Protein contacts, inter-residue interactions and side-chain modelling

Three-dimensional structures of proteins are the support of their biological functions. Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-C alpha distances. In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria. First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted. Detailed analyses have been done concerning the proximity of contacts in the sequence, the size of the proteins and fold classes. The strongest differences have been extracted, highlighting important residues. Then, we studied the influence of five different side-chain conformation prediction methods (SCWRL, IRECS, SCAP, SCATD and SCCOMP) on the distribution of contacts. The prediction rates of these different methods are quite similar. However, using a distance criterion between side chains, the results are quite different, e.g. SCAP predicts 50% more contacts than observed, unlike other methods that predict fewer contacts than observed. Contacts deduced are quite distinct from one method to another with at most 75% contacts in common. Moreover, distributions of amino acid preferential contacts present unexpected behaviours distinct from previously observed in the X-ray structures, especially at the surface of proteins. For instance, the interactions involving Tryptophan greatly decrease. (C) 2007 Elsevier Masson SAS. All rights reserved.