920104 0.832 CIDH920105 0.818 BIOV880101 0.816 BIOV880102 0.814 CHOC760103 0.813 VENT840101 0.805 BEGF750102 0.803 ROSG850102 0.803 LIFS790101 0.801 RADA880108 0.800 CHOP780203 -0.818 OOBM770103 -0.819 CHOP780210 -0.820 WOLS870101 -0.852 MEIH800102 -0.858 PARJ860101 -0.868 RACS770102 -0.878 RACS770101 -0.905 MEIH800101 -0.909 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 3.70 2.53 2.12 2.60 3.03 2.70 3.30 3.13 3.57 7.69 5.88 1.79 5.21 6.60 2.12 2.43 2.60 6.25 3.03 7.14 // H PONP800108 D Average number of surrounding residues (Ponnuswamy et al., 1980) R LIT:0608056 PMID:7397216 A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. T Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins J Biochim. Biophys. Acta 623, 301-316 (1980) C NISK800101 0.976 PONP800102 0.948 PONP930101 0.944 PONP800101 0.938 MANP780101 0.935 PONP800103 0.931 NISK860101 0.921 ROSG850102 0.919 CIDH920104 0.909 BIOV880101 0.907 NADH010103 0.907 NADH010104 0.902 NADH010102 0.890 RADA880108 0.889 JANJ790101 0.881 FAUJ830101 0.875 JANJ780102 0.863 MEIH800103 0.862 JURD980101 0.856 BIOV880102 0.854 KYTJ820101 0.850 KANM800102 0.849 KANM800104 0.849 MIYS850101 0.847 NADH010105 0.845 WERD780101 0.843 CIDH920105 0.843 CIDH920103 0.841 DESM900102 0.833 ROBB790101 0.831 LIFS790101 0.828 NADH010101 0.820 ROBB760105 0.820 GEIM800107 0.817 QIAN880122 0.811 EISD860103 0.809 CHOC760103 0.809 CHOP780202 0.809 ROBB760106 0.808 QIAN880121 0.802 JANJ790102 0.802 MEIH800101 -0.825 WOEC730101 -0.831 MEIH800102 -0.836 OOBM770101 -0.851 KRIW790101 -0.860 VINM940102 -0.871 VINM940101 -0.891 OOBM770103 -0.896 GRAR740102 -0.907 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.05 5.70 5.04 4.95 7.86 5.45 5.10 6.16 5.80 7.51 7.37 4.88 6.39 6.62 5.65 5.53 5.81 6.98 6.73 7.62 // H PRAM820101 D Intercept in regression analysis (Prabhakaran-Ponnuswamy, 1982) R LIT:2004113b A Prabhakaran, M. and Ponnuswamy, P.K. T Shape and surface features of globular proteins J Macromolecules 15, 314-320 (1982) * Regression analysis of solvent contact area and spatial position C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.305 0.227 0.322 0.335 0.339 0.306 0.282 0.352 0.215 0.278 0.262 0.391 0.280 0.195 0.346 0.326 0.251 0.291 0.293 0.291 // H PRAM820102 D Slope in regression analysis x 1.0E1 (Prabhakaran-Ponnuswamy, 1982) R LIT:2004113b A Prabhakaran, M. and Ponnuswamy, P.K. T Shape and surface features of globular proteins J Macromolecules 15, 314-320 (1982) * Regression analysis of solvent contact area and spatial position C LEVM760104 0.812 PRAM820103 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.175 0.083 0.090 0.140 0.074 0.093 0.135 0.201 0.125 0.100 0.104 0.058 0.054 0.104 0.136 0.155 0.152 0.092 0.081 0.096 // H PRAM820103 D Correlation coefficient in regression analysis (Prabhakaran-Ponnuswamy, 1982) R LIT:2004113b A Prabhakaran, M. and Ponnuswamy, P.K. T Shape and surface features of globular proteins J Macromolecules 15, 314-320 (1982) * Regression analysis of solvent contact area and spatial position C PRAM820102 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.687 0.590 0.489 0.632 0.263 0.527 0.669 0.670 0.594 0.564 0.541 0.407 0.328 0.577 0.600 0.692 0.713 0.632 0.495 0.529 // H PRAM900101 D Hydrophobicity (Prabhakaran, 1990) R LIT:1614053b PMID:2390062 A Prabhakaran, M. T The distribution of physical, chemical and conformational properties in signal and nascent peptides J Biochem. J. 269, 691-696 (1990) * Original references: * Engelman, D.M., Steitz, T.A. and Terwilliger, T.C. * Annu. Rev. Biophys. Chem. 15, 321-353 (1986) C ROSM880101 0.917 VHEG790101 0.909 KUHL950101 0.908 OOBM770101 0.907 JANJ780101 0.901 ROSM880102 0.892 JANJ780103 0.884 HOPT810101 0.881 LEVM760101 0.881 WOEC730101 0.871 GRAR740102 0.855 ZIMJ680103 0.854 CHOC760102 0.826 MONM990101 0.820 GUYH850101 0.820 FAUJ880109 0.815 RADA880104 -0.803 CHOC760103 -0.814 NADH010103 -0.815 WARP780101 -0.827 EISD860103 -0.831 NADH010101 -0.843 KYTJ820101 -0.850 FAUJ830101 -0.853 JANJ780102 -0.860 EISD860101 -0.862 JURD980101 -0.862 RADA880107 -0.865 NADH010102 -0.870 WOLR810101 -0.887 JANJ790102 -0.890 DESM900102 -0.890 RADA880101 -0.932 EISD840101 -0.936 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -6.70 51.50 20.10 38.50 -8.40 17.20 34.30 -4.20 12.60 -13. -11.70 36.80 -14.20 -15.50 0.80 -2.50 -5. -7.90 2.90 -10.90 // H PRAM900102 D Relative frequency in alpha-helix (Prabhakaran, 1990) R LIT:1614053b PMID:2390062 A Prabhakaran, M. T The distribution of physical, chemical and conformational properties in signal and nascent peptides J Biochem. J. 269, 691-696 (1990) * Original reference of these three data: * Creighton, T.E. * In "Protein Structure and Melecular Properties", (Freeman, W.H., ed.), * San Francisco P.235 (1983) C LEVM780101 1.000 LEVM780104 0.964 PALJ810101 0.943 KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924 ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907 RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898 NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873 TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829 QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.29 0.96 0.90 1.04 1.11 1.27 1.44 0.56 1.22 0.97 1.30 1.23 1.47 1.07 0.52 0.82 0.82 0.99 0.72 0.91 // H PRAM900103 D Relative frequency in beta-sheet (Prabhakaran, 1990) R LIT:1614053b PMID:2390062 A Prabhakaran, M. T The distribution of physical, chemical and conformational properties in signal and nascent peptides J Biochem. J. 269, 691-696 (1990) * Original reference of these three data: * Creighton, T.E. * In "Protein Structure and Melecular Properties", (Freeman, W.H., ed.), * San Francisco P.235 (1983) C LEVM780102 1.000 PALJ810112 0.913 LEVM780105 0.899 PALJ810104 0.868 PTIO830102 0.865 LIFS790101 0.864 QIAN880120 0.858 KANM800102 0.856 PALJ810103 0.846 GEIM800107 0.842 BEGF750102 0.834 QIAN880119 0.834 CHOP780202 0.833 AVBF000101 0.815 QIAN880121 0.805 MUNV940103 -0.848 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.90 0.99 0.76 0.72 0.74 0.80 0.75 0.92 1.08 1.45 1.02 0.77 0.97 1.32 0.64 0.95 1.21 1.14 1.25 1.49 // H PRAM900104 D Relative frequency in reverse-turn (Prabhakaran, 1990) R LIT:1614053b PMID:2390062 A Prabhakaran, M. T The distribution of physical, chemical and conformational properties in signal and nascent peptides J Biochem. J. 269, 691-696 (1990) * Original reference of these three data: * Creighton, T.E. * In "Protein Structure and Melecular Properties", (Freeman, W.H., ed.), * San Francisco P.235 (1983) C LEVM780103 1.000 LEVM780106 0.983 GEIM800111 0.954 CHOP780216 0.951 QIAN880133 0.947 QIAN880134 0.934 ISOY800103 0.934 QIAN880132 0.932 GEIM800108 0.931 CHOP780203 0.928 CHAM830101 0.909 PALJ810105 0.906 QIAN880135 0.903 CHOP780101 0.891 TANS770110 0.873 CHOP780210 0.850 PALJ810106 0.844 RACS770101 0.809 KANM800103 -0.814 AURR980109 -0.815 QIAN880108 -0.819 QIAN880107 -0.829 AVBF000102 -0.834 ROBB760103 -0.840 FAUJ880102 -0.844 QIAN880109 -0.846 PTIO830101 -0.858 SUEM840101 -0.865 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.78 0.88 1.28 1.41 0.80 0.97 1. 1.64 0.69 0.51 0.59 0.96 0.39 0.58 1.91 1.33 1.03 0.75 1.05 0.47 // H PTIO830101 D Helix-coil equilibrium constant (Ptitsyn-Finkelstein, 1983) R LIT:0904057 PMID:6673754 A Ptitsyn, O.B. and Finkelstein, A.V. T Theory of protein secondary structure and algorithm of its prediction J Biopolymers 22, 15-25 (1983) * Charged state for Arg, His, Lys, Asp, and Glu C ROBB760103 0.903 QIAN880109 0.886 QIAN880108 0.884 SUEM840101 0.877 BLAM930101 0.868 QIAN880111 0.857 ONEK900101 0.847 QIAN880107 0.846 QIAN880110 0.835 AURR980113 0.833 FAUJ880102 0.832 FINA770101 0.826 AURR980109 0.820 ROBB760104 0.817 AURR980114 0.809 MUNV940104 -0.807 QIAN880131 -0.826 ONEK900102 -0.830 ISOY800104 -0.832 MUNV940105 -0.833 QIAN880132 -0.833 CHOP780213 -0.835 GEIM800108 -0.840 CHAM830101 -0.841 MUNV940102 -0.844 LEVM780106 -0.854 CHOP780216 -0.855 PRAM900104 -0.858 LEVM780103 -0.860 QIAN880133 -0.864 GEIM800111 -0.876 MUNV940101 -0.880 QIAN880135 -0.899 QIAN880134 -0.920 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.10 0.95 0.80 0.65 0.95 1.00 1.00 0.60 0.85 1.10 1.25 1.00 1.15 1.10 0.10 0.75 0.75 1.10 1.10 0.95 // H PTIO830102 D Beta-coil equilibrium constant (Ptitsyn-Finkelstein, 1983) R LIT:0904057 PMID:6673754 A Ptitsyn, O.B. and Finkelstein, A.V. T Theory of protein secondary structure and algorithm of its prediction J Biopolymers 22, 15-25 (1983) * Charged state for Arg, His, Lys, Asp, and Glu C LIFS790101 0.941 PALJ810104 0.937 KANM800102 0.917 CHOP780202 0.913 QIAN880120 0.908 LEVM780105 0.894 ROBB760106 0.882 QIAN880121 0.880 PONP930101 0.879 ROBB760105 0.878 LIFS790102 0.874 PALJ810103 0.867 QIAN880119 0.865 PRAM900103 0.865 LEVM780102 0.865 AVBF000101 0.861 MANP780101 0.861 KANM800104 0.858 SWER830101 0.856 GEIM800107 0.850 VENT840101 0.842 CIDH920104 0.842 PONP800107 0.837 NISK860101 0.825 LIFS790103 0.822 CRAJ730102 0.820 PONP800101 0.819 CHOP780209 0.814 CIDH920105 0.813 NAGK730102 0.811 PALJ810112 0.811 GEIM800105 0.810 CIDH920103 0.807 BEGF750102 0.807 MIYS850101 0.807 OOBM770103 -0.801 KRIW790101 -0.801 MEIH800101 -0.828 MUNV940103 -0.903 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.00 0.70 0.60 0.50 1.90 1.00 0.70 0.30 0.80 4.00 2.00 0.70 1.90 3.10 0.20 0.90 1.70 2.20 2.80 4.00 // H QIAN880101 D Weights for alpha-helix at the window position of -6 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.12 0.04 -0.10 0.01 -0.25 -0.03 -0.02 -0.02 -0.06 -0.07 0.05 0.26 0.00 0.05 -0.19 -0.19 -0.04 -0.06 -0.14 -0.03 // H QIAN880102 D Weights for alpha-helix at the window position of -5 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.26 -0.14 -0.03 0.15 -0.15 -0.13 0.21 -0.37 0.10 -0.03 -0.02 0.12 0.00 0.12 -0.08 0.01 -0.34 -0.01 -0.29 0.02 // H QIAN880103 D Weights for alpha-helix at the window position of -4 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.64 -0.10 0.09 0.33 0.03 -0.23 0.51 -0.09 -0.23 -0.22 0.41 -0.17 0.13 -0.03 -0.43 -0.10 -0.07 -0.02 -0.38 -0.01 // H QIAN880104 D Weights for alpha-helix at the window position of -3 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880106 0.851 QIAN880105 0.824 AURR980108 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.29 -0.03 -0.04 0.11 -0.05 0.26 0.28 -0.67 -0.26 0.00 0.47 -0.19 0.27 0.24 -0.34 -0.17 -0.20 0.25 -0.30 -0.01 // H QIAN880105 D Weights for alpha-helix at the window position of -2 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C ROBB760101 0.874 QIAN880106 0.846 CHOP780201 0.835 AURR980113 0.833 BEGF750101 0.833 QIAN880107 0.829 ISOY800101 0.828 KANM800101 0.827 QIAN880104 0.824 RACS820108 0.820 KANM800103 0.820 ROBB760103 0.811 MAXF760101 0.811 CHAM830101 -0.803 MUNV940102 -0.816 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.68 -0.22 -0.09 -0.02 -0.15 -0.15 0.44 -0.73 -0.14 -0.08 0.61 0.03 0.39 0.06 -0.76 -0.26 -0.10 0.20 -0.04 0.12 // H QIAN880106 D Weights for alpha-helix at the window position of -1 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C ROBB760101 0.904 ISOY800101 0.903 QIAN880107 0.896 KANM800103 0.889 MAXF760101 0.881 CHOP780201 0.874 PALJ810102 0.871 RACS820108 0.866 AURR980109 0.862 ROBB760103 0.854 KANM800101 0.854 QIAN880104 0.851 QIAN880105 0.846 AURR980112 0.839 AURR980108 0.838 AURR980113 0.835 RICJ880109 0.834 PRAM900102 0.827 LEVM780101 0.827 TANS770101 0.819 FINA770101 0.810 LEVM780104 0.804 AURR980110 0.804 AURR980114 0.803 QIAN880132 -0.813 MUNV940101 -0.835 CHAM830101 -0.856 MUNV940102 -0.867 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.34 0.22 -0.33 0.06 -0.18 0.01 0.20 -0.88 -0.09 -0.03 0.20 -0.11 0.43 0.15 -0.81 -0.35 -0.37 0.07 -0.31 0.13 // H QIAN880107 D Weights for alpha-helix at the window position of 0 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C KANM800103 0.908 QIAN880106 0.896 AURR980109 0.893 ROBB760103 0.889 ISOY800101 0.887 MAXF760101 0.885 AURR980114 0.876 QIAN880108 0.872 ROBB760101 0.867 QIAN880109 0.865 PALJ810102 0.856 KANM800101 0.854 QIAN880110 0.853 PTIO830101 0.846 CHOP780201 0.843 AURR980113 0.832 RACS820108 0.831 LEVM780101 0.829 PRAM900102 0.829 QIAN880105 0.829 LEVM780104 0.822 BEGF750101 0.815 AURR980110 0.815 FINA770101 0.814 TANS770101 0.804 AURR980108 0.803 SUEM840101 0.803 AURR980112 0.802 CHOP780216 -0.808 QIAN880133 -0.809 CHOP780101 -0.809 LEVM780106 -0.813 PALJ810106 -0.821 PRAM900104 -0.829 LEVM780103 -0.834 CRAJ730103 -0.840 CHAM830101 -0.858 MUNV940101 -0.880 MUNV940102 -0.882 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.57 0.23 -0.36 -0.46 -0.15 0.15 0.26 -0.71 -0.05 0.00 0.48 0.16 0.41 0.03 -1.12 -0.47 -0.54 -0.10 -0.35 0.31 // H QIAN880108 D Weights for alpha-helix at the window position of 1 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880109 0.951 ROBB760103 0.914 QIAN880110 0.901 PTIO830101 0.884 ROBB760104 0.879 QIAN880107 0.872 ONEK900101 0.866 BLAM930101 0.860 KANM800103 0.829 RACS820108 0.820 QIAN880111 0.819 PRAM900104 -0.819 LEVM780103 -0.820 QIAN880135 -0.836 MUNV940102 -0.839 QIAN880136 -0.843 QIAN880134 -0.845 ISOY800104 -0.847 ONEK900102 -0.860 MUNV940101 -0.864 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.33 0.10 -0.19 -0.44 -0.03 0.19 0.21 -0.46 0.27 -0.33 0.57 0.23 0.79 0.48 -1.86 -0.23 -0.33 0.15 -0.19 0.24 // H QIAN880109 D Weights for alpha-helix at the window position of 2 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880110 0.953 QIAN880108 0.951 QIAN880111 0.912 PTIO830101 0.886 ROBB760104 0.871 ROBB760103 0.868 QIAN880107 0.865 BLAM930101 0.828 KANM800103 0.824 QIAN880112 0.824 ONEK900101 0.824 AURR980114 0.810 AURR980109 0.807 CHOP780205 0.806 ONEK900102 -0.800 LEVM780106 -0.815 MUNV940101 -0.841 QIAN880134 -0.841 PRAM900104 -0.846 LEVM780103 -0.848 QIAN880135 -0.884 QIAN880136 -0.927 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.13 0.08 -0.07 -0.71 -0.09 0.12 0.13 -0.39 0.32 0.00 0.50 0.37 0.63 0.15 -1.40 -0.28 -0.21 0.02 -0.10 0.17 // H QIAN880110 D Weights for alpha-helix at the window position of 3 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880109 0.953 QIAN880111 0.922 QIAN880108 0.901 QIAN880107 0.853 PTIO830101 0.835 QIAN880112 0.828 KANM800103 0.820 AURR980114 0.819 ROBB760103 0.807 ROBB760104 0.806 AURR980109 0.802 QIAN880136 -0.890 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.31 0.18 -0.10 -0.81 -0.26 0.41 -0.06 -0.42 0.51 -0.15 0.56 0.47 0.58 0.10 -1.33 -0.49 -0.44 0.14 -0.08 -0.01 // H QIAN880111 D Weights for alpha-helix at the window position of 4 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880110 0.922 QIAN880109 0.912 QIAN880112 0.861 PTIO830101 0.857 QIAN880108 0.819 QIAN880135 -0.878 QIAN880136 -0.900 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.21 0.07 -0.04 -0.58 -0.12 0.13 -0.23 -0.15 0.37 0.31 0.70 0.28 0.61 -0.06 -1.03 -0.28 -0.25 0.21 0.16 0.00 // H QIAN880112 D Weights for alpha-helix at the window position of 5 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880111 0.861 QIAN880113 0.859 QIAN880110 0.828 QIAN880109 0.824 QIAN880136 -0.812 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.18 0.21 -0.03 -0.32 -0.29 -0.27 -0.25 -0.40 0.28 -0.03 0.62 0.41 0.21 0.05 -0.84 -0.05 -0.16 0.32 0.11 0.06 // H QIAN880113 D Weights for alpha-helix at the window position of 6 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880112 0.859 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.08 0.05 -0.08 -0.24 -0.25 -0.28 -0.19 -0.10 0.29 -0.01 0.28 0.45 0.11 0.00 -0.42 0.07 -0.33 0.36 0.00 -0.13 // H QIAN880114 D Weights for beta-sheet at the window position of -6 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880115 0.832 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.18 -0.13 0.28 0.05 -0.26 0.21 -0.06 0.23 0.24 -0.42 -0.23 0.03 -0.42 -0.18 -0.13 0.41 0.33 -0.10 -0.10 -0.07 // H QIAN880115 D Weights for beta-sheet at the window position of -5 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880114 0.832 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.01 0.02 0.41 -0.09 -0.27 0.01 0.09 0.13 0.22 -0.27 -0.25 0.08 -0.57 -0.12 0.26 0.44 0.35 -0.15 0.15 -0.09 // H QIAN880116 D Weights for beta-sheet at the window position of -4 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880126 0.823 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.19 0.03 0.02 -0.06 -0.29 0.02 -0.10 0.19 -0.16 -0.08 -0.42 -0.09 -0.38 -0.32 0.05 0.25 0.22 -0.19 0.05 -0.15 // H QIAN880117 D Weights for beta-sheet at the window position of -3 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.14 0.14 -0.27 -0.10 -0.64 -0.11 -0.39 0.46 -0.04 0.16 -0.57 0.04 0.24 0.08 0.02 -0.12 0.00 -0.10 0.18 0.29 // H QIAN880118 D Weights for beta-sheet at the window position of -2 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C PALJ810103 0.845 LEVM780105 0.819 QIAN880119 0.812 GEIM800105 0.810 KANM800102 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.31 0.25 -0.53 -0.54 -0.06 0.07 -0.52 0.37 -0.32 0.57 0.09 -0.29 0.29 0.24 -0.31 0.11 0.03 0.15 0.29 0.48 // H QIAN880119 D Weights for beta-sheet at the window position of -1 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880120 0.959 LIFS790101 0.929 LEVM780105 0.903 ROBB760106 0.897 KANM800102 0.888 LIFS790103 0.877 PTIO830102 0.865 QIAN880121 0.862 PALJ810103 0.861 ROBB760105 0.859 AVBF000101 0.859 CHOP780202 0.855 KANM800104 0.841 PONP930101 0.836 PRAM900103 0.834 LEVM780102 0.834 GEIM800105 0.829 OOBM850101 0.825 PALJ810110 0.824 PALJ810104 0.822 QIAN880118 0.812 BEGF750102 0.811 GEIM800107 0.807 CHOP780208 0.807 LEVM780106 -0.810 GEIM800108 -0.810 