This file is a Amino-acid similarity file for use with BOX. This file is used in colouring residues that are "similar" to a single consensus residue. Similarities contained in this file are not automatically set-forming. This means: The line I LVM means that I is similar to L,V and M and also that L,V,M are similar to I. It does not imply that L is similar to V or to M. For achieving this, more lines (the next ones) are necessary. Although is seems weird, this feature has been chosen DELIBERATELY because I think it could be helpful in some cases. This table was taken from ClustalX v1.3b: STRONG groups: These are all the positively scoring groups that occur in the Gonnet Pam250 matrix with score >0.5 .. S TA T AS A ST N EQK E QKN Q KNE K NEQ N HQK H QKN Q KNH K NHQ N DEQ D EQN E QND Q NDE Q HRK H RKQ R KQH K QHR M ILV I LVM L VMI V MIL M ILF I LFM L FMI F MIL H Y F YW Y WF W FY