title: Environment-dependent residue contact energies for proteins.
abstract: 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.
authors.affiliation: Department of Chemistry and E. O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
authors.forename: C
authors.initials: C
authors.lastname: Zhang
authors.forename: S H
authors.initials: SH
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D016208:Databases, Factual; D008962:Models, Theoretical; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics