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Protein X-ray crystallography produces an electron density map that rarely detects individual hydrogen atoms or distinguishes between carbon, nitrogen and oxygen atoms in the electron density. This makes it difficult to orientate the side chains of Asn, Gln and His, which appear symmetrical in the electron density; their orientation is usually judged on the basis of hydrogen bonding. Based on the observation that almost all buried donors and acceptors are satisfied, we have developed a simple algorithm to compare the alternative conformations of these residues and, where possible, identify the most favourable. In a cross-section of protein structures we found a few side chains (15.0% of Asn and Gln and 9.9% of His) which would be more favourable in the alternative orientation. We have also found that this proportion rises slightly with worsening resolution.

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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.