CHOP780203 -0.814 QIAN880131 -0.830 QIAN880133 -0.849 GEIM800110 -0.853 QIAN880132 -0.858 MUNV940103 -0.927 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.10 0.19 -0.89 -0.89 0.13 -0.04 -0.34 -0.45 -0.34 0.95 0.32 -0.46 0.43 0.36 -0.91 -0.12 0.49 0.34 0.42 0.76 // H QIAN880120 D Weights for beta-sheet at the window position of 0 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C LIFS790101 0.969 QIAN880119 0.959 LIFS790103 0.939 QIAN880121 0.935 CHOP780202 0.915 LEVM780105 0.913 PTIO830102 0.908 ROBB760106 0.908 KANM800102 0.896 PALJ810103 0.886 PALJ810104 0.886 PONP930101 0.879 AVBF000101 0.876 ROBB760105 0.860 PRAM900103 0.858 LEVM780102 0.858 GEIM800107 0.843 NISK860101 0.837 BEGF750102 0.829 SWER830101 0.825 GEIM800106 0.825 PALJ810110 0.824 GEIM800105 0.822 MANP780101 0.806 KANM800104 0.803 CHOP780208 0.800 CHOP780216 -0.800 QIAN880131 -0.801 GEIM800108 -0.804 VINM940102 -0.813 GEIM800111 -0.816 VINM940101 -0.823 OOBM770103 -0.824 LEVM780106 -0.831 QIAN880132 -0.839 QIAN880134 -0.842 PARS000101 -0.863 QIAN880133 -0.863 GEIM800110 -0.898 MUNV940103 -0.959 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.25 -0.02 -0.77 -1.01 0.13 -0.12 -0.62 -0.72 -0.16 1.10 0.23 -0.59 0.32 0.48 -1.24 -0.31 0.17 0.45 0.77 0.69 // H QIAN880121 D Weights for beta-sheet at the window position of 1 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880120 0.935 LIFS790101 0.930 CHOP780202 0.911 PALJ810104 0.910 ROBB760106 0.907 KANM800102 0.900 PONP930101 0.893 LIFS790103 0.882 PTIO830102 0.880 LEVM780105 0.876 PALJ810103 0.875 GEIM800107 0.875 QIAN880119 0.862 AVBF000101 0.855 QIAN880122 0.838 ROBB760105 0.834 NISK860101 0.829 KANM800104 0.829 NISK800101 0.818 PONP800101 0.815 PALJ810112 0.812 GEIM800105 0.811 CHOP780209 0.809 LEVM780102 0.805 PRAM900103 0.805 PONP800108 0.802 MANP780101 0.802 QIAN880133 -0.802 KRIW790101 -0.803 GEIM800110 -0.806 PARS000101 -0.809 VINM940101 -0.828 QIAN880134 -0.838 MUNV940103 -0.938 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.26 -0.09 -0.34 -0.55 0.47 -0.33 -0.75 -0.56 -0.04 0.94 0.25 -0.55 -0.05 0.20 -1.28 -0.28 0.08 0.22 0.53 0.67 // H QIAN880122 D Weights for beta-sheet at the window position of 2 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880121 0.838 PONP930101 0.837 PONP800108 0.811 NADH010103 0.809 NISK800101 0.808 NADH010104 0.804 PONP800101 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.05 -0.11 -0.40 -0.11 0.36 -0.67 -0.35 0.14 0.02 0.47 0.32 -0.51 -0.10 0.20 -0.79 0.03 -0.15 0.09 0.34 0.58 // H QIAN880123 D Weights for beta-sheet at the window position of 3 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.44 -0.13 0.05 -0.20 0.13 -0.58 -0.28 0.08 0.09 -0.04 -0.12 -0.33 -0.21 -0.13 -0.48 0.27 0.47 -0.22 -0.11 0.06 // H QIAN880124 D Weights for beta-sheet at the window position of 4 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.31 -0.10 0.06 0.13 -0.11 -0.47 -0.05 0.45 -0.06 -0.25 -0.44 -0.44 -0.28 -0.04 -0.29 0.34 0.27 -0.08 0.06 0.11 // H QIAN880125 D Weights for beta-sheet at the window position of 5 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.02 0.04 0.03 0.11 -0.02 -0.17 0.10 0.38 -0.09 -0.48 -0.26 -0.39 -0.14 -0.03 -0.04 0.41 0.36 -0.01 -0.08 -0.18 // H QIAN880126 D Weights for beta-sheet at the window position of 6 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880116 0.823 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.06 0.02 0.10 0.24 -0.19 -0.04 -0.04 0.17 0.19 -0.20 -0.46 -0.43 -0.52 -0.33 0.37 0.43 0.50 -0.32 0.35 0.00 // H QIAN880127 D Weights for coil at the window position of -6 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C OOBM850105 -0.813 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.05 0.06 0.00 0.15 0.30 -0.08 -0.02 -0.14 -0.07 0.26 0.04 -0.42 0.25 0.09 0.31 -0.11 -0.06 0.19 0.33 0.04 // H QIAN880128 D Weights for coil at the window position of -5 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.19 0.17 -0.38 0.09 0.41 0.04 -0.20 0.28 -0.19 -0.06 0.34 -0.20 0.45 0.07 0.04 -0.23 -0.02 0.16 0.22 0.05 // H QIAN880129 D Weights for coil at the window position of -4 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.43 0.06 0.00 -0.31 0.19 0.14 -0.41 -0.21 0.21 0.29 -0.10 0.33 -0.01 0.25 0.28 -0.23 -0.26 0.15 0.09 -0.10 // H QIAN880130 D Weights for coil at the window position of -3 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.19 -0.07 0.17 -0.27 0.42 -0.29 -0.22 0.17 0.17 -0.34 -0.22 0.00 -0.53 -0.31 0.14 0.22 0.10 -0.15 -0.02 -0.33 // H QIAN880131 D Weights for coil at the window position of -2 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C CHOP780216 0.873 TANS770110 0.873 QIAN880133 0.871 CHOP780203 0.861 CHAM830101 0.860 GEIM800108 0.860 GEIM800111 0.857 QIAN880132 0.847 QIAN880135 0.844 QIAN880134 0.832 CHOP780210 0.826 CHOP780101 0.824 PALJ810106 0.809 QIAN880120 -0.801 SUEM840101 -0.823 PTIO830101 -0.826 QIAN880119 -0.830 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.25 0.12 0.61 0.60 0.18 0.09 -0.12 0.09 0.42 -0.54 -0.55 0.14 -0.47 -0.29 0.89 0.24 0.16 -0.44 -0.19 -0.45 // H QIAN880132 D Weights for coil at the window position of -1 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880133 0.957 LEVM780106 0.943 PRAM900104 0.932 LEVM780103 0.931 CHOP780216 0.931 GEIM800111 0.929 CHOP780203 0.928 CHAM830101 0.925 QIAN880134 0.909 GEIM800108 0.906 TANS770110 0.903 CHOP780101 0.896 ISOY800103 0.892 PALJ810106 0.859 CHOP780210 0.852 QIAN880131 0.847 PALJ810105 0.830 QIAN880135 0.824 PALJ810115 0.804 ROBB760112 0.800 AURR980109 -0.806 LIFS790101 -0.806 AVBF000101 -0.809 QIAN880106 -0.813 ROBB760103 -0.827 PTIO830101 -0.833 QIAN880120 -0.839 AVBF000102 -0.849 FAUJ880102 -0.849 QIAN880119 -0.858 SUEM840101 -0.880 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.27 -0.40 0.71 0.54 0.00 -0.08 -0.12 1.14 0.18 -0.74 -0.54 0.45 -0.76 -0.47 1.40 0.40 -0.10 -0.46 -0.05 -0.86 // H QIAN880133 D Weights for coil at the window position of 0 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C LEVM780106 0.971 QIAN880132 0.957 LEVM780103 0.948 PRAM900104 0.947 GEIM800111 0.943 CHOP780216 0.939 QIAN880134 0.938 GEIM800108 0.930 TANS770110 0.920 CHOP780203 0.915 CHAM830101 0.913 ISOY800103 0.908 QIAN880135 0.907 CHOP780101 0.897 QIAN880131 0.871 PALJ810106 0.860 PALJ810105 0.843 MUNV940103 0.836 GEIM800110 0.822 CHOP780210 0.820 ROBB760112 0.814 QIAN880121 -0.802 ROBB760103 -0.807 AVBF000101 -0.807 QIAN880107 -0.809 AVBF000102 -0.823 LIFS790101 -0.848 QIAN880119 -0.849 FAUJ880102 -0.851 QIAN880120 -0.863 PTIO830101 -0.864 SUEM840101 -0.879 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.42 -0.23 0.81 0.95 -0.18 -0.01 -0.09 1.24 0.05 -1.17 -0.69 0.09 -0.86 -0.39 1.77 0.63 0.29 -0.37 -0.41 -1.32 // H QIAN880134 D Weights for coil at the window position of 1 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880135 0.961 QIAN880133 0.938 LEVM780103 0.935 PRAM900104 0.934 LEVM780106 0.932 GEIM800111 0.919 QIAN880132 0.909 CHOP780216 0.900 MUNV940105 0.899 MUNV940104 0.897 ISOY800104 0.893 GEIM800108 0.884 CHOP780213 0.870 MUNV940103 0.858 GEIM800110 0.853 CHAM830101 0.841 CHOP780203 0.838 TANS770104 0.837 QIAN880131 0.832 ISOY800103 0.828 ROBB760104 -0.802 LIFS790101 -0.804 AVBF000101 -0.822 BLAM930101 -0.836 QIAN880121 -0.838 QIAN880109 -0.841 QIAN880120 -0.842 QIAN880108 -0.845 FAUJ880102 -0.852 ROBB760103 -0.855 PTIO830101 -0.920 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.24 -0.04 0.45 0.65 -0.38 0.01 0.07 0.85 -0.21 -0.65 -0.80 0.17 -0.71 -0.61 2.27 0.33 0.13 -0.44 -0.49 -0.99 // H QIAN880135 D Weights for coil at the window position of 2 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) * (Gin !) C QIAN880134 0.961 QIAN880133 0.907 LEVM780103 0.906 PRAM900104 0.903 LEVM780106 0.902 GEIM800111 0.895 CHOP780216 0.884 GEIM800108 0.877 CHOP780213 0.851 QIAN880131 0.844 GEIM800110 0.842 QIAN880136 0.838 ISOY800104 0.837 MUNV940105 0.829 QIAN880132 0.824 MUNV940103 0.820 MUNV940104 0.819 CHAM830101 0.814 CHOP780203 0.811 ROBB760103 -0.834 QIAN880108 -0.836 QIAN880111 -0.878 QIAN880109 -0.884 PTIO830101 -0.899 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.14 0.21 0.35 0.66 -0.09 0.11 0.06 0.36 -0.31 -0.51 -0.80 -0.14 -0.56 -0.25 1.59 0.32 0.21 -0.17 -0.35 -0.70 // H QIAN880136 D Weights for coil at the window position of 3 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C QIAN880135 0.838 QIAN880112 -0.812 QIAN880108 -0.843 QIAN880110 -0.890 QIAN880111 -0.900 QIAN880109 -0.927 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.01 -0.13 -0.11 0.78 -0.31 -0.13 0.09 0.14 -0.56 -0.09 -0.81 -0.43 -0.49 -0.20 1.14 0.13 -0.02 -0.20 0.10 -0.11 // H QIAN880137 D Weights for coil at the window position of 4 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.30 -0.09 -0.12 0.44 0.03 0.24 0.18 -0.12 -0.20 -0.07 -0.18 0.06 -0.44 0.11 0.77 -0.09 -0.27 -0.09 -0.25 -0.06 // H QIAN880138 D Weights for coil at the window position of 5 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.23 -0.20 0.06 0.34 0.19 0.47 0.28 0.14 -0.22 0.42 -0.36 -0.15 -0.19 -0.02 0.78 -0.29 -0.30 -0.18 0.07 0.29 // H QIAN880139 D Weights for coil at the window position of 6 (Qian-Sejnowski, 1988) R LIT:1411084 PMID:3172241 A Qian, N. and Sejnowski, T.J. T Predicting the secondary structure of globular proteins using neural network models J J. Mol. Biol. 202, 865-884 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.08 -0.01 -0.06 0.04 0.37 0.48 0.36 -0.02 -0.45 0.09 0.24 -0.27 0.16 0.34 0.16 -0.35 -0.04 -0.06 -0.20 0.18 // H RACS770101 D Average reduced distance for C-alpha (Rackovsky-Scheraga, 1977) R LIT:2004126b PMID:271950 A Rackovsky, S. and Scheraga, H.A. T Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) C MEIH800101 0.973 RACS770102 0.946 MEIH800102 0.905 PARJ860101 0.871 KARP850102 0.869 GUYH850101 0.853 KARP850101 0.837 VINM940101 0.835 OOBM770103 0.835 VINM940103 0.829 KRIW790101 0.828 CHOP780203 0.827 FUKS010103 0.819 KRIW790102 0.814 PRAM900104 0.809 LEVM780103 0.808 PARS000101 0.804 RACS770103 0.801 SWER830101 -0.803 GUOD860101 -0.805 NISK800101 -0.805 NADH010103 -0.807 NADH010104 -0.813 CIDH920102 -0.825 PONP800102 -0.827 CIDH920101 -0.837 ROBB790101 -0.839 BEGF750102 -0.840 MEIH800103 -0.845 RICJ880111 -0.846 PONP800101 -0.863 CIDH920104 -0.864 PLIV810101 -0.868 BIOV880102 -0.875 MANP780101 -0.878 ROSG850102 -0.880 CIDH920103 -0.881 PONP930101 -0.886 RADA880108 -0.887 CIDH920105 -0.887 BIOV880101 -0.893 PONP800107 -0.905 WERD780101 -0.912 NISK860101 -0.923 MIYS850101 -0.940 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.934 0.962 0.986 0.994 0.900 1.047 0.986 1.015 0.882 0.766 0.825 1.040 0.804 0.773 1.047 1.056 1.008 0.848 0.931 0.825 // H RACS770102 D Average reduced distance for side chain (Rackovsky-Scheraga, 1977) R LIT:2004126b PMID:271950 A Rackovsky, S. and Scheraga, H.A. T Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) * (Gly 0.080) C MEIH800102 0.987 MEIH800101 0.963 RACS770101 0.946 GUYH850101 0.934 KRIW790102 0.895 RACS770103 0.889 KRIW790101 0.871 KARP850102 0.852 VINM940101 0.844 VINM940103 0.839 OOBM770101 0.838 PARJ860101 0.834 OOBM770103 0.828 ROSM880102 0.824 JANJ780103 0.823 CHOC760102 0.809 WOLS870101 0.802 NADH010105 -0.800 DESM900101 -0.801 NADH010101 -0.808 NISK800101 -0.818 CIDH920105 -0.830 CIDH920103 -0.834 FAUJ830101 -0.843 KYTJ820101 -0.844 JANJ790102 -0.851 CIDH920104 -0.854 JURD980101 -0.855 EISD860103 -0.858 PLIV810101 -0.859 PONP800103 -0.860 PONP800102 -0.864 MANP780101 -0.865 DESM900102 -0.867 JANJ780102 -0.869 PONP800101 -0.870 PONP930101 -0.871 CHOC760103 -0.875 PONP800107 -0.878 NADH010104 -0.883 NADH010103 -0.893 NADH010102 -0.899 WERD780101 -0.906 NISK860101 -0.913 MEIH800103 -0.918 BIOV880102 -0.932 BIOV880101 -0.937 ROSG850102 -0.940 RADA880108 -0.942 MIYS850101 -0.943 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.941 1.112 1.038 1.071 0.866 1.150 1.100 1.055 0.911 0.742 0.798 1.232 0.781 0.723 1.093 1.082 1.043 0.867 1.050 0.817 // H RACS770103 D Side chain orientational preference (Rackovsky-Scheraga, 1977) R LIT:2004126b PMID:271950 A Rackovsky, S. and Scheraga, H.A. T Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) * (Gly !) * (Ratio of the numbers of occurrences in two orientations) C MEIH800102 0.903 RACS770102 0.889 KRIW790102 0.889 OOBM770101 0.871 JANJ780103 0.847 MEIH800101 0.837 VINM940101 0.830 OOBM770103 0.823 GUYH850101 0.816 VINM940104 0.804 RACS770101 0.801 PONP800102 -0.809 MIYS850101 -0.818 PONP800103 -0.819 JANJ780102 -0.828 NADH010104 -0.832 JANJ790102 -0.834 DESM900101 -0.837 NISK860101 -0.837 WERD780101 -0.846 WARP780101 -0.848 NADH010103 -0.851 BIOV880101 -0.856 RADA880108 -0.863 DESM900102 -0.868 NADH010102 -0.876 ROSG850102 -0.901 BIOV880102 -0.906 MEIH800103 -0.919 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.16 1.72 1.97 2.66 0.50 3.87 2.40 1.63 0.86 0.57 0.51 3.90 0.40 0.43 2.04 1.61 1.48 0.75 1.72 0.59 // H RACS820101 D Average relative fractional occurrence in A0(i) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.85 2.02 0.88 1.50 0.90 1.71 1.79 1.54 1.59 0.67 1.03 0.88 1.17 0.85 1.47 1.50 1.96 0.83 1.34 0.89 // H RACS820102 D Average relative fractional occurrence in AR(i) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.58 1.14 0.77 0.98 1.04 1.24 1.49 0.66 0.99 1.09 1.21 1.27 1.41 1.00 1.46 1.05 0.87 1.23 0.68 0.88 // H RACS820103 D Average relative fractional occurrence in AL(i) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.82 2.60 2.07 2.64 0.00 0.00 2.62 1.63 0.00 2.32 0.00 2.86 0.00 0.00 0.00 1.23 2.48 0.00 1.90 1.62 // H RACS820104 D Average relative fractional occurrence in EL(i) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.78 1.75 1.32 1.25 3.14 0.93 0.94 1.13 1.03 1.26 0.91 0.85 0.41 1.07 1.73 1.31 1.57 0.98 1.31 1.11 // H RACS820105 D Average relative fractional occurrence in E0(i) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C NAKH900102 -0.839 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.88 0.99 1.02 1.16 1.14 0.93 1.01 0.70 1.87 1.61 1.09 0.83 1.71 1.52 0.87 1.14 0.96 1.96 1.68 1.56 // H RACS820106 D Average relative fractional occurrence in ER(i) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C ISOY800108 0.831 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.30 0.90 2.73 1.26 0.72 0.97 1.33 3.09 1.33 0.45 0.96 0.71 1.89 1.20 0.83 1.16 0.97 1.58 0.86 0.64 // H RACS820107 D Average relative fractional occurrence in A0(i-1) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.40 1.20 1.24 1.59 2.98 0.50 1.26 1.89 2.71 1.31 0.57 0.87 0.00 1.27 0.38 0.92 1.38 1.53 1.79 0.95 // H RACS820108 D Average relative fractional occurrence in AR(i-1) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C KANM800101 0.914 LEVM780101 0.904 PRAM900102 0.904 ISOY800101 0.904 ROBB760101 0.889 LEVM780104 0.889 PALJ810102 0.881 GEIM800101 0.880 PALJ810101 0.872 CHOP780201 0.868 QIAN880106 0.866 MAXF760101 0.860 KANM800103 0.858 ROBB760103 0.851 GEIM800104 0.851 TANS770101 0.845 AURR980112 0.840 CRAJ730101 0.839 QIAN880107 0.831 QIAN880108 0.820 NAGK730101 0.820 QIAN880105 0.820 AURR980114 0.818 BURA740101 0.809 AURR980109 0.804 AURR980115 0.802 MUNV940101 -0.859 MUNV940102 -0.894 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.48 1.02 0.99 1.19 0.86 1.42 1.43 0.46 1.27 1.12 1.33 1.36 1.41 1.30 0.25 0.89 0.81 1.27 0.91 0.93 // H RACS820109 D Average relative fractional occurrence in AL(i-1) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C ISOY800108 0.848 MAXF760104 0.844 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.00 0.00 4.14 2.15 0.00 0.00 0.00 6.49 0.00 0.00 0.00 0.00 0.00 2.11 1.99 0.00 1.24 0.00 1.90 0.00 // H RACS820110 D Average relative fractional occurrence in EL(i-1) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C MUNV940105 0.833 MUNV940104 0.831 AVBF000102 -0.801 ROBB760104 -0.818 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.02 1.00 1.31 1.76 1.05 1.05 0.83 2.39 0.40 0.83 1.06 0.94 1.33 0.41 2.73 1.18 0.77 1.22 1.09 0.88 // H RACS820111 D Average relative fractional occurrence in E0(i-1) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C TANS770103 0.841 MAXF760102 0.815 ROBB760105 0.803 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.93 1.52 0.92 0.60 1.08 0.94 0.73 0.78 1.08 1.74 1.03 1.00 1.31 1.51 1.37 0.97 1.38 1.12 1.65 1.70 // H RACS820112 D Average relative fractional occurrence in ER(i-1) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.99 1.19 1.15 1.18 2.32 1.52 1.36 1.40 1.06 0.81 1.26 0.91 1.00 1.25 0.00 1.50 1.18 1.33 1.09 1.01 // H RACS820113 D Value of theta(i) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 17.05 21.25 34.81 19.27 28.84 15.42 20.12 38.14 23.07 16.66 10.89 16.46 20.61 16.26 23.94 19.95 18.92 23.36 26.49 17.06 // H RACS820114 D Value of theta(i-1) (Rackovsky-Scheraga, 1982) R LIT:0903736 A Rackovsky, S. and Scheraga, H.A. T Differential geometry and polymer conformation. 