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

Various amino acid similarity matrices have been derived using data on physicochemical properties and molecular evolution. Conformational similarity indices, CSXX', between different residues are computed here using the distribution 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 (φ,ψ and χ 1) of different residues (X) with Ala (A) and is found to have strong correlation with α-helix propensities. However, no subset of CSXX' provides any linear relationship with β-sheet propensities, suggesting that the conformational feature favouring the location of a residue in an α-helix is different from the one favouring the β-sheet. Conformationally similar residues (close CSAX values) have similar steric framework of the side-chain (linear/branched, aliphatic/aromatic), irrespective of the polarity or hydrophobicity. Cooperative nucleation of helix may be facile for a contiguous stretch of residues with high overall CSAX values