Environment-dependent residue contact energies for proteins

We examine the interactions between amino acid residues in the context of their secondary structural environments (helix, strand, and coil) in proteins. Effective contact energies for an expanded 60-residue alphabet (20 aa x three secondary structural states) are estimated from the residue-residue contacts observed in known protein structures. Similar to the prototypical contact energies for 20 aa, the newly derived energy parameters reflect mainly the hydrophobic interactions; however, the relative strength of such interactions shows a strong dependence on the secondary structural environment, with nonlocal interactions in beta-sheet structures and alpha-helical structures dominating the energy table. Environment-dependent residue contact energies outperform existing residue pair potentials in both threading and three-dimensional contact prediction tests and should be generally applicable to protein structure prediction.