Simplification of protein representation from the contact potentials between residues

Abstract

Based on the concept of energy landscape a picture of the mismatch between the reduced interaction matrix of residues and the matrix of statistical contact potentials is presented. For the Miyazawa and Jernigan (MJ) matrix, rational groupings of 20 kinds of residues with minimal mismatches under the consideration of local minima and statistics on correlation between the residues are studied. A hierarchical tree of groupings relating to different numbers of groups $N$ is obtained, and a plateau around $N=8\sim 10$ is found, which may represent the basic degree of freedom of the sequence complexity of proteins.