A self-organizing map of amino acids with their local environments in proteins by using pairwise-contact energy parameters

Based on the 180 × 180 pairwise-contact energy parameters between 20 amino acids incorporating their 9 local environments in proteins, the classification of 180 types of amino acids is presented by the self-organizing map, We demonstrate that the physico-chemical features of the amino acids are well captured in the 180 × 180 pairwise-contact energy parameters and that they agree with their known biological characters in the simultaneous aspects of secondary structures, hydrophobicity, and the existence probability of amino acids under various environments in protein structures. Our result justifies the use of these energy parameters for the recognition of protein folds.