4. Conformational and nucleation properties of individual amino acids J Macromolecules 15, 1340-1346 (1982) C MUNV940102 0.877 ONEK900102 0.855 MUNV940101 0.828 ROBB760103 -0.806 BLAM930101 -0.862 ONEK900101 -0.880 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 14.53 17.82 13.59 19.78 30.57 22.18 18.19 37.16 22.63 20.28 14.30 14.07 20.61 19.61 52.63 18.56 21.09 19.78 26.36 21.87 // H RADA880101 D Transfer free energy from chx to wat (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro missing) C EISD840101 0.968 WOLR810101 0.939 NADH010101 0.902 RADA880104 0.901 JURD980101 0.893 EISD860101 0.891 KYTJ820101 0.884 RADA880107 0.881 FAUJ830101 0.873 JANJ780102 0.855 CHOC760103 0.853 EISD860103 0.850 NADH010102 0.845 JANJ790102 0.839 DESM900102 0.828 NADH010103 0.809 RADA880108 0.807 YUTK870101 0.803 WOEC730101 -0.812 CHOC760102 -0.814 GUYH850101 -0.815 JANJ780103 -0.817 WOLS870101 -0.823 HOPT810101 -0.829 FAUJ880110 -0.838 LEVM760101 -0.838 JANJ780101 -0.844 GRAR740102 -0.861 OOBM770101 -0.863 FAUJ880109 -0.873 ROSM880102 -0.917 VHEG790101 -0.925 PRAM900101 -0.932 KUHL950101 -0.950 ROSM880101 -0.978 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.81 -14.92 -6.64 -8.72 1.28 -5.54 -6.81 0.94 -4.66 4.92 4.92 -5.55 2.35 2.98 0. -3.40 -2.57 2.33 -0.14 4.04 // H RADA880102 D Transfer free energy from oct to wat (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro Cys Asp missing) C NOZY710101 0.917 EISD860101 0.912 MEEJ800102 0.900 CIDH920102 0.862 CIDH920105 0.861 ZIMJ680105 0.851 FAUJ830101 0.846 PLIV810101 0.845 TAKK010101 0.830 GUOD860101 0.829 VENT840101 0.826 MIYS850101 0.824 SWER830101 0.820 CIDH920103 0.819 CIDH920104 0.817 MEEJ810102 0.813 BROC820101 0.811 MEIH800101 -0.816 VHEG790101 -0.818 LEVM760101 -0.838 BULH740101 -0.856 HOPT810101 -0.859 WOLS870101 -0.873 PARJ860101 -0.883 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.52 -1.32 -0.01 0. 0. -0.07 -0.79 0. 0.95 2.04 1.76 0.08 1.32 2.09 0. 0.04 0.27 2.51 1.63 1.18 // H RADA880103 D Transfer free energy from vap to chx (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro missing) C FAUJ880104 -0.806 CHAM830105 -0.808 HUTJ700102 -0.812 ROSG850101 -0.814 FAUJ880106 -0.823 MCMT640101 -0.833 GOLD730102 -0.864 BIGC670101 -0.865 KRIW790103 -0.871 TSAJ990101 -0.875 TSAJ990102 -0.879 GRAR740103 -0.881 CHOC750101 -0.892 LEVM760105 -0.893 RADA880106 -0.895 CHAM830106 -0.901 CHAM820101 -0.912 LEVM760102 -0.913 FAUJ880103 -0.923 CHOC760101 -0.924 FASG760101 -0.954 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.13 -5. -3.04 -2.23 -2.52 -3.84 -3.43 1.45 -5.61 -2.77 -2.64 -3.97 -3.83 -3.74 0. -1.66 -2.31 -8.21 -5.97 -2.05 // H RADA880104 D Transfer free energy from chx to oct (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro Cys Asp missing) C RADA880105 0.918 WOLR810101 0.910 EISD840101 0.908 RADA880101 0.901 RADA880107 0.897 JURD980101 0.824 CHOC760103 0.821 KYTJ820101 0.819 NADH010101 0.819 PRAM900101 -0.803 JANJ780101 -0.825 CHOC760102 -0.830 KUHL950101 -0.847 ROSM880102 -0.855 ROSM880101 -0.863 FAUJ880109 -0.926 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.29 -13.60 -6.63 0. 0. -5.47 -6.02 0.94 -5.61 2.88 3.16 -5.63 1.03 0.89 0. -3.44 -2.84 -0.18 -1.77 2.86 // H RADA880105 D Transfer free energy from vap to oct (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro Cys Asp missing) C RADA880104 0.918 WOLR810101 0.875 RADA880107 0.846 FAUJ880109 -0.889 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.42 -18.60 -9.67 0. 0. -9.31 -9.45 2.39 -11.22 0.11 0.52 -9.60 -2.80 -2.85 0. -5.10 -5.15 -8.39 -7.74 0.81 // H RADA880106 D Accessible surface area (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro missing) C CHAM830106 0.922 GRAR740103 0.920 KRIW790103 0.883 CHOC760101 0.875 LEVM760102 0.871 LEVM760105 0.871 FASG760101 0.870 FAUJ880103 0.869 CHOC750101 0.867 TSAJ990102 0.864 TSAJ990101 0.861 BIGC670101 0.856 GOLD730102 0.854 CHAM820101 0.847 ROSG850101 0.814 RADA880103 -0.895 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 93.7 250.4 146.3 142.6 135.2 177.7 182.9 52.6 188.1 182.2 173.7 215.2 197.6 228.6 0. 109.5 142.1 271.6 239.9 157.2 // H RADA880107 D Energy transfer from out to in(95%buried) (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro missing) C EISD840101 0.927 JANJ790102 0.906 RADA880104 0.897 WOLR810101 0.890 RADA880101 0.881 CHOC760103 0.870 JANJ780102 0.856 RADA880105 0.846 JURD980101 0.842 KYTJ820101 0.828 NADH010102 0.823 EISD860103 0.812 EISD860102 -0.837 OOBM770101 -0.854 JANJ780103 -0.856 KUHL950101 -0.857 PRAM900101 -0.865 ROSM880101 -0.867 ROSM880102 -0.894 JANJ780101 -0.917 CHOC760102 -0.925 FAUJ880109 -0.957 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.29 -2.71 -1.18 -1.02 0. -1.53 -0.90 -0.34 -0.94 0.24 -0.12 -2.05 -0.24 0. 0. -0.75 -0.71 -0.59 -1.02 0.09 // H RADA880108 D Mean polarity (Radzicka-Wolfenden, 1988) R LIT:1405051b A Radzicka, A. and Wolfenden, R. T Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution J Biochemistry 27, 1664-1670 (1988) * (Pro missing) C BIOV880101 0.981 ROSG850102 0.967 MIYS850101 0.950 NISK860101 0.950 BIOV880102 0.942 PONP800102 0.938 PONP800103 0.934 PONP800101 0.934 FAUJ830101 0.932 WERD780101 0.930 NADH010103 0.919 MEIH800103 0.916 NADH010104 0.915 CIDH920104 0.914 NADH010102 0.911 PLIV810101 0.906 NISK800101 0.902 MANP780101 0.900 CIDH920105 0.898 PONP930101 0.891 CIDH920103 0.891 PONP800108 0.889 DESM900102 0.881 EISD860103 0.873 JANJ780102 0.869 ROBB790101 0.867 CIDH920101 0.858 JURD980101 0.857 JANJ790102 0.853 NADH010105 0.845 EISD860101 0.844 KYTJ820101 0.842 NADH010101 0.838 PONP800106 0.835 CIDH920102 0.833 CHOC760103 0.830 SWER830101 0.826 JANJ790101 0.824 EISD840101 0.817 GUOD860101 0.812 DESM900101 0.812 RADA880101 0.807 MEEJ810101 0.804 PONP800107 0.800 KARP850101 -0.804 JANJ780103 -0.805 FUKS010102 -0.815 LEVM760101 -0.824 WOEC730101 -0.825 ROSM880101 -0.831 HOPT810101 -0.831 KUHL950101 -0.839 FUKS010103 -0.840 WOLS870101 -0.840 VINM940102 -0.846 KRIW710101 -0.847 FUKS010104 -0.851 KRIW790102 -0.856 ROSM880102 -0.861 VINM940103 -0.862 RACS770103 -0.863 OOBM770101 -0.864 PARJ860101 -0.865 OOBM770103 -0.878 KARP850102 -0.879 RACS770101 -0.887 KRIW790101 -0.897 GRAR740102 -0.899 VINM940101 -0.906 MEIH800101 -0.940 RACS770102 -0.942 GUYH850101 -0.948 MEIH800102 -0.953 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.06 -0.84 -0.48 -0.80 1.36 -0.73 -0.77 -0.41 0.49 1.31 1.21 -1.18 1.27 1.27 0. -0.50 -0.27 0.88 0.33 1.09 // H RICJ880101 D Relative preference value at N" (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C RICJ880102 1.000 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.7 0.4 1.2 1.4 0.6 1. 1. 1.6 1.2 0.9 0.9 1. 0.3 1.2 0.7 1.6 0.3 1.1 1.9 0.7 // H RICJ880102 D Relative preference value at N' (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C RICJ880101 1.000 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.7 0.4 1.2 1.4 0.6 1. 1. 1.6 1.2 0.9 0.9 1. 0.3 1.2 0.7 1.6 0.3 1.1 1.9 0.7 // H RICJ880103 D Relative preference value at N-cap (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.5 0.4 3.5 2.1 0.6 0.4 0.4 1.8 1.1 0.2 0.2 0.7 0.8 0.2 0.8 2.3 1.6 0.3 0.8 0.1 // H RICJ880104 D Relative preference value at N1 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.2 0.7 0.7 0.8 0.8 0.7 2.2 0.3 0.7 0.9 0.9 0.6 0.3 0.5 2.6 0.7 0.8 2.1 1.8 1.1 // H RICJ880105 D Relative preference value at N2 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.6 0.9 0.7 2.6 1.2 0.8 2. 0.9 0.7 0.7 0.3 1. 1. 0.9 0.5 0.8 0.7 1.7 0.4 0.6 // H RICJ880106 D Relative preference value at N3 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C FAUJ880112 0.849 AURR980107 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1. 0.4 0.7 2.2 0.6 1.5 3.3 0.6 0.7 0.4 0.6 0.8 1. 0.6 0.4 0.4 1. 1.4 1.2 1.1 // H RICJ880107 D Relative preference value at N4 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C CHOP780210 -0.818 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.1 1.5 0. 0.3 1.1 1.3 0.5 0.4 1.5 1.1 2.6 0.8 1.7 1.9 0.1 0.4 0.5 3.1 0.6 1.5 // H RICJ880108 D Relative preference value at N5 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.4 1.2 1.2 0.6 1.6 1.4 0.9 0.6 0.9 0.9 1.1 1.9 1.7 1. 0.3 1.1 0.6 1.4 0.2 0.8 // H RICJ880109 D Relative preference value at Mid (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C QIAN880106 0.834 ROBB760103 0.831 KANM800103 0.829 AURR980109 0.828 AURR980113 0.808 CHAM830101 -0.826 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.8 1.3 0.9 1. 0.7 1.3 0.8 0.5 1. 1.2 1.2 1.1 1.5 1.3 0.3 0.6 1. 1.5 0.8 1.2 // H RICJ880110 D Relative preference value at C5 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.8 1. 0.6 0.7 0. 1. 1.1 0.5 2.4 1.3 1.2 1.4 2.7 1.9 0.3 0.5 0.5 1.1 1.3 0.4 // H RICJ880111 D Relative preference value at C4 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C MEIH800101 -0.802 CHOP780210 -0.804 BHAR880101 -0.813 RACS770101 -0.846 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.3 0.8 0.6 0.5 0.7 0.2 0.7 0.5 1.9 1.6 1.4 1. 2.8 2.9 0. 0.5 0.6 2.1 0.8 1.4 // H RICJ880112 D Relative preference value at C3 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.7 0.8 0.8 0.6 0.2 1.3 1.6 0.1 1.1 1.4 1.9 2.2 1. 1.8 0. 0.6 0.7 0.4 1.1 1.3 // H RICJ880113 D Relative preference value at C2 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.4 2.1 0.9 0.7 1.2 1.6 1.7 0.2 1.8 0.4 0.8 1.9 1.3 0.3 0.2 1.6 0.9 0.4 0.3 0.7 // H RICJ880114 D Relative preference value at C1 (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.1 1. 1.2 0.4 1.6 2.1 0.8 0.2 3.4 0.7 0.7 2. 1. 0.7 0. 1.7 1. 0. 1.2 0.7 // H RICJ880115 D Relative preference value at C-cap (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C AURR980117 0.921 MAXF760104 0.919 ISOY800108 0.889 TANS770107 0.807 MAXF760105 0.802 LEVM760103 -0.829 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.8 0.9 1.6 0.7 0.4 0.9 0.3 3.9 1.3 0.7 0.7 1.3 0.8 0.5 0.7 0.8 0.3 0. 0.8 0.2 // H RICJ880116 D Relative preference value at C' (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1. 1.4 0.9 1.4 0.8 1.4 0.8 1.2 1.2 1.1 0.9 1.2 0.8 0.1 1.9 0.7 0.8 0.4 0.9 0.6 // H RICJ880117 D Relative preference value at C" (Richardson-Richardson, 1988) R LIT:1408116 PMID:3381086 A Richardson, J.S. and Richardson, D.C. T Amino acid preferences for specific locations at the ends of alpha helices J Science 240, 1648-1652 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.7 1.1 1.5 1.4 0.4 1.1 0.7 0.6 1. 0.7 0.5 1.3 0. 1.2 1.5 0.9 2.1 2.7 0.5 1. // H ROBB760101 D Information measure for alpha-helix (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C CHOP780201 0.969 ISOY800101 0.957 MAXF760101 0.956 TANS770101 0.948 PALJ810102 0.946 KANM800101 0.945 PRAM900102 0.916 LEVM780101 0.916 PALJ810101 0.914 BURA740101 0.912 LEVM780104 0.911 NAGK730101 0.910 QIAN880106 0.904 GEIM800101 0.897 RACS820108 0.889 KANM800103 0.886 CRAJ730101 0.875 QIAN880105 0.874 QIAN880107 0.867 GEIM800104 0.855 AURR980108 0.814 AURR980109 0.810 ROBB760103 0.807 AURR980112 0.806 PALJ810109 0.805 MUNV940101 -0.822 MUNV940102 -0.827 CHAM830101 -0.828 NAGK730103 -0.861 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.5 -0.9 -5.1 0.5 -1.3 1.0 7.8 -8.6 1.2 0.6 3.2 2.3 5.3 1.6 -7.7 -3.9 -2.6 1.2 -4.5 1.4 // H ROBB760102 D Information measure for N-terminal helix (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C CHOP780204 0.911 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.3 -5.2 0.3 7.4 0.8 -0.7 10.3 -5.2 -2.8 -4.0 -2.1 -4.1 -3.5 -1.1 8.1 -3.5 2.3 -0.9 -3.7 -4.4 // H ROBB760103 D Information measure for middle helix (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C QIAN880108 0.914 PTIO830101 0.903 QIAN880107 0.889 KANM800103 0.887 BLAM930101 0.883 ONEK900101 0.878 QIAN880109 0.868 AURR980109 0.857 QIAN880106 0.854 BEGF750101 0.852 RACS820108 0.851 ISOY800101 0.841 AURR980113 0.838 AURR980108 0.835 RICJ880109 0.831 QIAN880105 0.811 ROBB760101 0.807 QIAN880110 0.807 CHOP780201 0.806 FAUJ880113 0.802 AURR980114 0.801 GEIM800108 -0.802 RACS820114 -0.806 QIAN880133 -0.807 QIAN880132 -0.827 ISOY800104 -0.830 QIAN880135 -0.834 PRAM900104 -0.840 CHOP780216 -0.841 LEVM780103 -0.843 GEIM800111 -0.843 QIAN880134 -0.855 ONEK900102 -0.867 CHAM830101 -0.878 MUNV940102 -0.913 MUNV940101 -0.918 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.7 0.3 -6.1 -3.1 -4.9 0.6 2.2 -6.8 -1.0 3.2 5.5 0.5 7.2 2.8 -22.8 -3.0 -4.0 4.0 -4.6 2.5 // H ROBB760104 D Information measure for C-terminal helix (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C QIAN880108 0.879 BLAM930101 0.878 QIAN880109 0.871 ONEK900101 0.844 CHOP780205 0.841 BUNA790101 0.823 PTIO830101 0.817 QIAN880110 0.806 QIAN880134 -0.802 MUNV940102 -0.803 ISOY800104 -0.817 RACS820110 -0.818 MUNV940101 -0.831 MUNV940104 -0.840 FINA910102 -0.844 MUNV940105 -0.859 ONEK900102 -0.861 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.3 1.4 -3.3 -4.4 6.1 2.7 2.5 -8.3 5.9 -0.5 0.1 7.3 3.5 1.6 -24.4 -1.9 -3.7 -0.9 -0.6 2.3 // H ROBB760105 D Information measure for extended (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C ROBB760106 0.949 KANM800102 0.898 KANM800104 0.885 CHOP780202 0.885 PTIO830102 0.878 GEIM800105 0.877 TANS770103 0.871 PALJ810103 0.869 LIFS790101 0.867 QIAN880120 0.860 QIAN880119 0.859 ISOY800102 0.847 LEVM780105 0.842 GEIM800107 0.836 PALJ810104 0.835 QIAN880121 0.834 PONP930101 0.829 PONP800102 0.828 PONP800101 0.823 PONP800103 0.823 BURA740102 0.821 PONP800108 0.820 NAGK730102 0.815 MANP780101 0.805 PALJ810110 0.804 RACS820111 0.803 MUNV940103 -0.832 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -2.3 0.4 -4.1 -4.4 4.4 1.2 -5.0 -4.2 -2.5 6.7 2.3 -3.3 2.3 2.6 -1.8 -1.7 1.3 -1.0 4.0 6.8 // H ROBB760106 D Information measure for pleated-sheet (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C ROBB760105 0.949 KANM800102 0.938 CHOP780202 0.931 QIAN880120 0.908 QIAN880121 0.907 LIFS790101 0.906 GEIM800107 0.899 QIAN880119 0.897 PALJ810104 0.894 NAGK730102 0.887 PALJ810103 0.886 PTIO830102 0.882 KANM800104 0.877 LEVM780105 0.869 PONP930101 0.866 CRAJ730102 0.865 GEIM800105 0.856 CHOP780208 0.846 GEIM800106 0.838 PALJ810110 0.836 AVBF000101 0.834 PONP800101 0.829 LIFS790103 0.827 MANP780101 0.824 PONP800102 0.822 PONP800103 0.812 NISK860101 0.810 BEGF750102 0.809 PONP800108 0.808 GEIM800110 -0.819 MUNV940103 -0.888 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -2.7 0.4 -4.2 -4.4 3.7 0.8 -8.1 -3.9 -3.0 7.7 3.7 -2.9 3.7 3.0 -6.6 -2.4 1.7 0.3 3.3 7.1 // H ROBB760107 D Information measure for extended without H-bond (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.0 1.1 -2.0 -2.6 5.4 2.4 3.1 -3.4 0.8 -0.1 -3.7 -3.1 -2.1 0.7 7.4 1.3 0.0 -3.4 4.8 2.7 // H ROBB760108 D Information measure for turn (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C ROBB760113 0.994 ROBB760110 0.960 BEGF750103 0.922 CRAJ730103 0.912 CHOP780101 0.887 PALJ810106 0.882 TANS770110 0.839 CHAM830101 0.812 BEGF750101 -0.819 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -5.0 2.1 4.2 3.1 4.4 0.4 -4.7 5.7 -0.3 -4.6 -5.6 1.0 -4.8 -1.8 2.6 2.6 0.3 3.4 2.9 -6.0 // H ROBB760109 D Information measure for N-terminal turn (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -3.3 0.0 5.4 3.9 -0.3 -0.4 -1.8 -1.2 3.0 -0.5 -2.3 -1.2 -4.3 0.8 6.5 1.8 -0.7 -0.8 3.1 -3.5 // H ROBB760110 D Information measure for middle turn (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C ROBB760108 0.960 ROBB760113 0.957 BEGF750103 0.903 CRAJ730103 0.887 PALJ810106 0.864 CHOP780101 0.863 TANS770110 0.805 CHAM830101 0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -4.7 2.0 3.9 1.9 6.2 -2.0 -4.2 5.7 -2.6 -7.0 -6.2 2.8 -4.8 -3.7 3.6 2.1 0.6 3.3 3.8 -6.2 // H ROBB760111 D Information measure for C-terminal turn (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C CHOP780215 0.825 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -3.7 1.0 -0.6 -0.6 4.0 3.4 -4.3 5.9 -0.8 -0.5 -2.8 1.3 -1.6 1.6 -6.0 1.5 1.2 6.5 1.3 -4.6 // H ROBB760112 D Information measure for coil (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C PALJ810115 0.885 CHOP780211 0.841 QIAN880133 0.814 ISOY800103 0.807 QIAN880132 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -2.5 -1.2 4.6 0.0 -4.7 -0.5 -4.4 4.9 1.6 -3.3 -2.0 -0.8 -4.1 -4.1 5.8 2.5 1.7 1.2 -0.6 -3.5 // H ROBB760113 D Information measure for loop (Robson-Suzuki, 1976) R PMID:1003471 A Robson, B. and Suzuki, E. T Conformational properties of amino acid residues in globular proteins J J. Mol. Biol. 107, 327-356 (1976) C ROBB760108 0.994 ROBB760110 0.957 BEGF750103 0.924 CRAJ730103 0.916 CHOP780101 0.907 PALJ810106 0.895 TANS770110 0.853 CHAM830101 0.841 NAGK730103 0.811 CHOP780201 -0.811 BEGF750101 -0.826 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -5.1 2.6 4.7 3.1 3.8 0.2 -5.2 5.6 -0.9 -4.5 -5.4 1.0 -5.3 -2.4 3.5 3.2 0.0 2.9 3.2 -6.3 // H ROBB790101 D Hydration free energy (Robson-Osguthorpe, 1979) R LIT:0511124 PMID:513136 A Robson, B. and Osguthorpe, D.J. T Refined models for computer simulation of protein folding: Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor J J. Mol. Biol. 132, 19-51 (1979) * (Gly 0.67) C CIDH920105 0.921 NISK860101 0.912 CIDH920104 0.903 CIDH920102 0.896 MIYS850101 0.895 BIOV880101 0.890 CIDH920103 0.884 PLIV810101 0.875 WERD780101 0.872 FAUJ830101 0.868 RADA880108 0.867 MEEJ810101 0.861 PONP930101 0.858 ROSG850102 0.846 CIDH920101 0.846 SWER830101 0.835 MANP780101 0.834 PONP800108 0.831 NISK800101 0.830 PONP800101 0.822 MEEJ810102 0.821 BIOV880102 0.821 GUOD860101 0.815 MEEJ800102 0.807 PONP800102 0.807 LEVM760106 0.804 MEIH800103 0.801 BULH740101 -0.813 PARS000101 -0.819 WOLS870101 -0.831 GRAR740102 -0.832 RACS770101 -0.839 VINM940101 -0.858 FUKS010103 -0.865 VINM940102 -0.866 MEIH800101 -0.868 PARJ860101 -0.893 OOBM770103 -0.909 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -1.0 0.3 -0.7 -1.2 2.1 -0.1 -0.7 0.3 1.1 4.0 2.0 -0.9 1.8 2.8 0.4 -1.2 -0.5 3.0 2.1 1.4 // H ROSG850101 D Mean area buried on transfer (Rose et al., 1985) R LIT:1109092 PMID:4023714 A Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H. T Hydrophobicity of amino acid residues in globular proteins J Science 229, 834-838 (1985) C GRAR740103 0.922 KRIW790103 0.920 CHAM820101 0.917 TSAJ990101 0.914 BIGC670101 0.910 GOLD730102 0.909 