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 of 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 Identification Research database (release 63). Using various threshold values of the proposed measure, amino acid residues were classified into several groups. The classification elaborated differs essentially from groupings previously used. The numerical measure of amino acid residues similarity can be used in site-directed mutagenesis studies for the prediction of probability of local spatial rearrangements in proteins.
Rogov
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Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, GSP-7, Moscow 117997, Russia.
Nekrasov
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D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D016208:Databases, Factual; D030562:Databases, Protein; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008433:Mathematics; D016297:Mutagenesis, Site-Directed; D009716:Numerical Analysis, Computer-Assisted; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation
D000596:Amino Acids; D010455:Peptides