title: Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron.
abstract: The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with several simple lattices (Bagci et al., Proteins 2003;53:56-67; Raghunathan et al., Protein Sci 1997;6:2072-2083). 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 < 1.5 A). 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 are considered in detail and a theoretical description of these packing regularities is proposed.
authors.affiliation: Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-0320, USA.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Feng
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kloczkowski
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012044:Regression Analysis
chemical_list: D011506:Proteins