Atomic environments of arginine side chains in proteins.
A statistical analysis of the atomic environments of arginine side chains from 62 high resolution protein structures has been made. Using the definition of F.M. Richards (J. Mol. Biol., 82, 1-14, 1974), the protein data set was subdivided into 19 different atom types and their propensities to form atom contacts with the side chain atoms of arginine residues were calculated. For those arginine side chain-atom pairs classed as interacting, a detailed analysis of their geometries was carried out. This has included the contact separation (R) and the spatial distribution in terms of the spherical polar angles theta and phi. The geometrical distributions of the 19 different atom types were compared and contrasted to identify factors that are important for packing. From the results we find that polarity, covalent constraints, volume occlusion and solvent accessibility are the key determinants governing packing around arginine side chains.
Nandi
C L
CL
Department of Biochemistry and Molecular Biology, University College London, UK.
Singh
J
J
Thornton
J M
JM
D001120:Arginine / Q000737:chemistry*; D003198:Computer Simulation; D016208:Databases, Factual; D008956:Models, Chemical; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins; D001120:Arginine