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Abstract
Energies required to transfer amino acid side chains from water to less polar environments
were calculated from results of several studies and compared with several statistical
analyses of residue distributions in soluble proteins. An analysis that divides proteins
into layers parallel with their surfaces is more informative than those that simply
classify residues as exposed or buried. Most residues appear to be distributed as
a function of the distance from the protein-water interface in a manner consistent
with partition energies calculated from partitioning of amino acids between water
and octanol phases and from solubilities of amino acids in water, ethanol, and methanol.
Lys, Arg, Tyr, and Trp residues tend to concentrate near the water-protein interface
where their apolar side-chain components are more buried than their polar side-chain
components. Residue distributions calculated in this manner do not correlate well
with side-chain solvation energies calculated from vapor pressures of side-chain analogs
over a water phase. Results of statistical studies that classify residues as exposed
to solvent or buried inside the protein interior appear to depend on the method used
to classify residues. Data from some of these studies correlate better with solvation
energies, but other data correlate better with partition energies. Most other statistical
methods that have been used to evaluate effects of water on residue distributions
yield results that correlate better with partition energies than with solvation energies.