Conformational similarity indices between different residues in proteins and alpha-helix propensities

Various amino acid similarity matrices have been derived using data on phys icochemical properties and molecular evolution. Conformational similarity i ndices, CSXX, between different residues are computed here using the distri bution of the main-chain and side-chain torsion angles and the values have been used to cluster amino acids in proteins. A subset of these parameters, CSAX, indicates the extent of similarity in the main-chain and side-chain conformations (phi,psi and chi (1)) of different residues (X) with Ala (A) and is found to have strong correlation with alpha -helix propensities. How ever, no subset of CSXX, provides any linear relationship with beta -sheet propensities, suggesting that the conformational feature favouring the loca tion of a residue in an alpha -helix is different from the one favouring th e beta -sheet. Conformationally similar residues (close CSAX values) have s imilar steric framework of the side-chain (linear/branched. aliphatic/aroma tic), irrespective of the polarity or hydrophobicity. Cooperative nucleatio n of helix may be facile for a contiguous stretch of residues with high ove rall CSAX values.