TSAJ990102 0.909 CHOC750101 0.908 LEVM760106 0.896 FAUJ880103 0.892 CIDH920102 0.866 MCMT640101 0.857 LEVM760107 0.852 CHOC760101 0.842 FASG760101 0.838 NOZY710101 0.834 CIDH920101 0.831 RADA880106 0.814 PARS000101 -0.805 KARP850101 -0.807 VINM940102 -0.810 RADA880103 -0.814 WEBA780101 -0.817 FUKS010103 -0.819 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 86.6 162.2 103.3 97.8 132.3 119.2 113.9 62.9 155.8 158.0 164.1 115.5 172.9 194.1 92.9 85.6 106.5 224.6 177.7 141.0 // H ROSG850102 D Mean fractional area loss (Rose et al., 1985) R LIT:1109092 PMID:4023714 A Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H. T Hydrophobicity of amino acid residues in globular proteins J Science 229, 834-838 (1985) C BIOV880101 0.981 RADA880108 0.967 NISK860101 0.962 BIOV880102 0.960 NADH010103 0.958 NADH010104 0.953 PONP800102 0.949 MEIH800103 0.948 NADH010102 0.948 PONP800103 0.947 WERD780101 0.943 NISK800101 0.942 PONP800101 0.938 MIYS850101 0.937 PONP930101 0.928 PONP800108 0.919 DESM900102 0.914 JANJ780102 0.909 FAUJ830101 0.904 MANP780101 0.903 CIDH920104 0.896 JANJ790102 0.892 DESM900101 0.866 NADH010105 0.865 CIDH920105 0.858 JANJ790101 0.857 JURD980101 0.854 CHOC760103 0.851 CIDH920103 0.846 EISD860103 0.846 ROBB790101 0.846 PLIV810101 0.841 KYTJ820101 0.841 NADH010101 0.833 WARP780101 0.823 PONP800106 0.807 EISD840101 0.806 PONP800107 0.803 WOEC730101 -0.804 FUKS010103 -0.808 VINM940104 -0.809 CHOC760102 -0.819 PARS000101 -0.820 ROSM880102 -0.822 PARJ860101 -0.823 HOPT810101 -0.825 JANJ780101 -0.836 VINM940102 -0.849 KRIW710101 -0.852 FUKS010104 -0.877 JANJ780103 -0.879 GRAR740102 -0.880 RACS770101 -0.880 KARP850102 -0.897 VINM940103 -0.901 RACS770103 -0.901 OOBM770101 -0.903 OOBM770103 -0.916 KRIW790102 -0.922 GUYH850101 -0.929 MEIH800101 -0.930 KRIW790101 -0.935 RACS770102 -0.940 VINM940101 -0.943 MEIH800102 -0.959 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.74 0.64 0.63 0.62 0.91 0.62 0.62 0.72 0.78 0.88 0.85 0.52 0.85 0.88 0.64 0.66 0.70 0.85 0.76 0.86 // H ROSM880101 D Side chain hydropathy, uncorrected for solvation (Roseman, 1988) R LIT:1405111b PMID:3398047 A Roseman, M.A. T Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds J J. Mol. Biol. 200, 513-522 (1988) C KUHL950101 0.962 ROSM880102 0.938 PRAM900101 0.917 FAUJ880110 0.888 GRAR740102 0.887 VHEG790101 0.883 LEVM760101 0.876 WOLS870101 0.866 OOBM770101 0.854 HOPT810101 0.848 FAUJ880109 0.846 WOEC730101 0.844 JANJ780101 0.822 JANJ780103 0.810 GUYH850101 0.803 PARJ860101 0.803 NAKH900110 -0.812 DESM900102 -0.812 WARP780101 -0.816 CHOC760103 -0.819 BIOV880102 -0.824 JANJ790102 -0.824 CIDH920104 -0.828 BIOV880101 -0.830 NADH010102 -0.830 RADA880108 -0.831 PLIV810101 -0.834 JANJ780102 -0.835 KYTJ820101 -0.845 JURD980101 -0.851 RADA880104 -0.863 NADH010101 -0.866 RADA880107 -0.867 EISD860103 -0.871 WOLR810101 -0.884 FAUJ830101 -0.907 EISD860101 -0.917 EISD840101 -0.947 RADA880101 -0.978 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.67 12.1 7.23 8.72 -0.34 6.39 7.35 0.00 3.82 -3.02 -3.02 6.13 -1.30 -3.24 -1.75 4.35 3.86 -2.86 0.98 -2.18 // H ROSM880102 D Side chain hydropathy, corrected for solvation (Roseman, 1988) R LIT:1405111b PMID:3398047 A Roseman, M.A. T Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds J J. Mol. Biol. 200, 513-522 (1988) C ROSM880101 0.938 KUHL950101 0.922 PRAM900101 0.892 WOLS870101 0.877 GRAR740102 0.870 OOBM770101 0.867 MEIH800102 0.859 JANJ780101 0.853 CHOC760102 0.845 JANJ780103 0.838 GUYH850101 0.837 VHEG790101 0.828 FAUJ880109 0.824 RACS770102 0.824 LEVM760101 0.823 WOEC730101 0.801 PARJ860101 0.801 WARP780101 -0.801 DESM900102 -0.816 ROSG850102 -0.822 MIYS850101 -0.825 GUOD860101 -0.829 WOLR810101 -0.829 MEIH800103 -0.829 CIDH920104 -0.831 BIOV880102 -0.837 NADH010104 -0.839 BIOV880101 -0.854 RADA880104 -0.855 NADH010103 -0.857 RADA880108 -0.861 PLIV810101 -0.864 JANJ790102 -0.866 EISD860101 -0.868 CHOC760103 -0.869 NADH010101 -0.870 JANJ780102 -0.870 KYTJ820101 -0.878 NADH010102 -0.881 JURD980101 -0.894 RADA880107 -0.894 RADA880101 -0.917 EISD840101 -0.925 FAUJ830101 -0.927 EISD860103 -0.943 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.67 3.89 2.27 1.57 -2.00 2.12 1.78 0.00 1.09 -3.02 -3.02 2.46 -1.67 -3.24 -1.75 0.10 -0.42 -2.86 0.98 -2.18 // H ROSM880103 D Loss of Side chain hydropathy by helix formation (Roseman, 1988) R LIT:1405111b PMID:3398047 A Roseman, M.A. T Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds J J. Mol. Biol. 200, 513-522 (1988) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.4 0.3 0.9 0.8 0.5 0.7 1.3 0.0 1.0 0.4 0.6 0.4 0.3 0.7 0.9 0.4 0.4 0.6 1.2 0.4 // H SIMZ760101 D Transfer free energy (Simon, 1976), Cited by Charton-Charton (1982) R A Simon, Z. T J Quantum Biochemistry and Specific Interactions, Abacus Press, Tunbridge Wells, Kent, England (1976) * Cited by Charton-Charton (1982) C ARGP820101 0.967 JOND750101 0.966 GOLD730101 0.939 TAKK010101 0.936 MEEJ800102 0.861 LEVM760106 0.848 CIDH920105 0.837 MEEJ810101 0.836 CIDH920102 0.832 ZIMJ680101 0.821 BULH740102 0.815 LAWE840101 0.815 ZIMJ680102 0.810 MEEJ810102 0.808 NOZY710101 0.807 VENT840101 0.806 ZIMJ680105 0.805 PLIV810101 0.805 PARJ860101 -0.825 WOLS870101 -0.830 BULH740101 -0.894 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.73 0.73 -0.01 0.54 0.70 -0.10 0.55 0.00 1.10 2.97 2.49 1.50 1.30 2.65 2.60 0.04 0.44 3.00 2.97 1.69 // H SNEP660101 D Principal component I (Sneath, 1966) R PMID:4291386 A Sneath, P.H.A. T Relations between chemical structure and biological activity in peptides J J. Theor. Biol. 12, 157-195 (1966) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.239 0.211 0.249 0.171 0.220 0.260 0.187 0.160 0.205 0.273 0.281 0.228 0.253 0.234 0.165 0.236 0.213 0.183 0.193 0.255 // H SNEP660102 D Principal component II (Sneath, 1966) R PMID:4291386 A Sneath, P.H.A. T Relations between chemical structure and biological activity in peptides J J. Theor. Biol. 12, 157-195 (1966) C FAUJ880110 -0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.330 -0.176 -0.233 -0.371 0.074 -0.254 -0.409 0.370 -0.078 0.149 0.129 -0.075 -0.092 -0.011 0.370 0.022 0.136 -0.011 -0.138 0.245 // H SNEP660103 D Principal component III (Sneath, 1966) R PMID:4291386 A Sneath, P.H.A. T Relations between chemical structure and biological activity in peptides J J. Theor. Biol. 12, 157-195 (1966) C LEVM760107 0.818 CHAM820101 0.808 ZASB820101 0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.110 0.079 -0.136 -0.285 -0.184 -0.067 -0.246 -0.073 0.320 0.001 -0.008 0.049 -0.041 0.438 -0.016 -0.153 -0.208 0.493 0.381 -0.155 // H SNEP660104 D Principal component IV (Sneath, 1966) R PMID:4291386 A Sneath, P.H.A. T Relations between chemical structure and biological activity in peptides J J. Theor. Biol. 12, 157-195 (1966) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.062 -0.167 0.166 -0.079 0.380 -0.025 -0.184 -0.017 0.056 -0.309 -0.264 -0.371 0.077 0.074 -0.036 0.470 0.348 0.050 0.220 -0.212 // H SUEM840101 D Zimm-Bragg parameter s at 20 C (Sueki et al., 1984) R LIT:1004141 A Sueki, M., Lee, S., Powers, S.P., Denton, J.B., Konishi, Y. and Scheraga, H.A. T Helix-coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly{(hydroxybutyl)glutamine-co-L-histidine} J Macromolecules 17, 148-155 (1984) * Charged state for Arg, His, Asp, and Glu * (Cys Pro 0.100) C AURR980113 0.887 FINA770101 0.883 AURR980109 0.882 PTIO830101 0.877 AURR980114 0.845 KANM800103 0.820 QIAN880107 0.803 QIAN880131 -0.823 PALJ810106 -0.832 CHOP780101 -0.845 ISOY800103 -0.850 LEVM780103 -0.864 TANS770110 -0.864 PRAM900104 -0.865 CHOP780216 -0.874 GEIM800108 -0.875 LEVM780106 -0.878 QIAN880133 -0.879 QIAN880132 -0.880 GEIM800111 -0.885 CHAM830101 -0.891 CHOP780203 -0.892 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.071 1.033 0.784 0.680 0.922 0.977 0.970 0.591 0.850 1.140 1.140 0.939 1.200 1.086 0.659 0.760 0.817 1.107 1.020 0.950 // H SUEM840102 D Zimm-Bragg parameter sigma x 1.0E4 (Sueki et al., 1984) R LIT:1004141 A Sueki, M., Lee, S., Powers, S.P., Denton, J.B., Konishi, Y. and Scheraga, H.A. T Helix-coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly{(hydroxybutyl)glutamine-co-L-histidine} J Macromolecules 17, 148-155 (1984) * Charged state for Arg, His, Asp, and Glu * (Cys Pro !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.0 0.1 0.1 70.0 26.0 33.0 6.0 0.1 0.1 55.0 33.0 1.0 54.0 18.0 42.0 0.1 0.1 77.0 66.0 0.1 // H SWER830101 D Optimal matching hydrophobicity (Sweet-Eisenberg, 1983) R LIT:2004095b PMID:6663622 A Sweet, R.M. and Eisenberg, D. T Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure J J. Mol. Biol. 171, 479-488 (1983) C CIDH920105 0.890 MIYS850101 0.889 PLIV810101 0.875 CIDH920102 0.870 CIDH920103 0.865 NISK860101 0.865 CIDH920104 0.862 PTIO830102 0.856 GUOD860101 0.853 CIDH920101 0.853 BIOV880101 0.839 VENT840101 0.836 NOZY710101 0.836 ROBB790101 0.835 PONP930101 0.835 FAUJ830101 0.833 ZIMJ680105 0.829 RADA880108 0.826 QIAN880120 0.825 EISD860101 0.824 CHOP780202 0.823 MANP780101 0.821 RADA880102 0.820 LIFS790101 0.815 PALJ810104 0.809 MEEJ810101 0.806 WERD780101 0.804 MUNV940103 -0.802 RACS770101 -0.803 VINM940102 -0.811 VINM940101 -0.817 MEIH800101 -0.830 WOEC730101 -0.832 OOBM770103 -0.833 PARS000101 -0.846 WOLS870101 -0.887 PARJ860101 -0.893 GRAR740102 -0.896 BULH740101 -0.923 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.40 -0.59 -0.92 -1.31 0.17 -0.91 -1.22 -0.67 -0.64 1.25 1.22 -0.67 1.02 1.92 -0.49 -0.55 -0.28 0.50 1.67 0.91 // H TANS770101 D Normalized frequency of alpha-helix (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C ROBB760101 0.948 CHOP780201 0.947 MAXF760101 0.930 KANM800101 0.927 NAGK730101 0.925 PALJ810102 0.923 GEIM800101 0.918 PALJ810101 0.918 BURA740101 0.917 LEVM780104 0.908 ISOY800101 0.906 PRAM900102 0.854 LEVM780101 0.854 RACS820108 0.845 KANM800103 0.843 CRAJ730101 0.843 GEIM800104 0.841 AURR980115 0.834 QIAN880106 0.819 AURR980111 0.817 QIAN880107 0.804 AURR980114 0.800 NAGK730103 -0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.42 1.06 0.71 1.01 0.73 1.02 1.63 0.50 1.20 1.12 1.29 1.24 1.21 1.16 0.65 0.71 0.78 1.05 0.67 0.99 // H TANS770102 D Normalized frequency of isolated helix (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.946 1.128 0.432 1.311 0.481 1.615 0.698 0.360 2.168 1.283 1.192 1.203 0.000 0.963 2.093 0.523 1.961 1.925 0.802 0.409 // H TANS770103 D Normalized frequency of extended structure (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C ISOY800102 0.929 MAXF760102 0.891 ROBB760105 0.871 GEIM800105 0.850 RACS820111 0.841 PALJ810103 0.824 WOEC730101 -0.806 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.790 1.087 0.832 0.530 1.268 1.038 0.643 0.725 0.864 1.361 1.111 0.735 1.092 1.052 1.249 1.093 1.214 1.114 1.340 1.428 // H TANS770104 D Normalized frequency of chain reversal R (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C CHOP780213 0.954 ISOY800104 0.918 FINA910102 0.876 MUNV940104 0.870 MUNV940105 0.846 QIAN880134 0.837 ONEK900102 0.826 FODM020101 -0.802 BLAM930101 -0.837 BUNA790101 -0.867 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.194 0.795 0.659 1.056 0.678 1.290 0.928 1.015 0.611 0.603 0.595 1.060 0.831 0.377 3.159 1.444 1.172 0.452 0.816 0.640 // H TANS770105 D Normalized frequency of chain reversal S (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C CHOP780214 0.862 ISOY800105 0.836 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.497 0.677 2.072 1.498 1.348 0.711 0.651 1.848 1.474 0.471 0.656 0.932 0.425 1.348 0.179 1.151 0.749 1.283 1.283 0.654 // H TANS770106 D Normalized frequency of chain reversal D (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.937 1.725 1.080 1.640 1.004 1.078 0.679 0.901 1.085 0.178 0.808 1.254 0.886 0.803 0.748 1.145 1.487 0.803 1.227 0.625 // H TANS770107 D Normalized frequency of left-handed helix (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C MAXF760104 0.913 ISOY800108 0.827 RICJ880115 0.807 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.289 1.380 3.169 0.917 1.767 2.372 0.285 4.259 1.061 0.262 0.000 1.288 0.000 0.393 0.000 0.160 0.218 0.000 0.654 0.167 // H TANS770108 D Normalized frequency of zeta R (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.328 2.088 1.498 3.379 0.000 0.000 0.000 0.500 1.204 2.078 0.414 0.835 0.982 1.336 0.415 1.089 1.732 1.781 0.000 0.946 // H TANS770109 D Normalized frequency of coil (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C MAXF760105 0.878 MAXF760104 0.821 ISOY800108 0.816 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.945 0.364 1.202 1.315 0.932 0.704 1.014 2.355 0.525 0.673 0.758 0.947 1.028 0.622 0.579 1.140 0.863 0.777 0.907 0.561 // H TANS770110 D Normalized frequency of chain reversal (Tanaka-Scheraga, 1977) R PMID:557155 A Tanaka, S. and Scheraga, H.A. T Statistical mechanical treatment of protein conformation. 5. A multiphasic model for specific-sequence copolymers of amino acids J Macromolecules 10, 9-20 (1977) * Recalculated by Kidera as normalized frequencies C CHOP780101 0.956 CHOP780203 0.940 CHOP780216 0.930 PALJ810106 0.925 QIAN880133 0.920 CHAM830101 0.917 QIAN880132 0.903 ISOY800103 0.897 LEVM780106 0.892 GEIM800108 0.886 GEIM800111 0.883 LEVM780103 0.875 PRAM900104 0.873 QIAN880131 0.873 PALJ810105 0.860 CRAJ730103 0.859 CHOP780210 0.858 ROBB760113 0.853 ROBB760108 0.839 BEGF750103 0.834 ROBB760110 0.805 AURR980109 -0.816 SUEM840101 -0.864 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.842 0.936 1.352 1.366 1.032 0.998 0.758 1.349 1.079 0.459 0.665 1.045 0.668 0.881 1.385 1.257 1.055 0.881 1.101 0.643 // H VASM830101 D Relative population of conformational state A (Vasquez et al., 1983) R LIT:0908110 A Vasquez, M., Nemethy, G. and Scheraga, H.A. T Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue alpha-aminobutyric acid J Macromolecules 16, 1043-1049 (1983) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.135 0.296 0.196 0.289 0.159 0.236 0.184 0.051 0.223 0.173 0.215 0.170 0.239 0.087 0.151 0.010 0.100 0.166 0.066 0.285 // H VASM830102 D Relative population of conformational state C (Vasquez et al., 1983) R LIT:0908110 A Vasquez, M., Nemethy, G. and Scheraga, H.A. T Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue alpha-aminobutyric acid J Macromolecules 16, 1043-1049 (1983) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.507 0.459 0.287 0.223 0.592 0.383 0.445 0.390 0.310 0.111 0.619 0.559 0.431 0.077 0.739 0.689 0.785 0.160 0.060 0.356 // H VASM830103 D Relative population of conformational state E (Vasquez et al., 1983) R LIT:0908110 A Vasquez, M., Nemethy, G. and Scheraga, H.A. T Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue alpha-aminobutyric acid J Macromolecules 16, 1043-1049 (1983) * (Pro !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.159 0.194 0.385 0.283 0.187 0.236 0.206 0.049 0.233 0.581 0.083 0.159 0.198 0.682 0.366 0.150 0.074 0.463 0.737 0.301 // H VELV850101 D Electron-ion interaction potential (Veljkovic et al., 1985) R LIT:2004067b A Veljkovic, V., Cosic, I., Dimitrijevic, B. and Lalovic, D. T Is it possible to analyze DNA and protein sequences by the method of digital signal processing? J IEEE Trans. Biomed. Eng. 32, 337-341 (1985) C COSI940101 1.000 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V .03731 .09593 .00359 .12630 .08292 .07606 .00580 .00499 .02415 .00000 .00000 .03710 .08226 .09460 .01979 .08292 .09408 .05481 .05159 .00569 // H VENT840101 D Bitterness (Venanzi, 1984) R LIT:1103107b PMID:6521488 A Venanzi, T.J. T Hydrophobicity parameters and the bitter taste of L-amino acids J J. Theor. Biol. 111, 447-450 (1984) C NOZY710101 0.897 GUOD860101 0.848 PTIO830102 0.842 WILM950101 0.840 SWER830101 0.836 MEEJ810102 0.831 PALJ810104 0.831 RADA880102 0.826 CHOP780209 0.817 LIFS790101 0.814 MEEJ810101 0.813 CIDH920105 0.813 TAKK010101 0.812 SIMZ760101 0.806 PONP800107 0.805 CHOP780202 0.805 GOLD730101 0.802 WOLS870101 -0.835 PARJ860101 -0.846 BULH740101 -0.907 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1. 0. 0. 1. 0. 0. 0. 1. 1. 1. // H VHEG790101 D Transfer free energy to lipophilic phase (von Heijne-Blomberg, 1979) R LIT:0509382 PMID:477664 A von Heijne, G. and Blomberg, C. T Trans-membrane translocation of proteins: The direct transfer model J Eur. J. Biochem. 