The influence of side chain structures on the residue-residue associations in globular proteins

Abstract

The relationship between the physical make-up of the side chain structure of an amino acid and its capacity to associate with other side chains in the crystalline state of protein molecules has been investigated by a linear regression study. Relevant inter- and intra-molecular forces and steric factors are taken to represent the side chain structure, while the observed atom-atom interactions in a set of protein crystals are taken to represent the residue-residue association potentials. Correlation equations are set up in such a way that, (i) the dependence of the association potential of a residue on the side chain structures of associating residues, and (ii) the dependence of the association potential of a residue on its own side chain structure are brought out separately. The results show definite quantitative relationships in each of the above two views. Particularly, the behaviour of the charged residues is highly correlated to the structural make of their side chains. It is demonstrated how and to what extent the effects of associating/preferring residues are taken care of when they associate with a certain kind of residue in the protein environment.