The goal of this project is to identify common features of packing interactionsin protein crystals, by statistical survey of structures in the Brookhaven Protein Data Bank. We will consider residue types involved, specific pairwise interactions, and examine the relationship of packing contacts to crystal habit. We have used new functions in the PKB suite to identify a non-redundant subset of structures in the Protein Data Bank which have valid crystal symmetry information. For these structure we have tabulated atomic contacts by residue and residue-pair type, and conducted a preliminary statistical analyses. The most interesting feature identified to date is the low participation of lysine, arginine and glutamic acid side chains in packing contacts. Salt bridges involving these residues are important in protein tertiary structure, but it appears that interactions of smaller, uncharged side chains predominate in crystal packing. Statistical methods for detailed analysis of these datahave been developed. These will be used to quantitate precisely the participation different residues in packing interactions, while adjusting for their abundance, occurrence on the protein surface, and specific stereochemistry. This project will develop an empirical description of nonbonded interactions expected at protein-protein interfaces. This may prove useful in identification of docking sites of biological importance. It may also suggest ways to alter the strength of docking interactions, as a means to improve ordering in protein crystals, or as a means to identify the biological function of docking sites.