97, 175-181 (1979) C PRAM900101 0.909 ROSM880101 0.883 KUHL950101 0.858 HOPT810101 0.849 ROSM880102 0.828 LEVM760101 0.825 JURD980101 -0.814 RADA880102 -0.818 NADH010101 -0.827 NAKH900110 -0.848 EISD860101 -0.862 WOLR810101 -0.867 EISD840101 -0.924 RADA880101 -0.925 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -12.04 39.23 4.25 23.22 3.95 2.16 16.81 -7.85 6.28 -18.32 -17.79 9.71 -8.86 -21.98 5.82 -1.54 -4.15 -16.19 -1.51 -16.22 // H WARP780101 D Average interactions per side chain atom (Warme-Morgan, 1978) R LIT:0405099 PMID:633361 A Warme, P.K. and Morgan, R.S. T A survey of amino acid side-chain interactions in 21 proteins J J. Mol. Biol. 118, 289-304 (1978) * (Gly 0.81) C DESM900102 0.882 JANJ780102 0.878 JANJ790102 0.877 NADH010102 0.870 DESM900101 0.864 BIOV880102 0.853 KYTJ820101 0.845 MEIH800103 0.835 JURD980101 0.827 CHOC760103 0.824 ROSG850102 0.823 EISD860103 0.820 CHOC760104 0.815 NADH010103 0.811 ROSM880102 -0.801 KUHL950101 -0.811 ROSM880101 -0.816 MEIH800102 -0.826 PRAM900101 -0.827 RACS770103 -0.848 CHOC760102 -0.849 JANJ780101 -0.869 JANJ780103 -0.890 OOBM770101 -0.937 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 10.04 6.18 5.63 5.76 8.89 5.41 5.37 7.99 7.49 8.72 8.79 4.40 9.15 7.98 7.79 7.08 7.00 8.07 6.90 8.88 // H WEBA780101 D RF value in high salt chromatography (Weber-Lacey, 1978) R LIT:2004106b PMID:691071 A Weber, A.L. and Lacey, J.C.,Jr. T Genetic code correlations: Amino acids and their anticodon nucleotides J J. Mol. Evol. 11, 199-210 (1978) C MEEJ800102 -0.808 ROSG850101 -0.817 MEEJ810101 -0.831 MEEJ810102 -0.854 NOZY710101 -0.890 LEVM760107 -0.923 GARJ730101 -0.924 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.89 0.88 0.89 0.87 0.85 0.82 0.84 0.92 0.83 0.76 0.73 0.97 0.74 0.52 0.82 0.96 0.92 0.20 0.49 0.85 // H WERD780101 D Propensity to be buried inside (Wertz-Scheraga, 1978) R LIT:0405105 PMID:621952 A Wertz, D.H. and Scheraga, H.A. T Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule J Macromolecules 11, 9-15 (1978) * Adjusted values C NISK860101 0.966 BIOV880101 0.951 ROSG850102 0.943 MIYS850101 0.934 RADA880108 0.930 BIOV880102 0.929 CIDH920105 0.905 CIDH920104 0.896 PONP930101 0.895 MEIH800103 0.895 NISK800101 0.891 NADH010104 0.890 PONP800102 0.883 CIDH920103 0.881 NADH010103 0.880 PONP800101 0.880 CIDH920101 0.878 PONP800103 0.876 ROBB790101 0.872 CIDH920102 0.871 FAUJ830101 0.862 MANP780101 0.853 PONP800108 0.843 PLIV810101 0.841 NADH010102 0.841 NADH010105 0.837 MEEJ810101 0.825 DESM900102 0.814 SWER830101 0.804 FUKS010102 -0.801 BHAR880101 -0.803 KRIW710101 -0.819 GRAR740102 -0.826 FUKS010104 -0.832 KARP850101 -0.842 RACS770103 -0.846 PARS000101 -0.853 PARJ860101 -0.869 FUKS010103 -0.869 GUYH850101 -0.871 KRIW790102 -0.875 VINM940102 -0.886 KRIW790101 -0.899 MEIH800102 -0.903 RACS770102 -0.906 OOBM770103 -0.906 KARP850102 -0.909 RACS770101 -0.912 VINM940103 -0.926 VINM940101 -0.931 MEIH800101 -0.943 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.52 0.49 0.42 0.37 0.83 0.35 0.38 0.41 0.70 0.79 0.77 0.31 0.76 0.87 0.35 0.49 0.38 0.86 0.64 0.72 // H WERD780102 D Free energy change of epsilon(i) to epsilon(ex) (Wertz-Scheraga, 1978) R LIT:0405105 PMID:621952 A Wertz, D.H. and Scheraga, H.A. T Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule J Macromolecules 11, 9-15 (1978) * Adjusted values C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.16 -0.20 1.03 -0.24 -0.12 -0.55 -0.45 -0.16 -0.18 -0.19 -0.44 -0.12 -0.79 -0.25 -0.59 -0.01 0.05 -0.33 -0.42 -0.46 // H WERD780103 D Free energy change of alpha(Ri) to alpha(Rh) (Wertz-Scheraga, 1978) R LIT:0405105 PMID:621952 A Wertz, D.H. and Scheraga, H.A. T Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule J Macromolecules 11, 9-15 (1978) * Adjusted values * (Met !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.15 -0.37 0.69 -0.22 -0.19 -0.06 0.14 0.36 -0.25 0.02 0.06 -0.16 0.11 1.18 0.11 0.13 0.28 -0.12 0.19 -0.08 // H WERD780104 D Free energy change of epsilon(i) to alpha(Rh) (Wertz-Scheraga, 1978) R LIT:0405105 PMID:621952 A Wertz, D.H. and Scheraga, H.A. T Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule J Macromolecules 11, 9-15 (1978) * Adjusted values C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.07 -0.40 -0.57 -0.80 0.17 -0.26 -0.63 0.27 -0.49 0.06 -0.17 -0.45 0.03 0.40 -0.47 -0.11 0.09 -0.61 -0.61 -0.11 // H WOEC730101 D Polar requirement (Woese, 1973) R PMID:4588588 A Woese, C.R. T Evolution of genetic code J Naturwiss. 60, 447-459 (1973) C GRAR740102 0.960 HOPT810101 0.886 HOPA770101 0.876 LEVM760101 0.872 PRAM900101 0.871 ROSM880101 0.844 WOLS870101 0.841 KUHL950101 0.837 OOBM770103 0.835 VINM940101 0.834 PARJ860101 0.821 FUKS010102 0.820 FAUJ880110 0.812 OOBM770101 0.804 ROSM880102 0.801 NADH010102 -0.800 CIDH920105 -0.800 MEIH800103 -0.802 ISOY800102 -0.803 EISD860103 -0.803 ROSG850102 -0.804 TANS770103 -0.806 RADA880101 -0.812 BIOV880102 -0.819 WIMW960101 -0.821 NISK860101 -0.822 PONP800103 -0.823 CIDH920104 -0.823 RADA880108 -0.825 BIOV880101 -0.829 PONP800108 -0.831 SWER830101 -0.832 EISD860101 -0.838 MAXF760102 -0.842 DESM900102 -0.847 FAUJ830101 -0.880 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.0 9.1 10.0 13.0 5.5 8.6 12.5 7.9 8.4 4.9 4.9 10.1 5.3 5.0 6.6 7.5 6.6 5.3 5.7 5.6 // H WOLR810101 D Hydration potential (Wolfenden et al., 1981) R LIT:0704095 PMID:7213619 A Wolfenden, R. andersson, L., Cullis, P.M. and Southgate, C.C.B. T Affinties of amino acid side chains for solvent water J Biochemistry 20, 849-855 (1981) * (Pro 2.9) C RADA880101 0.939 EISD840101 0.914 RADA880104 0.910 RADA880107 0.890 KYTJ820101 0.885 JURD980101 0.881 RADA880105 0.875 CHOC760103 0.873 CHOC760104 0.868 JANJ780102 0.851 NADH010101 0.848 JANJ790102 0.828 JANJ780103 -0.822 ROSM880102 -0.829 CHOC760102 -0.840 OOBM770101 -0.847 JANJ780101 -0.864 VHEG790101 -0.867 ROSM880101 -0.884 PRAM900101 -0.887 KUHL950101 -0.898 FAUJ880109 -0.904 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.94 -19.92 -9.68 -10.95 -1.24 -9.38 -10.20 2.39 -10.27 2.15 2.28 -9.52 -1.48 -0.76 -3.68 -5.06 -4.88 -5.88 -6.11 1.99 // H WOLS870101 D Principal property value z1 (Wold et al., 1987) R LIT:1312098b A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg, B. and Wikstrom, C. T Principal property values for six non-natural amino acids and their application to a structure-activity relationship for oxytocin peptide analogues J Can. J. Chem. 65, 1814-1820 (1987) C PARJ860101 0.964 BULH740101 0.929 GRAR740102 0.910 ROSM880102 0.877 ROSM880101 0.866 MEIH800101 0.852 OOBM770103 0.852 LEVM760101 0.845 WOEC730101 0.841 HOPT810101 0.830 MEIH800102 0.813 RACS770102 0.802 MANP780101 -0.809 EISD840101 -0.820 RADA880101 -0.823 MEEJ800101 -0.823 SIMZ760101 -0.830 ROBB790101 -0.831 NAKH900110 -0.832 VENT840101 -0.835 JOND750101 -0.837 ARGP820101 -0.838 RADA880108 -0.840 EISD860103 -0.841 BIOV880102 -0.842 NISK860101 -0.848 WILM950101 -0.851 PONP800107 -0.852 BIOV880101 -0.854 GOLD730101 -0.854 TAKK010101 -0.858 CIDH920102 -0.869 BROC820101 -0.871 RADA880102 -0.873 NOZY710101 -0.874 CIDH920103 -0.879 SWER830101 -0.887 CIDH920104 -0.891 CIDH920105 -0.899 MIYS850101 -0.899 MEEJ810102 -0.905 MEEJ810101 -0.906 EISD860101 -0.918 MEEJ800102 -0.925 FAUJ830101 -0.928 ZIMJ680105 -0.937 GUOD860101 -0.955 PLIV810101 -0.963 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.07 2.88 3.22 3.64 0.71 2.18 3.08 2.23 2.41 -4.44 -4.19 2.84 -2.49 -4.92 -1.22 1.96 0.92 -4.75 -1.39 -2.69 // H WOLS870102 D Principal property value z2 (Wold et al., 1987) R LIT:1312098b A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg, B. and Wikstrom, C. T Principal property values for six non-natural amino acids and their application to a structure-activity relationship for oxytocin peptide analogues J Can. J. Chem. 65, 1814-1820 (1987) C LEVM760102 0.881 FASG760101 0.866 FAUJ880106 0.866 CHOC760101 0.845 LEVM760105 0.836 FAUJ880103 0.814 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -1.73 2.52 1.45 1.13 -0.97 0.53 0.39 -5.36 1.74 -1.68 -1.03 1.41 -0.27 1.30 0.88 -1.63 -2.09 3.65 2.32 -2.53 // H WOLS870103 D Principal property value z3 (Wold et al., 1987) R LIT:1312098b A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg, B. and Wikstrom, C. T Principal property values for six non-natural amino acids and their application to a structure-activity relationship for oxytocin peptide analogues J Can. J. Chem. 65, 1814-1820 (1987) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.09 -3.44 0.84 2.36 4.13 -1.14 -0.07 0.30 1.11 -1.03 -0.98 -3.14 -0.41 0.45 2.23 0.57 -1.40 0.85 0.01 -1.29 // H YUTK870101 D Unfolding Gibbs energy in water, pH7.0 (Yutani et al., 1987) R LIT:2004127b PMID:3299367 A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. T Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) * (Arg missing) C YUTK870102 0.827 EISD840101 0.809 RADA880101 0.803 GUYH850101 -0.813 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.5 0. 8.2 8.5 11.0 6.3 8.8 7.1 10.1 16.8 15.0 7.9 13.3 11.2 8.2 7.4 8.8 9.9 8.8 12.0 // H YUTK870102 D Unfolding Gibbs energy in water, pH9.0 (Yutani et al., 1987) R LIT:2004127b PMID:3299367 A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. T Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) * (Arg missing) C YUTK870101 0.827 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.8 0. 6.2 7.0 8.3 8.5 4.9 6.4 9.2 10.0 12.2 7.5 8.4 8.3 6.9 8.0 7.0 5.7 6.8 9.4 // H YUTK870103 D Activation Gibbs energy of unfolding, pH7.0 (Yutani et al., 1987) R LIT:2004127b PMID:3299367 A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. T Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) * (Arg missing) C YUTK870104 0.997 EISD860102 -0.839 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 18.08 0. 17.47 17.36 18.17 17.93 18.16 18.24 18.49 18.62 18.60 17.96 18.11 17.30 18.16 17.57 17.54 17.19 17.99 18.30 // H YUTK870104 D Activation Gibbs energy of unfolding, pH9.0 (Yutani et al., 1987) R LIT:2004127b PMID:3299367 A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. T Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) * (Arg missing) C YUTK870103 0.997 EISD860102 -0.840 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 18.56 0. 18.24 17.94 17.84 18.51 17.97 18.57 18.64 19.21 19.01 18.36 18.49 17.95 18.77 18.06 17.71 16.87 18.23 18.98 // H ZASB820101 D Dependence of partition coefficient on ionic strength (Zaslavsky et al., 1982) R LIT:0806206 A Zaslavsky, B.Yu, Mestechkina, N.M., Miheeva, L.M. and Rogozhin, S.V. T Measurement of relative hydrophobicity of amino acid side-chains by partition in an aqueous two-phase polymeric system: Hydrophobicity scale for non-polar and ionogenic side-chains J J. Chromatogr. 240, 21-28 (1982) * (C H Y missing?) C WIMW960101 0.885 CIDH920102 0.809 SNEP660103 0.804 OOBM850102 -0.853 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.152 -0.089 -0.203 -0.355 0. -0.181 -0.411 -0.190 0. -0.086 -0.102 -0.062 -0.107 0.001 -0.181 -0.203 -0.170 0.275 0. -0.125 // H ZIMJ680101 D Hydrophobicity (Zimmerman et al., 1968) R LIT:2004109b PMID:5700434 A Zimmerman, J.M., Eliezer, N. and Simha, R. T The characterization of amino acid sequences in proteins by statistical methods J J. Theor. Biol. 21, 170-201 (1968) C SIMZ760101 0.821 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.83 0.83 0.09 0.64 1.48 0.00 0.65 0.10 1.10 3.07 2.52 1.60 1.40 2.75 2.70 0.14 0.54 0.31 2.97 1.79 // H ZIMJ680102 D Bulkiness (Zimmerman et al., 1968) R LIT:2004109b PMID:5700434 A Zimmerman, J.M., Eliezer, N. and Simha, R. T The characterization of amino acid sequences in proteins by statistical methods J J. Theor. Biol. 21, 170-201 (1968) C FAUJ880101 0.888 LEVM760106 0.873 TAKK010101 0.840 BULH740102 0.825 GOLD730101 0.818 SIMZ760101 0.810 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 11.50 14.28 12.82 11.68 13.46 14.45 13.57 3.40 13.69 21.40 21.40 15.71 16.25 19.80 17.43 9.47 15.77 21.67 18.03 21.57 // H ZIMJ680103 D Polarity (Zimmerman et al., 1968) R LIT:2004109b PMID:5700434 A Zimmerman, J.M., Eliezer, N. and Simha, R. T The characterization of amino acid sequences in proteins by statistical methods J J. Theor. Biol. 21, 170-201 (1968) C PRAM900101 0.854 HOPA770101 0.815 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.00 52.00 3.38 49.70 1.48 3.53 49.90 0.00 51.60 0.13 0.13 49.50 1.43 0.35 1.58 1.67 1.66 2.10 1.61 0.13 // H ZIMJ680104 D Isoelectric point (Zimmerman et al., 1968) R LIT:2004109b PMID:5700434 A Zimmerman, J.M., Eliezer, N. and Simha, R. T The characterization of amino acid sequences in proteins by statistical methods J J. Theor. Biol. 21, 170-201 (1968) C KLEP840101 0.941 FAUJ880111 0.813 FINA910103 0.805 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.00 10.76 5.41 2.77 5.05 5.65 3.22 5.97 7.59 6.02 5.98 9.74 5.74 5.48 6.30 5.68 5.66 5.89 5.66 5.96 // H ZIMJ680105 D RF rank (Zimmerman et al., 1968) R LIT:2004109b PMID:5700434 A Zimmerman, J.M., Eliezer, N. and Simha, R. T The characterization of amino acid sequences in proteins by statistical methods J J. Theor. Biol. 21, 170-201 (1968) C MEEJ800102 0.921 EISD860101 0.900 BROC820101 0.896 PLIV810101 0.875 BROC820102 0.865 TAKK010101 0.856 RADA880102 0.851 GUOD860101 0.850 MEEJ800101 0.842 NOZY710101 0.837 SWER830101 0.829 GOLD730101 0.820 FAUJ830101 0.816 LAWE840101 0.809 SIMZ760101 0.805 HOPT810101 -0.816 LEVM760101 -0.844 BULH740101 -0.879 PARJ860101 -0.886 WOLS870101 -0.937 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.9 4.6 5.4 2.8 2.8 9.0 3.2 5.6 8.2 17.1 17.6 3.5 14.9 18.8 14.8 6.9 9.5 17.1 15.0 14.3 // H AURR980101 D Normalized positional residue frequency at helix termini N4'(Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.94 1.15 0.79 1.19 0.60 0.94 1.41 1.18 1.15 1.07 0.95 1.03 0.88 1.06 1.18 0.69 0.87 0.91 1.04 0.90 // H AURR980102 D Normalized positional residue frequency at helix termini N"' (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.98 1.14 1.05 1.05 0.41 0.90 1.04 1.25 1.01 0.88 0.80 1.06 1.12 1.12 1.31 1.02 0.80 0.90 1.12 0.87 // H AURR980103 D Normalized positional residue frequency at helix termini N" (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.05 0.81 0.91 1.39 0.60 0.87 1.11 1.26 1.43 0.95 0.96 0.97 0.99 0.95 1.05 0.96 1.03 1.06 0.94 0.62 // H AURR980104 D Normalized positional residue frequency at helix termini N'(Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980105 0.839 FINA910101 0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.75 0.90 1.24 1.72 0.66 1.08 1.10 1.14 0.96 0.80 1.01 0.66 1.02 0.88 1.33 1.20 1.13 0.68 0.80 0.58 // H AURR980105 D Normalized positional residue frequency at helix termini Nc (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980104 0.839 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.67 0.76 1.28 1.58 0.37 1.05 0.94 0.98 0.83 0.78 0.79 0.84 0.98 0.96 1.12 1.25 1.41 0.94 0.82 0.67 // H AURR980106 D Normalized positional residue frequency at helix termini N1 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.10 1.05 0.72 1.14 0.26 1.31 2.30 0.55 0.83 1.06 0.84 1.08 0.90 0.90 1.67 0.81 0.77 1.26 0.99 0.76 // H AURR980107 D Normalized positional residue frequency at helix termini N2 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C RICJ880106 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.39 0.95 0.67 1.64 0.52 1.60 2.07 0.65 1.36 0.64 0.91 0.80 1.10 1.00 0.94 0.69 0.92 1.10 0.73 0.70 // H AURR980108 D Normalized positional residue frequency at helix termini N3 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980112 0.910 PALJ810102 0.871 CHOP780201 0.867 KANM800103 0.857 ISOY800101 0.856 AURR980109 0.848 MAXF760101 0.841 QIAN880106 0.838 ROBB760103 0.835 AURR980113 0.821 QIAN880104 0.815 ROBB760101 0.814 BEGF750101 0.810 BURA740101 0.808 QIAN880107 0.803 MUNV940102 -0.803 MUNV940101 -0.814 CHAM830101 -0.834 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.43 1.33 0.55 0.90 0.52 1.43 1.70 0.56 0.66 1.18 1.52 0.82 1.68 1.10 0.15 0.61 0.75 1.68 0.65 1.14 // H AURR980109 D Normalized positional residue frequency at helix termini N4 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C KANM800103 0.944 AURR980114 0.939 ISOY800101 0.894 QIAN880107 0.893 AURR980113 0.892 SUEM840101 0.882 PALJ810102 0.877 AURR980112 0.875 MAXF760101 0.865 QIAN880106 0.862 CHOP780201 0.859 ROBB760103 0.857 KANM800101 0.852 AURR980108 0.848 RICJ880109 0.828 BEGF750101 0.821 PTIO830101 0.820 AURR980110 0.817 ROBB760101 0.810 QIAN880109 0.807 RACS820108 0.804 QIAN880110 0.802 FINA770101 0.802 QIAN880132 -0.806 LEVM780103 -0.814 GEIM800111 -0.814 PRAM900104 -0.815 TANS770110 -0.816 MUNV940102 -0.818 MUNV940101 -0.828 CHOP780101 -0.837 PALJ810106 -0.845 CHAM830101 -0.896 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.55 1.39 0.60 0.61 0.59 1.43 1.34 0.37 0.89 1.47 1.36 1.27 2.13 1.39 0.03 0.44 0.65 1.10 0.93 1.18 // H AURR980110 D Normalized positional residue frequency at helix termini N5 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980115 0.907 AURR980111 0.867 MAXF760101 0.860 ISOY800101 0.855 KANM800101 0.830 AURR980109 0.817 AURR980112 0.816 QIAN880107 0.815 CHOP780201 0.814 PALJ810102 0.812 AURR980114 0.811 QIAN880106 0.804 MUNV940101 -0.822 MUNV940102 -0.846 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.80 1.73 0.73 0.90 0.55 0.97 1.73 0.32 0.46 1.09 1.47 1.24 1.64 0.96 0.15 0.67 0.70 0.68 0.91 0.81 // H AURR980111 D Normalized positional residue frequency at helix termini C5 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980110 0.867 AURR980115 0.835 PALJ810102 0.830 TANS770101 0.817 CHOP780201 0.813 AURR980114 0.811 MAXF760101 0.811 ISOY800101 0.801 AURR980112 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.52 1.49 0.58 1.04 0.26 1.41 1.76 0.30 0.83 1.25 1.26 1.10 1.14 1.14 0.44 0.66 0.73 0.68 1.04 1.03 // H AURR980112 D Normalized positional residue frequency at helix termini C4 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980108 0.910 PALJ810102 0.888 AURR980109 0.875 KANM800103 0.871 ISOY800101 0.870 CHOP780201 0.856 AURR980114 0.853 AURR980115 0.850 AURR980113 0.848 KANM800101 0.847 RACS820108 0.840 QIAN880106 0.839 MAXF760101 0.838 PALJ810109 0.817 AURR980110 0.816 GEIM800104 0.815 ROBB760101 0.806 QIAN880107 0.802 GEIM800101 0.802 AURR980111 0.800 MUNV940101 -0.819 MUNV940102 -0.853 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.49 1.41 0.67 0.94 0.37 1.52 1.55 0.29 0.96 1.04 1.40 1.17 1.84 0.86 0.20 0.68 0.79 1.52 1.06 0.94 // H AURR980113 D Normalized positional residue frequency at helix termini C3 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C KANM800103 0.905 AURR980109 0.892 SUEM840101 0.887 BEGF750101 0.857 FINA770101 0.849 AURR980112 0.848 ROBB760103 0.838 AURR980114 0.836 QIAN880106 0.835 QIAN880105 0.833 PTIO830101 0.833 QIAN880107 0.832 AURR980108 0.821 ISOY800101 0.815 RICJ880109 0.808 CHAM830101 -0.828 