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An approximate but rapid method for estimating hydrophobic energy is proposed. Aside from a scale factor, it is given by the pairwise sum of the surface area buried by each neighbor atom, but excluding those atoms in the same residue or in its sequence neighbor residues. This sum is found to be linearly related to the true buried area as calculated by the algorithm of Lee and Richards 1971, J. Mol. Biol., 55, 379-400, and to the contact potential of Miyazawa and Jernigan 1985, Macromolecules, 18, 534-552. It correlates with experimental transfer free energies to approximately the same degree as that calculated using the true buried area. Furthermore, in a simple test of helix packing with ROP protein monomer, the new hydrophobic energy clearly discriminated one structure, with the lowest r.m.s. deviation from the crystal structure, against an exhaustive set of others.
Kurochkina et al. (Sun,) studied this question.