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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.

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The rapid increase in the number of high-quality protein structures provides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes they form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of side chain/atom interactions to assess three different methods for modelling atomic interactions in proteins. We have also derived a new empirical solvation potential which aims to reproduce the hydrophobic effect. To conclude we address the problem of molecular recognition and consider what we can deduce about the interactions involved in the binding of peptides to proteins.