The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with several simple lattices.1,2 In this work, instead of a lattice we use the regular polyhedron, the icosahedron, as the model to describe the orientational distribution of contacts in clusters derived from a high-resolution protein dataset (522 protein structures with high resolution < 1.5Å). We find that the order parameter (orientation function) measuring the angular overlap of directions in coordination clusters with directions of the icosahedron is 0.91, which is a significant improvement in comparison with the value 0.82 for the order parameter with the face-centered cubic (fcc) lattice. Close packing tendencies and patterns of residue packing in proteins is considered in detail and a theoretical description of these packing regularities is proposed.
Available at: http://works.bepress.com/robert-jernigan/202/
This is the peer reviewed version of the following article: Feng, Yaping, Robert L. Jernigan, and Andrzej Kloczkowski. "Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron." Proteins: Structure, Function, and Bioinformatics 73, no. 3 (2008): 730-741, which has been published in final form at doi: 10.1002/prot.22092. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.