Contact Curve Based Simulation of Side Chains from Two Amino Acids in a Protein Molecule

Abstract

In this paper, an algorithm to compute the contact configuration between the rotating side chains from two amino acids in a protein molecule is proposed. The main chain and side chain parts in one amino acid are considered as two rigidbody parts combined with a revolute joint. While the atom positions in the main chain parts of two amino acids are fixed, the side chains possibly rotate, which can cause the collision between amino acids. On the plane of rotation angle parameters, we find the region for two side chains colliding each other. Then, by extracting the boundary of the region, the contact curve of the amino acids is found, where by using it, the amino acids with rotating side chains can be simulated.