Grouping of residues based on their contact interactions.
Based on the concept of energy landscape a grouping method of residues for reducing the sequence complexity in proteins is presented. For the Miyazawa and Jernigan 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=8-10 is found, which may represent the basic degree of freedom of the sequence complexity in proteins.
Wang
Jun
J
National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China.
Wang
Wei
W
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry* / Q000145:classification*; D019295:Computational Biology / Q000379:methods; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000145:classification; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*; D013499:Surface Properties
D000596:Amino Acids; D010455:Peptides; D011506:Proteins