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 struc- tural environment, with nonlocal interactions in beta-sheet structures and o-helical structures dominating the energy table. Environ- ment-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.
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