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.73 1.24 0.70 0.68 0.63 0.88 1.16 0.32 0.76 1.15 1.80 1.22 2.21 1.35 0.07 0.65 0.46 1.57 1.10 0.94 // H AURR980114 D Normalized positional residue frequency at helix termini C2 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980109 0.939 KANM800103 0.916 QIAN880107 0.876 FINA770101 0.875 ISOY800101 0.857 MAXF760101 0.853 AURR980112 0.853 KANM800101 0.852 PALJ810102 0.848 SUEM840101 0.845 AURR980113 0.836 CHOP780201 0.828 QIAN880110 0.819 RACS820108 0.818 AURR980111 0.811 AURR980110 0.811 QIAN880109 0.810 PTIO830101 0.809 AURR980115 0.804 QIAN880106 0.803 ROBB760103 0.801 TANS770101 0.800 CHOP780101 -0.803 MUNV940102 -0.820 MUNV940101 -0.821 CHAM830101 -0.842 PALJ810106 -0.842 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.33 1.39 0.64 0.60 0.44 1.37 1.43 0.20 1.02 1.58 1.63 1.71 1.76 1.22 0.07 0.42 0.57 1.00 1.02 1.08 // H AURR980115 D Normalized positional residue frequency at helix termini C1 (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C AURR980110 0.907 KANM800101 0.858 MAXF760101 0.852 AURR980112 0.850 ISOY800101 0.844 AURR980111 0.835 TANS770101 0.834 PALJ810102 0.827 LEVM780104 0.818 CHOP780201 0.816 GEIM800101 0.804 AURR980114 0.804 RACS820108 0.802 MUNV940101 -0.807 MUNV940102 -0.852 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.87 1.66 0.70 0.91 0.33 1.24 1.88 0.33 0.89 0.90 1.65 1.63 1.35 0.67 0.03 0.71 0.50 1.00 0.73 0.51 // H AURR980116 D Normalized positional residue frequency at helix termini Cc (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.19 1.45 1.33 0.72 0.44 1.43 1.27 0.74 1.55 0.61 1.36 1.45 1.35 1.20 0.10 1.02 0.82 0.58 1.06 0.46 // H AURR980117 D Normalized positional residue frequency at helix termini C' (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C RICJ880115 0.921 MAXF760104 0.849 ISOY800108 0.822 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.77 1.11 1.39 0.79 0.44 0.95 0.92 2.74 1.65 0.64 0.66 1.19 0.74 1.04 0.66 0.64 0.82 0.58 0.93 0.53 // H AURR980118 D Normalized positional residue frequency at helix termini C" (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.93 0.96 0.82 1.15 0.67 1.02 1.07 1.08 1.40 1.14 1.16 1.27 1.11 1.05 1.01 0.71 0.84 1.06 1.15 0.74 // H AURR980119 D Normalized positional residue frequency at helix termini C"' (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C MUNV940104 0.804 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.09 1.29 1.03 1.17 0.26 1.08 1.31 0.97 0.88 0.97 0.87 1.13 0.96 0.84 2.01 0.76 0.79 0.91 0.64 0.77 // H AURR980120 D Normalized positional residue frequency at helix termini C4' (Aurora-Rose, 1998) R LIT:2409041 PMID:9514257 A Aurora, R. and Rose, G. T Helix capping J Protein Science 7, 21-38 (1998) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.71 1.09 0.95 1.43 0.65 0.87 1.19 1.07 1.13 1.05 0.84 1.10 0.80 0.95 1.70 0.65 .086 1.25 0.85 1.12 // H ONEK900101 D Delta G values for the peptides extrapolated to 0 M urea (O'Neil-DeGrado, 1990) R LIT:1701155 PMID:2237415 A O'Neil, K.T. and DeGrado, W.F. T A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids J Science 250, 646-651 (1990) C BLAM930101 0.965 BUNA790101 0.902 ROBB760103 0.878 QIAN880108 0.866 PTIO830101 0.847 ROBB760104 0.844 QIAN880109 0.824 FAUJ880113 0.820 MUNV940105 -0.839 RACS820114 -0.880 MUNV940101 -0.890 AVBF000104 -0.899 MUNV940102 -0.910 FINA910102 -0.920 ONEK900102 -0.982 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 13.4 13.3 12.0 11.7 11.6 12.8 12.2 11.3 11.6 12.0 13.0 13.0 12.8 12.1 6.5 12.2 11.7 12.4 12.1 11.9 // H ONEK900102 D Helix formation parameters (delta delta G) (O'Neil-DeGrado, 1990) R LIT:1701155 PMID:2237415 A O'Neil, K.T. and DeGrado, W.F. T A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids J Science 250, 646-651 (1990) C FINA910102 0.964 AVBF000104 0.919 MUNV940105 0.876 MUNV940101 0.861 MUNV940102 0.860 RACS820114 0.855 MUNV940104 0.845 ISOY800104 0.828 TANS770104 0.826 QIAN880109 -0.800 PTIO830101 -0.830 FAUJ880113 -0.839 QIAN880108 -0.860 ROBB760104 -0.861 ROBB760103 -0.867 BUNA790101 -0.949 BLAM930101 -0.974 ONEK900101 -0.982 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.77 -0.68 -0.07 -0.15 -0.23 -0.33 -0.27 0.00 -0.06 -0.23 -0.62 -0.65 -0.50 -0.41 3 -0.35 -0.11 -0.45 -0.17 -0.14 // H VINM940101 D Normalized flexibility parameters (B-values), average (Vihinen et al., 1994) R LIT:2014123 PMID:8090708 A Vihinen, M., Torkkila, E. and Riikonen, P. T Accuracy of protein flexibility predictions J Proteins 19, 141-149 (1994) C VINM940102 0.940 OOBM770103 0.936 VINM940103 0.921 FUKS010104 0.919 PARS000101 0.919 MEIH800101 0.900 KRIW790101 0.890 KARP850102 0.885 PARS000102 0.877 FUKS010102 0.876 MEIH800102 0.872 GRAR740102 0.869 HOPT810101 0.859 KRIW790102 0.853 RACS770102 0.844 PARJ860101 0.837 RACS770101 0.835 WOEC730101 0.834 RACS770103 0.830 GUYH850101 0.829 FUKS010103 0.827 KARP850101 0.821 VINM940104 0.815 LEVM760101 0.815 MUNV940103 0.811 PALJ810104 -0.801 WIMW960101 -0.804 DESM900101 -0.806 NADH010105 -0.808 SWER830101 -0.817 GEIM800107 -0.819 QIAN880120 -0.823 QIAN880121 -0.828 LIFS790103 -0.829 DESM900102 -0.829 CHOP780202 -0.831 LIFS790101 -0.834 MANP780101 -0.836 CIDH920103 -0.837 CIDH920101 -0.854 ROBB790101 -0.858 NADH010102 -0.859 MEIH800103 -0.861 FAUJ830101 -0.871 CIDH920102 -0.872 PONP800103 -0.878 PONP800101 -0.878 CIDH920104 -0.883 MIYS850101 -0.883 PONP800102 -0.883 CIDH920105 -0.885 NADH010103 -0.889 PONP800108 -0.891 NADH010104 -0.891 RADA880108 -0.906 PONP930101 -0.913 NISK800101 -0.922 BIOV880102 -0.929 WERD780101 -0.931 BIOV880101 -0.941 ROSG850102 -0.943 NISK860101 -0.959 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.984 1.008 1.048 1.068 0.906 1.037 1.094 1.031 0.950 0.927 0.935 1.102 0.952 0.915 1.049 1.046 0.997 0.904 0.929 0.931 // H VINM940102 D Normalized flexibility parameters (B-values) for each residue surrounded by none rigid neighbours (Vihinen et al., 1994) R LIT:2014123 PMID:8090708 A Vihinen, M., Torkkila, E. and Riikonen, P. T Accuracy of protein flexibility predictions J Proteins 19, 141-149 (1994) C VINM940101 0.940 PARS000101 0.917 OOBM770103 0.891 KARP850101 0.874 FUKS010103 0.864 VINM940103 0.855 GRAR740102 0.837 KARP850102 0.834 KRIW790101 0.834 PARJ860101 0.833 MEIH800101 0.833 FUKS010102 0.808 FUKS010104 0.807 MUNV940103 0.803 PARS000102 0.803 PLIV810101 -0.808 NADH010105 -0.809 ROSG850101 -0.810 CHOP780202 -0.810 SWER830101 -0.811 NADH010103 -0.812 QIAN880120 -0.813 PONP800103 -0.820 MANP780101 -0.821 BIOV880102 -0.826 MIYS850101 -0.832 NADH010104 -0.834 MEEJ810101 -0.839 PONP800102 -0.842 LIFS790101 -0.843 FAUJ830101 -0.844 PONP800101 -0.845 RADA880108 -0.846 ROSG850102 -0.849 CIDH920103 -0.855 LIFS790103 -0.862 ROBB790101 -0.866 PONP930101 -0.869 PONP800108 -0.871 BIOV880101 -0.876 CIDH920104 -0.884 CIDH920101 -0.885 WERD780101 -0.886 NISK800101 -0.900 CIDH920105 -0.910 NISK860101 -0.919 CIDH920102 -0.925 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.315 1.310 1.380 1.372 1.196 1.342 1.376 1.382 1.279 1.241 1.234 1.367 1.269 1.247 1.342 1.381 1.324 1.186 1.199 1.235 // H VINM940103 D Normalized flexibility parameters (B-values) for each residue surrounded by one rigid neighbours (Vihinen et al., 1994) R LIT:2014123 PMID:8090708 A Vihinen, M., Torkkila, E. and Riikonen, P. T Accuracy of protein flexibility predictions J Proteins 19, 141-149 (1994) C VINM940101 0.921 MEIH800101 0.875 KRIW790101 0.875 BHAR880101 0.869 GUYH850101 0.865 KARP850102 0.863 VINM940102 0.855 OOBM770103 0.845 MEIH800102 0.841 RACS770102 0.839 FUKS010104 0.838 KARP850101 0.837 KRIW790102 0.836 RACS770101 0.829 PARS000101 0.823 FUKS010102 0.809 PARS000102 0.808 FAUJ830101 -0.804 NADH010106 -0.813 PONP800101 -0.813 CIDH920101 -0.814 PONP800103 -0.817 PONP930101 -0.818 PONP800102 -0.820 NADH010102 -0.824 DESM900102 -0.824 CIDH920102 -0.826 MEIH800103 -0.830 CIDH920105 -0.832 CIDH920104 -0.835 NISK800101 -0.836 MIYS850101 -0.849 RADA880108 -0.862 NADH010103 -0.882 NADH010105 -0.884 BIOV880102 -0.889 NADH010104 -0.899 ROSG850102 -0.901 BIOV880101 -0.901 NISK860101 -0.903 WERD780101 -0.926 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.994 1.026 1.022 1.022 0.939 1.041 1.052 1.018 0.967 0.977 0.982 1.029 0.963 0.934 1.050 1.025 0.998 0.938 0.981 0.968 // H VINM940104 D Normalized flexibility parameters (B-values) for each residue surrounded by two rigid neighbours (Vihinen et al., 1994) R LIT:2014123 PMID:8090708 A Vihinen, M., Torkkila, E. and Riikonen, P. T Accuracy of protein flexibility predictions J Proteins 19, 141-149 (1994) C VINM940101 0.815 JANJ780103 0.811 MEIH800102 0.808 RACS770103 0.804 DESM900102 -0.803 ROSG850102 -0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.783 0.807 0.799 0.822 0.785 0.817 0.826 0.784 0.777 0.776 0.783 0.834 0.806 0.774 0.809 0.811 0.795 0.796 0.788 0.781 // H MUNV940101 D Free energy in alpha-helical conformation (Munoz-Serrano, 1994) R LIT:2105109 PMID:7731949 A Munoz, V. and Serrano, L. T Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales J Proteins 20, 301-311 (1994) C MUNV940102 0.964 ONEK900102 0.861 RACS820114 0.828 CHOP780201 -0.802 AURR980115 -0.807 AURR980108 -0.814 PALJ810102 -0.815 AURR980112 -0.819 AURR980114 -0.821 ROBB760101 -0.822 AURR980110 -0.822 KANM800103 -0.826 AURR980109 -0.828 ROBB760104 -0.831 MAXF760101 -0.833 QIAN880106 -0.835 FAUJ880113 -0.836 QIAN880109 -0.841 KANM800101 -0.846 RACS820108 -0.859 QIAN880108 -0.864 ISOY800101 -0.875 QIAN880107 -0.880 PTIO830101 -0.880 BLAM930101 -0.882 ONEK900101 -0.890 ROBB760103 -0.918 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.423 0.503 0.906 0.870 0.877 0.594 0.167 1.162 0.802 0.566 0.494 0.615 0.444 0.706 1.945 0.928 0.884 0.690 0.778 0.706 // H MUNV940102 D Free energy in alpha-helical region (Munoz-Serrano, 1994) R LIT:2105109 PMID:7731949 A Munoz, V. and Serrano, L. T Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales J Proteins 20, 301-311 (1994) C MUNV940101 0.964 RACS820114 0.877 ONEK900102 0.860 AURR980108 -0.803 ROBB760104 -0.803 CHOP780201 -0.812 QIAN880105 -0.816 AURR980109 -0.818 AURR980114 -0.820 KANM800103 -0.823 PALJ810102 -0.824 FAUJ880113 -0.826 ROBB760101 -0.827 MAXF760101 -0.829 QIAN880108 -0.839 KANM800101 -0.843 PTIO830101 -0.844 AURR980110 -0.846 AURR980115 -0.852 AURR980112 -0.853 QIAN880106 -0.867 BLAM930101 -0.876 ISOY800101 -0.877 QIAN880107 -0.882 RACS820108 -0.894 ONEK900101 -0.910 ROBB760103 -0.913 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.619 0.753 1.089 0.932 1.107 0.770 0.675 1.361 1.034 0.876 0.740 0.784 0.736 0.968 1.780 0.969 1.053 0.910 1.009 0.939 // H MUNV940103 D Free energy in beta-strand conformation (Munoz-Serrano, 1994) R LIT:2105109 PMID:7731949 A Munoz, V. and Serrano, L. T Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales J Proteins 20, 301-311 (1994) C GEIM800110 0.880 QIAN880134 0.858 QIAN880133 0.836 PARS000101 0.826 QIAN880135 0.820 LEVM780106 0.815 VINM940101 0.811 GEIM800108 0.806 OOBM770103 0.805 VINM940102 0.803 GEIM800106 -0.800 PONP800102 -0.802 SWER830101 -0.802 NISK800101 -0.813 MANP780101 -0.815 PONP800101 -0.819 PALJ810112 -0.830 ROBB760105 -0.832 NISK860101 -0.840 GEIM800105 -0.841 PALJ810110 -0.845 PRAM900103 -0.848 LEVM780102 -0.848 PALJ810103 -0.857 KANM800104 -0.857 PONP930101 -0.864 GEIM800107 -0.869 PALJ810104 -0.888 ROBB760106 -0.888 LEVM780105 -0.891 CHOP780202 -0.892 LIFS790103 -0.902 PTIO830102 -0.903 KANM800102 -0.916 AVBF000101 -0.917 QIAN880119 -0.927 QIAN880121 -0.938 LIFS790101 -0.941 QIAN880120 -0.959 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.080 0.976 1.197 1.266 0.733 1.050 1.085 1.104 0.906 0.583 0.789 1.026 0.812 0.685 1.412 0.987 0.784 0.755 0.665 0.546 // H MUNV940104 D Free energy in beta-strand region (Munoz-Serrano, 1994) R LIT:2105109 PMID:7731949 A Munoz, V. and Serrano, L. T Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales J Proteins 20, 301-311 (1994) C MUNV940105 0.987 QIAN880134 0.897 FINA910102 0.896 TANS770104 0.870 ISOY800104 0.866 ONEK900102 0.845 CHOP780213 0.836 RACS820110 0.831 QIAN880135 0.819 AURR980119 0.804 PTIO830101 -0.807 AVBF000101 -0.821 FAUJ880102 -0.824 ROBB760104 -0.840 BUNA790101 -0.865 BLAM930101 -0.904 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.978 0.784 0.915 1.038 0.573 0.863 0.962 1.405 0.724 0.502 0.766 0.841 0.729 0.585 2.613 0.784 0.569 0.671 0.560 0.444 // H MUNV940105 D Free energy in beta-strand region (Munoz-Serrano, 1994) R LIT:2105109 PMID:7731949 A Munoz, V. and Serrano, L. T Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales J Proteins 20, 301-311 (1994) C MUNV940104 0.987 FINA910102 0.911 QIAN880134 0.899 ONEK900102 0.876 TANS770104 0.846 ISOY800104 0.844 RACS820110 0.833 QIAN880135 0.829 CHOP780213 0.826 PTIO830101 -0.833 ONEK900101 -0.839 ROBB760104 -0.859 BUNA790101 -0.874 BLAM930101 -0.925 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.40 1.23 1.61 1.89 1.14 1.33 1.42 2.06 1.25 1.02 1.33 1.34 1.12 1.07 3.90 1.20 0.99 1.10 0.98 0.87 // H WIMW960101 D Free energies of transfer of AcWl-X-LL peptides from bilayer interface to water (Wimley-White, 1996) R LIT:2223095 PMID:8836100 A Wimley, W.C. and White, S. T Experimentally determined hydrophobicity scale for proteins at membrane interfaces J Nature Structual biol. 3, 842-848 (1996) C ZASB820101 0.885 MEEJ800101 0.838 CIDH920102 0.837 MEEJ800102 0.821 NOZY710101 0.818 PARJ860101 -0.804 VINM940101 -0.804 GRAR740102 -0.804 FUKS010102 -0.808 LEVM760101 -0.812 OOBM770103 -0.814 WOEC730101 -0.821 HOPT810101 -0.855 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.08 3.91 3.83 3.02 4.49 3.67 2.23 4.24 4.08 4.52 4.81 3.77 4.48 5.38 3.80 4.12 4.11 6.10 5.19 4.18 // H KIMC930101 D Thermodynamic beta sheet propensity (Kim-Berg, 1993) R LIT:1909070 PMID:8459852 A Kim, C.A. and Berg, J.M. T Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide J Nature 362, 267-270 (1993) C LEVM760104 0.842 AVBF000101 -0.814 CHAM810101 -0.848 LEVM760103 -0.861 FAUJ880102 -0.886 AVBF000102 -0.900 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.35 -0.44 -0.38 -0.41 -0.47 -0.40 -0.41 0.0 -0.46 -0.56 -0.48 -0.41 -0.46 -0.55 -0.23 -0.39 -0.48 -0.48 -0.50 -0.53 // H MONM990101 D Turn propensity scale for transmembrane helices (Monne et al., 1999) R PMID:10329132 A Monne, M., Hermansson, M. and von Heijne, G. T A turn propensity scale for transmembrane helices J J. Mol. Biol. 288, 141-145 (1999) C GRAR740102 0.831 KRIW790101 0.830 PRAM900101 0.820 NADH010105 -0.815 KYTJ820101 -0.842 DESM900101 -0.848 NADH010104 -0.848 DESM900102 -0.850 JURD980101 -0.853 NADH010101 -0.860 NADH010103 -0.862 NADH010102 -0.871 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.5 1.7 1.7 1.6 0.6 1.6 1.6 1.3 1.6 0.6 0.4 1.6 0.5 0.4 1.7 0.7 0.4 0.7 0.6 0.5 // H BLAM930101 D Alpha helix propensity of position 44 in T4 lysozyme (Blaber et al., 1993) R LIT:1915114 PMID:8503008 A Blaber, M., Zhang, X.J. and Matthews, B.W. T Structural basis of amino acid alpha helix propensity J Science 260, 1637-1640 (1993) C ONEK900101 0.965 BUNA790101 0.945 ROBB760103 0.883 ROBB760104 0.878 PTIO830101 0.868 QIAN880108 0.860 FAUJ880113 0.839 QIAN880109 0.828 CHOP780213 -0.824 QIAN880134 -0.836 TANS770104 -0.837 ISOY800104 -0.860 RACS820114 -0.862 AVBF000104 -0.872 MUNV940102 -0.876 MUNV940101 -0.882 MUNV940104 -0.904 MUNV940105 -0.925 FINA910102 -0.961 ONEK900102 -0.974 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.96 0.77 0.39 0.42 0.42 0.80 0.53 0.00 0.57 0.84 0.92 0.73 0.86 0.59 -2.50 0.53 0.54 0.58 0.72 0.63 // H PARS000101 D p-Values of mesophilic proteins based on the distributions of B values (Parthasarathy-Murthy, 2000) R PMID:10679524 A Parthasarathy, S. and Murthy, M.R. T Protein thermal stability: insights from atomic displacement parameters (B values) J Protein Eng. 13, 9-13 (2000) C VINM940101 0.919 VINM940102 0.917 OOBM770103 0.864 KARP850102 0.852 GEIM800110 0.831 MUNV940103 0.826 VINM940103 0.823 KARP850101 0.816 MEIH800101 0.813 PARJ860101 0.812 RACS770101 0.804 KRIW790101 0.804 ROSG850101 -0.805 QIAN880121 -0.809 BIOV880102 -0.813 BIOV880101 -0.819 ROBB790101 -0.819 ROSG850102 -0.820 CIDH920103 -0.821 MIYS850101 -0.821 NOZY710101 -0.829 NISK800101 -0.832 LIFS790101 -0.844 SWER830101 -0.846 PONP930101 -0.849 WERD780101 -0.853 CIDH920105 -0.860 LIFS790103 -0.861 QIAN880120 -0.863 CIDH920102 -0.871 CIDH920101 -0.877 NISK860101 -0.884 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.343 0.353 0.409 0.429 0.319 0.395 0.405 0.389 0.307 0.296 0.287 0.429 0.293 0.292 0.432 0.416 0.362 0.268 0.22 0.307 // H PARS000102 D p-Values of thermophilic proteins based on the distributions of B values (Parthasarathy-Murthy, 2000) R PMID:10679524 A Parthasarathy, S. and Murthy, M.R. T Protein thermal stability: insights from atomic displacement parameters (B values) J Protein Eng. 13, 9-13 (2000) C VINM940101 0.877 FUKS010102 0.868 FUKS010104 0.850 VINM940103 0.808 VINM940102 0.803 NISK800101 -0.814 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.320 0.327 0.384 0.424 0.198 0.436 0.514 0.374 0.299 0.306 0.340 0.446 0.313 0.314 0.354 0.376 0.339 0.291 0.287 0.294 // H KUMS000101 D Distribution of amino acid residues in the 18 non-redundant families of thermophilic proteins (Kumar et al., 2000) R PMID:10775659 A Kumar, S., Tsai, C.J. and Nussinov, R. T Factors enhancing protein thermostability J Protein Eng. 13, 179-191 (2000) C KUMS000102 0.971 FUKS010110 0.947 FUKS010109 0.894 JUKT750101 0.879 CEDJ970104 0.871 DAYM780101 0.866 JOND920101 0.863 NAKH900101 0.856 JUNJ780101 0.854 CEDJ970101 0.830 CEDJ970102 0.826 FUKS010111 