Clustering of non-polar contacts in proteins

Motivation: Hydrophobic or non-polar contacts in proteins are important for protein folding, protein stability and protein-protein inter-actions. In particular; in the interior of a protein, in the hydrophobic core, a large number of such contacts are found. The residues involved in these contacts often form a tightly packed cluster of atoms. It is useful for the under-standing of protein structure to be able to identify and analyse such clusters. Results: Tools for hierarchical cluster analysis of non-polar contacts in proteins are described. These tools allow for efficient identification of clusters of non-polar interactions in proteins, both internal clusters and clusters involved in protein-protein contacts. The non-polar contacts are represented by a dendrogram structure, which is a simple approach for flexible identification of clusters by visual inspection. The tools are demonstrated on the structure of crambin, the structure of the complex between human growth hormone and the human growth hormone binding protein, and a pair of lipase/esterase structures.