Importance of solvent accessibility and contact surfaces in modeling side‐chain conformations in proteins

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Abstract
Contact surface area and chemical properties of atoms are used to concurrently predict conformations of multiple amino acid side chains on a fixed protein backbone. The combination of surface complementarity and solvent‐accessible surface accounts for van der Waals forces and solvation free energy. The scoring function is particularly suitable for modeling partially buried side chains. Both iterative and stochastic searching approaches are used. Our programs (Sccomp‐I and Sccomp‐S), with relatively fast execution times, correctly predict χ1 angles for 92–93% of buried residues and 82–84% for all residues, with an RMSD of ∼1.7 Å for side chain heavy atoms. We find that the differential between the atomic solvation parameters and the contact surface parameters (including those between noncomplementary atoms) is positive; i.e., most protein atoms prefer surface contact with other protein atoms rather than with the solvent. This might correspond to the driving force for maximizing packing of the protein. The influence of the crystal packing, completeness of rotamer library and precise positioning of Cβ atoms on the accuracy of side‐chain prediction are examined. The Sccomp‐S and Sccomp‐I programs can be accessed through the Web ( http://sgedg.weizmann.ac.il/sccomp.html) and are available for several platforms. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 712–724, 2004