The goal of this project is to identify common features of packing interactions in protein crystals, by statistical survey of structures in the Brookhaven Protein Data Bank. We have used 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 crystal-packing contacts by residue and residue-pair type, and conducted statistical analyses. An interesting feature identified is the preferential participation of amino acids with small side chains, suggesting that lattice packing in diffraction-quality crystals must involve rigid intra-molecular contact of the polypeptide backbone. Another interesting feature is a clear correlation between the density of packing contacts and the resolution of available diffraction data, suggesting that lattice packing can reduce crystal disorder. The significance of this project is in providing a summary of protein-protein interactions as observed in crystals. These are very different from intra-molecular or oligomer-docking contacts, and they may provide a model for interactions expected in loosely-associated biological complexes.
NIH ExPorter
NIH ExPorter