A numerical measure of amino acid residues similarity based on the analysis of their surroundings in natural protein sequences

A measure of similarity between amino acid residues based on the analysis o f the surroundings of each residue in primary structures of native proteins is proposed. The statistical data used for this purpose were obtained from the analysis of 168,808 protein sequences, which comprise the Protein Iden tification Research database (release 63). Using various threshold values o f the proposed measure, amino acid residues were classified into several gr oups. The classification elaborated differs essentially from groupings prev iously used. The numerical measure of amino acid residues similarity can be used in site-directed mutagenesis studies for the prediction of probabilit y of local spatial rearrangements in proteins.