Estimation of quality of approximation of atom-atom contacts of amino acid residues in proteins by the contacts of the residue force centers

摘要

How precisely the atom-atom contacts of amino acid residues in proteins can be approximated by the contacts of amino acid residue "force centers"? To answer this question, we examined the force centers positioned in the C_#alpha#-atom, the C_#beta#-atom, in the optimal point of the C#alpha# - C_#beta# axis, and in tile geometrical center of residues. The maximal coefficient of correlation between the residue force center contacts and the presence of atom-atom contacts of tile residues (85%) was obtained for the force centers positioned in geometrical centers of the residues. The correlation is 80% for the optimal position of the centers on the C_#alpha# - C_#beta# axes; a somewhat smaller value (78%) is obtained for the force centers positioned in C_#beta#-atoms, and 71% only for the centers positioned in C#alpha#-atoms. The obtained results allow one to estimate the limit of precision of calculations which replace the atom-atom interactions by interactions of amino acid residues taken as a whole.