0.826 NAKH920107 0.800 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.9 4.6 4.4 6.3 0.6 2.8 6.9 9.4 2.2 7.0 7.4 6.1 2.3 3.3 4.2 4.0 5.7 1.3 4.5 8.2 // H KUMS000102 D Distribution of amino acid residues in the 18 non-redundant families of mesophilic proteins (Kumar et al., 2000) R PMID:10775659 A Kumar, S., Tsai, C.J. and Nussinov, R. T Factors enhancing protein thermostability J Protein Eng. 13, 179-191 (2000) C KUMS000101 0.971 JUKT750101 0.948 FUKS010110 0.943 JUNJ780101 0.927 DAYM780101 0.925 CEDJ970101 0.914 JOND920101 0.909 CEDJ970104 0.908 FUKS010111 0.898 NAKH900101 0.894 CEDJ970102 0.881 FUKS010109 0.850 NAKH920107 0.839 NAKH900109 0.837 FUKS010112 0.819 CEDJ970103 0.812 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.2 3.6 5.1 6.0 1.0 2.9 6.0 9.4 2.1 6.0 7.7 6.5 2.4 3.4 4.2 5.5 5.7 1.2 3.7 8.2 // H KUMS000103 D Distribution of amino acid residues in the alpha-helices in thermophilic proteins (Kumar et al., 2000) R PMID:10775659 A Kumar, S., Tsai, C.J. and Nussinov, R. T Factors enhancing protein thermostability J Protein Eng. 13, 179-191 (2000) C KUMS000104 0.961 FUKS010110 0.827 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 14.1 5.5 3.2 5.7 0.1 3.7 8.8 4.1 2.0 7.1 9.1 7.7 3.3 5.0 0.7 3.9 4.4 1.2 4.5 5.9 // H KUMS000104 D Distribution of amino acid residues in the alpha-helices in mesophilic proteins (Kumar et al., 2000) R PMID:10775659 A Kumar, S., Tsai, C.J. and Nussinov, R. T Factors enhancing protein thermostability J Protein Eng. 13, 179-191 (2000) C KUMS000103 0.961 FUKS010110 0.861 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 13.4 3.9 3.7 4.6 0.8 4.8 7.8 4.6 3.3 6.5 10.6 7.5 3.0 4.5 1.3 3.8 4.6 1.0 3.3 7.1 // H TAKK010101 D Side-chain contribution to protein stability (kJ/mol) (Takano-Yutani, 2001) R PMID:11579219 A Takano, K., Yutani, K. T A new scale for side-chain contribution to protein stability based on the empirical stability analysis of mutant proteins J Protein Eng. 14, 525-528 (2001) C SIMZ760101 0.936 ARGP820101 0.906 JOND750101 0.906 MEEJ800102 0.891 NOZY710101 0.884 GOLD730101 0.872 CIDH920102 0.859 ZIMJ680105 0.856 LEVM760106 0.841 ZIMJ680102 0.840 CIDH920105 0.840 BROC820102 0.839 BROC820101 0.836 MEEJ810101 0.836 RADA880102 0.830 PLIV810101 0.822 MEEJ810102 0.819 LEVM760107 0.819 VENT840101 0.812 WOLS870101 -0.858 BULH740101 -0.865 PARJ860101 -0.870 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.8 7.3 3.6 4.9 3.0 2.4 4.4 0 11.9 17.2 17.0 10.5 11.9 23.0 15.0 2.6 6.9 24.2 17.2 15.3 // H FODM020101 D Propensity of amino acids within pi-helices (Fodje-Al-Karadaghi, 2002) R PMID:12034854 A Fodje, M.N. and Al-Karadaghi, S. T Occurrence, conformational features and amino acid propensities for the pi-helix J Protein Eng. 15, 353-358 (2002) C TANS770104 -0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.70 0.95 1.47 0.87 1.17 0.73 0.96 0.64 1.39 1.29 1.44 0.91 0.91 1.34 0.12 0.84 0.74 1.80 1.68 1.20 // H NADH010101 D Hydropathy scale based on self-information values in the two-state model (5% accessibility) (Naderi-Manesh et al., 2001) R PMID:11170200 A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. T Prediction of protein surface accessibility with information theory J Proteins. 42, 452-459 (2001) C JURD980101 0.925 KYTJ820101 0.918 NADH010105 0.912 DESM900102 0.905 NADH010103 0.904 RADA880101 0.902 NADH010102 0.898 NADH010104 0.895 JANJ780102 0.892 CHOC760103 0.881 EISD860103 0.868 CIDH920104 0.865 EISD840101 0.861 WOLR810101 0.848 JANJ790101 0.847 MANP780101 0.847 RADA880108 0.838 BIOV880101 0.838 FAUJ830101 0.837 PONP800103 0.833 ROSG850102 0.833 PONP800102 0.832 PONP800101 0.826 DESM900101 0.825 MEIH800103 0.824 PONP800108 0.820 RADA880104 0.819 MIYS850101 0.815 PONP930101 0.813 NISK800101 0.813 NISK860101 0.810 JANJ790102 0.808 CHOC760104 0.804 BIOV880102 0.804 JANJ780103 -0.804 RACS770102 -0.808 FAUJ880110 -0.813 MEIH800102 -0.818 KRIW790101 -0.827 VHEG790101 -0.827 PRAM900101 -0.843 GRAR740102 -0.859 MONM990101 -0.860 OOBM770101 -0.861 GUYH850101 -0.862 ROSM880101 -0.866 ROSM880102 -0.870 KUHL950101 -0.898 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 58 -184 -93 -97 116 -139 -131 -11 -73 107 95 -24 78 92 -79 -34 -7 59 -11 100 // H NADH010102 D Hydropathy scale based on self-information values in the two-state model (9% accessibility) (Naderi-Manesh et al., 2001) R PMID:11170200 A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. T Prediction of protein surface accessibility with information theory J Proteins. 42, 452-459 (2001) C NADH010103 0.986 NADH010104 0.968 JANJ780102 0.949 ROSG850102 0.948 JANJ790102 0.945 DESM900102 0.933 JURD980101 0.931 BIOV880101 0.921 PONP800103 0.921 KYTJ820101 0.920 BIOV880102 0.914 RADA880108 0.911 CHOC760103 0.910 MEIH800103 0.907 PONP800102 0.901 NADH010101 0.898 FAUJ830101 0.891 PONP800108 0.890 EISD840101 0.887 DESM900101 0.885 NISK800101 0.881 PONP930101 0.880 MIYS850101 0.878 NISK860101 0.878 NADH010105 0.876 PONP800101 0.875 JANJ790101 0.872 EISD860103 0.872 WARP780101 0.870 MANP780101 0.863 CIDH920104 0.856 RADA880101 0.845 WERD780101 0.841 RADA880107 0.823 CHOC760104 0.817 NADH010106 0.808 WOEC730101 -0.800 FUKS010104 -0.801 KARP850102 -0.807 HOPT810101 -0.820 VINM940103 -0.824 KRIW710101 -0.825 ROSM880101 -0.830 KUHL950101 -0.836 OOBM770103 -0.838 MEIH800101 -0.847 VINM940101 -0.859 PRAM900101 -0.870 MONM990101 -0.871 RACS770103 -0.876 ROSM880102 -0.881 GRAR740102 -0.881 KRIW790102 -0.890 CHOC760102 -0.893 RACS770102 -0.899 GUYH850101 -0.910 JANJ780101 -0.924 MEIH800102 -0.928 KRIW790101 -0.929 JANJ780103 -0.938 OOBM770101 -0.944 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 51 -144 -84 -78 137 -128 -115 -13 -55 106 103 -205 73 108 -79 -26 -3 69 11 108 // H NADH010103 D Hydropathy scale based on self-information values in the two-state model (16% accessibility) (Naderi-Manesh et al., 2001) R PMID:11170200 A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. T Prediction of protein surface accessibility with information theory J Proteins. 42, 452-459 (2001) C NADH010104 0.996 NADH010102 0.986 ROSG850102 0.958 BIOV880101 0.939 NADH010105 0.936 PONP800103 0.932 JANJ780102 0.923 RADA880108 0.919 PONP800102 0.919 BIOV880102 0.913 NISK860101 0.910 DESM900102 0.910 NISK800101 0.908 PONP800108 0.907 NADH010101 0.904 MEIH800103 0.901 JURD980101 0.900 JANJ790102 0.899 FAUJ830101 0.899 PONP930101 0.898 MIYS850101 0.896 PONP800101 0.894 KYTJ820101 0.885 CIDH920104 0.885 NADH010106 0.881 WERD780101 0.880 JANJ790101 0.879 MANP780101 0.878 CHOC760103 0.875 DESM900101 0.866 EISD860103 0.855 EISD840101 0.840 WARP780101 0.811 CIDH920105 0.810 QIAN880122 0.809 RADA880101 0.809 PLIV810101 0.804 GUOD860101 0.803 FUKS010104 -0.805 HOPT810101 -0.805 RACS770101 -0.807 KUHL950101 -0.807 VINM940102 -0.812 PRAM900101 -0.815 KARP850102 -0.834 CHOC760102 -0.840 RACS770103 -0.851 ROSM880102 -0.857 KRIW710101 -0.860 OOBM770103 -0.861 MONM990101 -0.862 MEIH800101 -0.868 JANJ780101 -0.868 GRAR740102 -0.881 VINM940103 -0.882 KRIW790102 -0.887 VINM940101 -0.889 JANJ780103 -0.892 RACS770102 -0.893 OOBM770101 -0.902 MEIH800102 -0.916 GUYH850101 -0.916 KRIW790101 -0.954 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 41 -109 -74 -47 169 -104 -90 -18 -35 104 103 -148 77 128 -81 -31 10 102 36 116 // H NADH010104 D Hydropathy scale based on self-information values in the two-state model (20% accessibility) (Naderi-Manesh et al., 2001) R PMID:11170200 A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. T Prediction of protein surface accessibility with information theory J Proteins. 42, 452-459 (2001) C NADH010103 0.996 NADH010102 0.968 NADH010105 0.957 ROSG850102 0.953 BIOV880101 0.937 PONP800103 0.926 PONP800102 0.917 NISK860101 0.915 RADA880108 0.915 NADH010106 0.914 NISK800101 0.909 PONP800108 0.902 BIOV880102 0.900 JANJ780102 0.898 MIYS850101 0.897 NADH010101 0.895 PONP930101 0.895 FAUJ830101 0.894 PONP800101 0.892 MEIH800103 0.890 WERD780101 0.890 CIDH920104 0.888 DESM900102 0.886 MANP780101 0.873 JURD980101 0.873 JANJ790101 0.871 JANJ790102 0.868 KYTJ820101 0.856 CHOC760103 0.848 DESM900101 0.843 EISD860103 0.840 CIDH920105 0.817 EISD840101 0.809 PLIV810101 0.806 QIAN880122 0.804 GUOD860101 0.803 CHOC760102 -0.809 RACS770101 -0.813 RACS770103 -0.832 JANJ780101 -0.832 VINM940102 -0.834 KARP850102 -0.835 ROSM880102 -0.839 MONM990101 -0.848 JANJ780103 -0.860 OOBM770103 -0.863 MEIH800101 -0.867 GRAR740102 -0.868 OOBM770101 -0.871 KRIW710101 -0.874 KRIW790102 -0.882 RACS770102 -0.883 VINM940101 -0.891 VINM940103 -0.899 MEIH800102 -0.900 GUYH850101 -0.910 KRIW790101 -0.958 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 32 -95 -73 -29 182 -95 -74 -22 -25 106 104 -124 82 132 -82 -34 20 118 44 113 // H NADH010105 D Hydropathy scale based on self-information values in the two-state model (25% accessibility) (Naderi-Manesh et al., 2001) R PMID:11170200 A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. T Prediction of protein surface accessibility with information theory J Proteins. 42, 452-459 (2001) C NADH010106 0.958 NADH010104 0.957 NADH010103 0.936 NADH010101 0.912 NADH010102 0.876 PONP800102 0.869 CIDH920104 0.869 BIOV880101 0.867 PONP800103 0.866 ROSG850102 0.865 NISK860101 0.863 NISK800101 0.860 PONP800101 0.853 PONP800108 0.845 RADA880108 0.845 MIYS850101 0.844 JANJ790101 0.843 MANP780101 0.842 PONP930101 0.839 WERD780101 0.837 FAUJ830101 0.822 JURD980101 0.821 DESM900102 0.816 MEIH800103 0.816 JANJ780102 0.814 KYTJ820101 0.804 CIDH920105 0.800 RACS770102 -0.800 MEIH800101 -0.806 VINM940101 -0.808 VINM940102 -0.809 GRAR740102 -0.812 MONM990101 -0.815 KRIW710101 -0.842 GUYH850101 -0.855 VINM940103 -0.884 KRIW790101 -0.898 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 24 -79 -76 0 194 -87 -57 -28 -31 102 103 -9 90 131 -85 -36 34 116 43 111 // H NADH010106 D Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001) R PMID:11170200 A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. T Prediction of protein surface accessibility with information theory J Proteins. 42, 452-459 (2001) C NADH010105 0.958 NADH010104 0.914 NADH010103 0.881 NADH010107 0.811 NADH010102 0.808 PONP800103 0.803 VINM940103 -0.813 KRIW710101 -0.846 KRIW790101 -0.861 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5 -57 -77 45 224 -67 -8 -47 -50 83 82 -38 83 117 -103 -41 79 130 27 117 // H NADH010107 D Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-Manesh et al., 2001) R PMID:11170200 A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A. T Prediction of protein surface accessibility with information theory J Proteins. 42, 452-459 (2001) C NADH010106 0.811 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -2 -41 -97 248 329 -37 117 -66 -70 28 36 115 62 120 -132 -52 174 179 -7 114 // H MONM990201 D Averaged turn propensities in a transmembrane helix (Monne et al., 1999) R PMID:10543969 A Monne, M., Nilsson, I., Elofsson, A. and von Heijne, G. T Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale J J Mol Biol. 293, 807-814 (1999) C FINA910101 0.812 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.4 1.5 1.6 15. 0.7 1.4 1.3 1.1 1.4 0.5 0.3 1.4 0.5 0.3 1.6 0.9 0.7 0.9 0.9 0.4 // H KOEP990101 D Alpha-helix propensity derived from designed sequences (Koehl-Levitt, 1999) R PMID:10535955 A Koehl, P. and Levitt, M. T Structure-based conformational preferences of amino acids J Proc Natl Acad Sci U S A. 96, 12524-12529 (1999) * (Pro missing) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.04 -0.30 0.25 0.27 0.57 -0.02 -0.33 1.24 -0.11 -0.26 -0.38 -0.18 -0.09 -0.01 0. 0.15 0.39 0.21 0.05 -0.06 // H KOEP990102 D Beta-sheet propensity derived from designed sequences (Koehl-Levitt, 1999) R PMID:10535955 A Koehl, P. and Levitt, M. T Structure-based conformational preferences of amino acids J Proc Natl Acad Sci U S A. 96, 12524-12529 (1999) * (Pro!) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.12 0.34 1.05 1.12 -0.63 1.67 0.91 0.76 1.34 -0.77 0.15 0.29 -0.71 -0.67 0. 1.45 -0.70 -0.14 -0.49 -0.70 // H CEDJ970101 D Composition of amino acids in extracellular proteins (percent) (Cedano et al., 1997) R PMID:9067612 A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. T Relation between amino acid composition and cellular location of proteins J J Mol Biol. 266, 594-600 (1997) C JUKT750101 0.973 DAYM780101 0.970 JOND920101 0.968 JUNJ780101 0.968 CEDJ970102 0.965 NAKH900101 0.954 CEDJ970104 0.944 KUMS000102 0.914 FUKS010110 0.889 CEDJ970103 0.889 FUKS010112 0.882 FUKS010111 0.878 NAKH900109 0.861 NAKH920107 0.860 NAKH920104 0.859 NAKH920101 0.850 NAKH920103 0.843 NAKH900102 0.832 KUMS000101 0.830 NAKH920106 0.826 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.6 4.2 4.6 4.9 2.9 4.0 5.1 7.8 2.1 4.6 8.8 6.3 2.5 3.7 4.9 7.3 6.0 1.4 3.6 6.7 // H CEDJ970102 D Composition of amino acids in anchored proteins (percent) (Cedano et al., 1997) R PMID:9067612 A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. T Relation between amino acid composition and cellular location of proteins J J Mol Biol. 266, 594-600 (1997) C JOND920101 0.995 NAKH900101 0.988 CEDJ970104 0.976 CEDJ970101 0.965 FUKS010112 0.946 DAYM780101 0.945 JUKT750101 0.942 FUKS010110 0.921 JUNJ780101 0.920 CEDJ970103 0.912 NAKH920103 0.906 NAKH920104 0.905 NAKH920101 0.898 NAKH920107 0.891 NAKH920106 0.886 KUMS000102 0.881 NAKH900109 0.865 NAKH900102 0.841 FUKS010109 0.839 CEDJ970105 0.835 KUMS000101 0.826 FUKS010111 0.819 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.6 5.0 4.4 5.2 2.2 4.1 6.2 6.9 2.1 5.1 9.4 5.8 2.1 4.0 5.4 7.2 6.1 1.4 3.2 6.7 // H CEDJ970103 D Composition of amino acids in membrane proteins (percent) (Cedano et al., 1997) R PMID:9067612 A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. T Relation between amino acid composition and cellular location of proteins J J Mol Biol. 266, 594-600 (1997) C NAKH900109 0.970 FUKS010106 0.919 CEDJ970102 0.912 JOND920101 0.911 NAKH900101 0.908 FUKS010105 0.901 FUKS010108 0.897 CEDJ970101 0.889 NAKH900111 0.865 FUKS010107 0.860 CEDJ970104 0.854 FUKS010112 0.850 FUKS010110 0.848 NAKH920105 0.836 JUKT750101 0.835 NAKH900107 0.820 NAKH900103 0.815 KUMS000102 0.812 NAKH920108 0.811 DAYM780101 0.807 JUNJ780101 0.806 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.1 4.6 3.7 3.8 2.0 3.1 4.6 7.0 2.0 6.7 11.0 4.4 2.8 5.6 4.7 7.3 5.6 1.8 3.3 7.7 // H CEDJ970104 D Composition of amino acids in intracellular proteins (percent) (Cedano et al., 1997) R PMID:9067612 A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. T Relation between amino acid composition and cellular location of proteins J J Mol Biol. 266, 594-600 (1997) C JOND920101 0.983 NAKH900101 0.978 CEDJ970102 0.976 FUKS010112 0.956 FUKS010110 0.956 DAYM780101 0.952 CEDJ970101 0.944 JUKT750101 0.942 NAKH920106 0.923 JUNJ780101 0.921 NAKH920101 0.920 KUMS000102 0.908 FUKS010109 0.901 KUMS000101 0.871 NAKH920104 0.865 NAKH920103 0.863 NAKH900102 0.860 NAKH920107 0.857 CEDJ970103 0.854 CEDJ970105 0.852 NAKH920102 0.834 NAKH900109 0.821 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.9 4.9 4.0 5.5 1.9 4.4 7.1 7.1 2.1 5.2 8.6 6.7 2.4 3.9 5.3 6.6 5.3 1.2 3.1 6.8 // H CEDJ970105 D Composition of amino acids in nuclear proteins (percent) (Cedano et al., 1997) R PMID:9067612 A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E. T Relation between amino acid composition and cellular location of proteins J J Mol Biol. 266, 594-600 (1997) C NAKH920101 0.942 NAKH920106 0.930 NAKH900102 0.903 NAKH900101 0.860 CEDJ970104 0.852 NAKH920102 0.843 DAYM780101 0.839 CEDJ970102 0.835 JOND920101 0.834 JUNJ780101 0.803 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.3 8.7 3.7 4.7 1.6 4.7 6.5 6.3 2.1 3.7 7.4 7.9 2.3 2.7 6.9 8.8 5.1 0.7 2.4 5.3 // H FUKS010101 D Surface composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C FUKS010102 0.932 FUKS010104 0.885 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 4.47 8.48 3.89 7.05 0.29 2.87 16.56 8.29 1.74 3.30 5.06 12.98 1.71 2.32 5.41 4.27 3.83 0.67 2.75 4.05 // H FUKS010102 D Surface composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C FUKS010104 0.938 FUKS010101 0.932 VINM940101 0.876 PARS000102 0.868 HOPT810101 0.854 LEVM760101 0.837 WOEC730101 0.820 VINM940103 0.809 VINM940102 0.808 WERD780101 -0.801 FAUJ830101 -0.805 WIMW960101 -0.808 BIOV880102 -0.810 RADA880108 -0.815 BIOV880101 -0.820 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.77 6.87 5.50 8.57 0.31 5.24 12.93 7.95 2.80 2.72 4.43 10.20 1.87 1.92 4.79 5.41 5.36 0.54 2.26 3.57 // H FUKS010103 D Surface composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C VINM940102 0.864 KARP850102 0.835 KARP850101 0.834 MEIH800101 0.832 VINM940101 0.827 RACS770101 0.819 PONP800101 -0.801 CIDH920103 -0.804 PLIV810101 -0.805 ROSG850102 -0.808 ROSG850101 -0.819 CIDH920105 -0.821 CIDH920102 -0.826 MIYS850101 -0.828 LEVM760106 -0.829 BIOV880101 -0.840 RADA880108 -0.840 NISK860101 -0.850 CIDH920101 -0.854 ROBB790101 -0.865 WERD780101 -0.869 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.43 4.51 9.12 8.71 0.42 5.42 5.86 9.40 1.49 1.76 2.74 9.67 0.60 1.18 5.60 9.60 8.95 1.18 3.26 3.10 // H FUKS010104 D Surface composition of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C FUKS010102 0.938 VINM940101 0.919 FUKS010101 0.885 HOPT810101 0.884 LEVM760101 0.869 KRIW790102 0.853 PARS000102 0.850 OOBM770103 0.849 VINM940103 0.838 KRIW790101 0.828 MEIH800102 0.822 KARP850102 0.822 NAKH920106 0.818 VINM940102 0.807 NADH010102 -0.801 NADH010103 -0.805 WERD780101 -0.832 NISK860101 -0.832 FAUJ830101 -0.832 RADA880108 -0.851 BIOV880101 -0.873 ROSG850102 -0.877 BIOV880102 -0.887 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 5.22 7.30 6.06 7.91 1.01 6.00 10.66 5.81 2.27 2.36 4.52 12.68 1.85 1.68 5.70 6.99 5.16 0.56 2.16 4.10 // H FUKS010105 D Interior composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C FUKS010106 0.982 NAKH920105 0.929 FUKS010108 0.923 NAKH900111 0.911 CEDJ970103 0.901 NAKH900109 0.892 FUKS010107 0.891 NAKH920108 0.890 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.88 3.71 2.35 3.50 1.12 1.66 4.02 6.88 1.88 10.08 13.21 3.39 2.44 5.27 3.80 4.10 4.98 1.11 4.07 12.53 // H FUKS010106 D Interior composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C FUKS010105 0.982 NAKH900111 0.933 NAKH920105 0.931 NAKH900109 0.927 FUKS010108 0.927 FUKS010107 0.924 CEDJ970103 0.919 NAKH920108 0.898 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 10.98 3.26 2.85 3.37 1.47 2.30 3.51 7.48 2.20 9.74 12.79 2.54 3.10 4.97 3.42 4.93 5.55 1.28 3.55 10.69 // H FUKS010107 D Interior composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C FUKS010106 0.924 NAKH900109 0.903 FUKS010105 0.891 NAKH900111 0.867 CEDJ970103 0.860 NAKH920105 0.833 FUKS010108 0.832 NAKH920108 0.817 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.95 3.05 4.84 4.46 1.30 2.64 2.58 8.87 1.99 7.73 9.66 2.00 2.45 5.41 3.20 6.03 5.62 2.60 6.15 9.46 // H FUKS010108 D Interior composition of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C NAKH920105 0.968 NAKH900111 0.954 NAKH920108 0.948 FUKS010106 0.927 FUKS010105 0.923 CEDJ970103 0.897 NAKH900112 0.896 NAKH900109 0.872 NAKH900103 0.864 NAKH900105 0.846 FUKS010107 0.832 NAKH900107 0.830 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.26 2.80 2.54 2.80 2.67 2.86 2.67 5.62 1.98 8.95 16.46 1.89 2.67 7.32 3.30 6.00 5.00 2.01 3.96 10.24 // H FUKS010109 D Entire chain composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C FUKS010110 0.936 CEDJ970104 0.901 KUMS000101 0.894 FUKS010112 0.890 NAKH900101 0.868 JOND920101 0.861 KUMS000102 0.850 CEDJ970102 0.839 NAKH920106 0.814 DAYM780101 0.801 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 7.39 5.91 3.06 5.14 0.74 2.22 9.80 7.53 1.82 6.96 9.45 7.81 2.10 3.91 4.54 4.18 4.45 0.90 3.46 8.62 // H FUKS010110 D Entire chain composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C CEDJ970104 0.956 KUMS000101 0.947 NAKH900101 0.946 JOND920101 0.944 KUMS000102 0.943 FUKS010109 0.936 CEDJ970102 0.921 JUKT750101 0.908 FUKS010112 0.904 DAYM780101 0.897 CEDJ970101 0.889 JUNJ780101 0.868 KUMS000104 0.861 NAKH900109 0.853 CEDJ970103 0.848 NAKH920101 0.833 KUMS000103 0.827 NAKH920106 0.824 NAKH920107 0.810 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 9.07 4.90 4.05 5.73 0.95 3.63 7.77 7.69 2.47 6.56 9.00 6.01 2.54 3.59 4.04 5.15 5.46 0.95 2.96 7.47 // H FUKS010111 D Entire chain composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C JUKT750101 0.927 JUNJ780101 0.906 KUMS000102 0.898 DAYM780101 0.882 CEDJ970101 0.878 NAKH920107 0.841 JOND920101 0.832 KUMS000101 0.826 CEDJ970102 0.819 NAKH900101 0.812 MCMT640101 -0.806 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 8.82 3.71 6.77 6.38 0.90 3.89 4.05 9.11 1.77 5.05 6.54 5.45 1.62 3.51 4.28 7.64 7.12 1.96 4.85 6.60 // H FUKS010112 D Entire chain compositino of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001) R PMID:11399062 A Fukuchi, S. and Nishikawa, K. T Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria J J Mol Biol. 309, 835-843 (2001) C CEDJ970104 0.956 NAKH900101 0.948 CEDJ970102 0.946 JOND920101 0.943 NAKH920106 0.921 FUKS010110 0.904 FUKS010109 0.890 NAKH920104 0.882 CEDJ970101 0.882 JUKT750101 0.875 NAKH920101 0.856 DAYM780101 0.856 CEDJ970103 0.850 NAKH920103 0.842 JUNJ780101 0.836 NAKH920107 0.824 KUMS000102 0.819 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 6.65 5.17 4.40 5.50 1.79 4.52 6.89 5.72 2.13 5.47 10.15 7.59 2.24 4.34 4.56 6.52 5.08 1.24 3.01 7.00 // H AVBF000101 D Screening coefficients gamma, local (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C QIAN880120 0.876 PTIO830102 0.861 KANM800102 0.859 QIAN880119 0.859 LIFS790101 0.857 QIAN880121 0.855 CHAM830103 0.843 ROBB760106 0.834 LEVM780105 0.824 PALJ810104 0.818 PALJ810110 0.816 PRAM900103 0.815 LEVM780102 0.815 LIFS790103 0.814 AVBF000102 0.805 LEVM780106 -0.805 GEIM800111 -0.806 QIAN880133 -0.807 QIAN880132 -0.809 KIMC930101 -0.814 MUNV940104 -0.821 QIAN880134 -0.822 GEIM800110 -0.825 MUNV940103 -0.917 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.163 0.220 0.124 0.212 0.316 0.274 0.212 0.080 0.315 0.474 0.315 0.255 0.356 0.410 NA 0.290 0.412 0.325 0.354 0.515 // H AVBF000102 D Screening coefficients gamma, non-local (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C FAUJ880102 0.881 LEVM760103 0.816 AVBF000101 0.805 FAUJ880105 0.802 RACS820110 -0.801 CHAM830101 -0.803 PALJ810105 -0.815 ISOY800103 -0.821 QIAN880133 -0.823 LEVM780103 -0.834 PRAM900104 -0.834 QIAN880132 -0.849 LEVM780106 -0.860 KIMC930101 -0.900 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.236 0.233 0.189 0.168 0.259 0.314 0.306 -0.170 0.256 0.391 0.293 0.231 0.367 0.328 NA 0.202 0.308 0.197 0.223 0.436 // H AVBF000103 D Slopes tripeptide, FDPB VFF neutral (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C AVBF000105 0.965 AVBF000106 0.897 AVBF000107 0.875 FAUJ880107 0.873 AVBF000108 0.868 AVBF000104 0.865 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.490 -0.429 -0.387 -0.375 -0.352 -0.422 -0.382 -0.647 -0.357 -0.268 -0.450 -0.409 -0.375 -0.309 NA -0.426 -0.240 -0.325 -0.288 -0.220 // H AVBF000104 D Slopes tripeptides, LD VFF neutral (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C ONEK900102 0.919 FINA910102 0.901 AVBF000103 0.865 AVBF000107 0.839 AVBF000108 0.819 BLAM930101 -0.872 ONEK900101 -0.899 BUNA790101 -0.922 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.871 -0.727 -0.741 -0.737 -0.666 -0.728 -0.773 -0.822 -0.685 -0.617 -0.798 -0.715 -0.717 -0.649 NA -0.679 -0.629 -0.669 -0.655 -0.599 // H AVBF000105 D Slopes tripeptide, FDPB VFF noside (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C AVBF000103 0.965 AVBF000106 0.939 FAUJ880107 0.931 AVBF000107 0.879 AVBF000108 0.816 YANJ020101 0.807 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.393 -0.317 -0.268 -0.247 -0.222 -0.291 -0.260 -0.570 -0.244 -0.144 -0.281 -0.294 -0.274 -0.189 NA -0.280 -0.152 -0.206 -0.155 -0.080 // H AVBF000106 D Slopes tripeptide FDPB VFF all (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C AVBF000105 0.939 AVBF000103 0.897 FAUJ880107 0.853 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.378 -0.369 -0.245 -0.113 -0.206 -0.290 -0.165 -0.560 -0.295 -0.134 -0.266 -0.335 -0.260 -0.187 NA -0.251 -0.093 -0.188 -0.147 -0.084 // H AVBF000107 D Slopes tripeptide FDPB PARSE neutral (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C FAUJ880107 0.884 AVBF000105 0.879 AVBF000103 0.875 AVBF000104 0.839 AVBF000108 0.832 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.729 -0.535 -0.597 -0.545 -0.408 -0.492 -0.532 -0.860 -0.519 -0.361 -0.462 -0.508 -0.518 -0.454 NA -0.278 -0.367 -0.455 -0.439 -0.323 // H AVBF000108 D Slopes dekapeptide, FDPB VFF neutral (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C AVBF000103 0.868 AVBF000107 0.832 AVBF000104 0.819 AVBF000105 0.816 FAUJ880107 0.802 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.623 -0.567 -0.619 -0.626 -0.571 -0.559 -0.572 -0.679 -0.508 -0.199 -0.527 -0.581 -0.571 -0.461 NA -0.458 -0.233 -0.327 -0.451 -0.263 // H AVBF000109 D Slopes proteins, FDPB VFF neutral (Avbelj, 2000) R PMID:10903873 A Avbelj, F. T Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins J J Mol Biol. 300, 1335-1359 (2000) * (Pro missing) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.376 -0.280 -0.403 -0.405 -0.441 -0.362 -0.362 -0.392 -0.345 -0.194 -0.317 -0.412 -0.312 -0.237 NA -0.374 -0.243 -0.111 -0.171 -0.355 // H YANJ020101 D Side-chain conformation by gaussian evolutionary method (Yang et al., 2002) R PMID:12142444 A Yang, J.M., Tsai, C.H., Hwang, M.J., Tsai, H.K., Hwang, J.K. and Kao, C.Y. T GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations J Protein Sci. 11, 1897-1907 (2002) * (Gly Ala missing) C AVBF000105 0.807 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V NA 0.62 0.76 0.66 0.83 0.59 0.73 NA 0.92 0.88 0.89 0.77 0.77 0.92 0.94 0.58 0.73 0.86 0.93 0.88 // H MITS020101 D Amphiphilicity index (Mitaku et al., 2002) R PMID:12016058 A Mitaku, S., Hirokawa, T. and Tsuji, T. T Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces J Bioinformatics. 18, 608-616 (2002) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0 2.45 0 0 0 1.25 1.27 0 1.45 0 0 3.67 0 0 0 0 0 6.93 5.06 0 // H TSAJ990101 D Volumes including the crystallographic waters using the ProtOr (Tsai et al., 1999) R PMID:10388571 A Tsai, J., Taylor, R., Chothia, C. and Gerstein, M. T The packing density in proteins: standard radii and volumes J J Mol Biol. 290, 253-266 (1999) * (Cyh 112.8) C TSAJ990102 1.000 CHOC750101 0.995 BIGC670101 0.993 GOLD730102 0.993 KRIW790103 0.988 FAUJ880103 0.983 GRAR740103 0.979 CHAM820101 0.977 CHOC760101 0.968 FASG760101 0.935 LEVM760105 0.922 ROSG850101 0.914 LEVM760102 0.910 DAWD720101 0.903 CHAM830106 0.889 FAUJ880106 0.879 LEVM760107 0.866 RADA880106 0.861 LEVM760106 0.849 RADA880103 -0.875 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 89.3 190.3 122.4 114.4 102.5 146.9 138.8 63.8 157.5 163.0 163.1 165.1 165.8 190.8 121.6 94.2 119.6 226.4 194.6 138.2 // H TSAJ990102 D Volumes not including the crystallographic waters using the ProtOr (Tsai et al., 1999) R PMID:10388571 A Tsai, J., Taylor, R., Chothia, C. and Gerstein, M. T The packing density in proteins: standard radii and volumes J J Mol Biol. 290, 253-266 (1999) * (Cyh 113.7) C TSAJ990101 1.000 CHOC750101 0.996 BIGC670101 0.992 GOLD730102 0.991 KRIW790103 0.987 FAUJ880103 0.985 GRAR740103 0.978 CHAM820101 0.978 CHOC760101 0.972 FASG760101 0.940 LEVM760105 0.928 LEVM760102 0.918 ROSG850101 0.909 DAWD720101 0.905 CHAM830106 0.896 FAUJ880106 0.882 RADA880106 0.864 LEVM760107 0.861 LEVM760106 0.841 RADA880103 -0.879 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 90.0 194.0 124.7 117.3 103.3 149.4 142.2 64.9 160.0 163.9 164.0 167.3 167.0 191.9 122.9 95.4 121.5 228.2 197.0 139.0 // H COSI940101 D Electron-ion interaction potential values (Cosic, 1994) R PMID:7851912 A Cosic, I. T Macromolecular bioactivity: is it resonant interaction between macromolecules?--Theory and applications J IEEE Trans Biomed Eng. 41, 1101-1114 (1994) * (values are cited from Protein Eng. 15:193-203) C VELV850101 1.000 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.0373 0.0959 0.0036 0.1263 0.0829 0.0761 0.0058 0.0050 0.0242 0.0000 0.0000 0.0371 0.0823 0.0946 0.0198 0.0829 0.0941 0.0548 0.0516 0.0057 // H PONP930101 D Hydrophobicity scales (Ponnuswamy, 1993) R PMID:8419986 A Ponnuswamy, P.K. T Hydrophobic characteristics of folded proteins J Prog Biophys Mol Biol. 59, 57-103 (1993) C MANP780101 0.967 NISK860101 0.961 NISK800101 0.956 PONP800101 0.945 PONP800108 0.944 PONP800102 0.934 CIDH920104 0.930 ROSG850102 0.928 BIOV880101 0.912 MIYS850101 0.910 PONP800103 0.909 LIFS790101 0.908 CIDH920103 0.899 NADH010103 0.898 WERD780101 0.895 NADH010104 0.895 QIAN880121 0.893 RADA880108 0.891 CIDH920105 0.891 NADH010102 0.880 QIAN880120 0.879 PTIO830102 0.879 BIOV880102 0.877 CHOP780202 0.867 ROBB760106 0.866 KANM800102 0.866 MEIH800103 0.863 ROBB790101 0.858 PALJ810104 0.857 PONP800107 0.851 JURD980101 0.849 KYTJ820101 0.844 FAUJ830101 0.843 NADH010105 0.839 GEIM800107 0.838 QIAN880122 0.837 QIAN880119 0.836 SWER830101 0.835 DESM900102 0.834 LIFS790102 0.833 KANM800104 0.833 ROBB760105 0.829 JANJ780102 0.825 CIDH920102 0.820 PLIV810101 0.819 JANJ790101 0.816 CHOC760103 0.816 NADH010101 0.813 DESM900101 0.807 GUOD860101 0.802 GUYH850101 -0.817 VINM940103 -0.818 KRIW790102 -0.821 PARJ860101 -0.846 PARS000101 -0.849 MUNV940103 -0.864 VINM940102 -0.869 RACS770102 -0.871 GRAR740102 -0.872 MEIH800102 -0.881 RACS770101 -0.886 KARP850102 -0.893 KRIW790101 -0.909 VINM940101 -0.913 OOBM770103 -0.914 MEIH800101 -0.916 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.85 0.20 -0.48 -1.10 2.10 -0.42 -0.79 0 0.22 3.14 1.99 -1.19 1.42 1.69 -1.14 -0.52 -0.08 1.76 1.37 2.53 // H WILM950101 D Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995) R A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides J Anal Chem. 67, 1210-1219 (1995) C GUOD860101 0.893 MEEJ810102 0.849 VENT840101 0.840 WILM950102 0.838 BULH740101 -0.845 WOLS870101 -0.851 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.06 -0.85 0.25 -0.20 0.49 0.31 -0.10 0.21 -2.24 3.48 3.50 -1.62 0.21 4.80 0.71 -0.62 0.65 2.29 1.89 1.59 // H WILM950102 D Hydrophobicity coefficient in RP-HPLC, C8 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995) R A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides J Anal Chem. 67, 1210-1219 (1995) C WILM950101 0.838 MEEJ810102 0.809 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 2.62 1.26 -1.27 -2.84 0.73 -1.69 -0.45 -1.15 -0.74 4.38 6.57 -2.78 -3.12 9.14 -0.12 -1.39 1.81 5.91 1.39 2.30 // H WILM950103 D Hydrophobicity coefficient in RP-HPLC, C4 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995) R A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides J Anal Chem. 67, 1210-1219 (1995) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -1.64 -3.28 0.83 0.70 9.30 -0.04 1.18 -1.85 7.17 3.02 0.83 -2.36 4.26 -1.36 3.12 1.59 2.31 2.61 2.37 0.52 // H WILM950104 D Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/2-PrOH/MeCN/H2O (Wilce et al. 1995) R A Wilce, M.C., Aguilar, M.I. and Hearn, M.T. T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides J Anal Chem. 67, 1210-1219 (1995) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -2.34 1.60 2.81 -0.48 5.03 0.16 1.30 -1.06 -3.00 7.26 1.09 1.56 0.62 2.57 -0.15 1.93 0.19 3.59 -2.58 2.06 // H KUHL950101 D Hydrophilicity scale (Kuhn et al., 1995) R PMID:8749849 A Kuhn, L.A., Swanson, C.A., Pique, M.E., Tainer, J.A. and Getzoff, E.D. T Atomic and residue hydrophilicity in the context of folded protein structures J Proteins. 23, 536-547 (1995) C ROSM880101 0.962 ROSM880102 0.922 FAUJ880110 0.922 PRAM900101 0.908 OOBM770101 0.876 GRAR740102 0.865 VHEG790101 0.858 JANJ780101 0.839 WOEC730101 0.837 GUYH850101 0.827 FAUJ880109 0.827 JANJ780103 0.826 MEIH800102 0.822 LEVM760101 0.807 NADH010103 -0.807 BIOV880102 -0.809 MEIH800103 -0.809 WARP780101 -0.811 JANJ790101 -0.811 CIDH920104 -0.822 BIOV880101 -0.834 EISD860101 -0.835 NADH010102 -0.836 RADA880108 -0.839 JANJ790102 -0.844 RADA880104 -0.847 RADA880107 -0.857 FAUJ830101 -0.863 DESM900102 -0.863 CHOC760103 -0.865 KYTJ820101 -0.883 JURD980101 -0.884 JANJ780102 -0.890 EISD860103 -0.894 WOLR810101 -0.898 NADH010101 -0.898 EISD840101 -0.907 RADA880101 -0.950 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 0.78 1.58 1.20 1.35 0.55 1.19 1.45 0.68 0.99 0.47 0.56 1.10 0.66 0.47 0.69 1.00 1.05 0.70 1.00 0.51 // H GUOD860101 D Retention coefficient at pH 2 (Guo et al., 1986) R A Guo, D., Mant, C.T., Taneja, A.K., Parker, J.M. and Hodges, R.S. T Prediction of peptide retention times in reversed-phase high-performance liquid chromatography; I. determination of retention coefficients of amino acid residues of model synthetic peptides J J Chromatogr. 359, 499-517 (1986) C MEEJ810102 0.949 PLIV810101 0.943 MEEJ810101 0.931 MIYS850101 0.908 FAUJ830101 0.900 WILM950101 0.893 NOZY710101 0.884 MEEJ800102 0.866 CIDH920104 0.860 CIDH920105 0.858 PONP800107 0.854 SWER830101 0.853 ZIMJ680105 0.850 VENT840101 0.848 CIDH920103 0.845 NISK860101 0.840 EISD860101 0.839 BIOV880101 0.839 BROC820101 0.832 CIDH920102 0.831 RADA880102 0.829 BIOV880102 0.817 MANP780101 0.815 ROBB790101 0.815 RADA880108 0.812 NAKH900110 0.805 NADH010104 0.803 NADH010103 0.803 PONP930101 0.802 RACS770101 -0.805 ROSM880102 -0.829 MEIH800101 -0.833 OOBM770103 -0.838 GRAR740102 -0.855 BULH740101 -0.922 PARJ860101 -0.925 WOLS870101 -0.955 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 25 -7 -7 2 32 0 14 -2 -26 91 100 -26 68 100 25 -2 7 109 56 62 // H JURD980101 D Modified Kyte-Doolittle hydrophobicity scale (Juretic et al., 1998) R A Juretic, D., Lucic, B., Zucic, D. and Trinajstic, N. T Protein transmembrane structure: recognition and prediction by using hydrophobicity scales through preference functions J Theoretical and Computational Chemistry, 5, 405-445 (1998) C KYTJ820101 0.996 CHOC760103 0.967 NADH010102 0.931 JANJ780102 0.928 NADH010101 0.925 EISD860103 0.901 DESM900102 0.900 NADH010103 0.900 EISD840101 0.895 RADA880101 0.893 MANP780101 0.887 WOLR810101 0.881 PONP800103 0.879 JANJ790102 0.879 NADH010104 0.873 CHOC760104 0.870 PONP800102 0.869 JANJ790101 0.868 MEIH800103 0.861 PONP800101 0.858 NAKH920108 0.858 RADA880108 0.857 PONP800108 0.856 ROSG850102 0.854 PONP930101 0.849 RADA880107 0.842 BIOV880101 0.840 MIYS850101 0.837 FAUJ830101 0.833 CIDH920104 0.832 DESM900101 0.829 WARP780101 0.827 KANM800104 0.826 LIFS790102 0.824 RADA880104 0.824 NADH010105 0.821 NISK800101 0.816 NISK860101 0.808 BIOV880102 0.805 ARGP820102 0.802 ARGP820103 0.800 VHEG790101 -0.814 KRIW790101 -0.824 CHOC760102 -0.851 ROSM880101 -0.851 MONM990101 -0.853 JANJ780103 -0.853 RACS770102 -0.855 PRAM900101 -0.862 JANJ780101 -0.862 GUYH850101 -0.864 GRAR740102 -0.864 MEIH800102 -0.879 KUHL950101 -0.884 ROSM880102 -0.894 OOBM770101 -0.903 I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V 1.10 -5.10 -3.50 -3.60 2.50 -3.68 -3.20 -0.64 -3.20 4.50 3.80 -4.11 1.90 2.80 -1.90 -0.50 -0.70 -0.46 -1.3 4.2 //