The hydrophobic amino acids that make up the core of a protein can be expected to be closer together than the rest of the residues in the molecule and are likely to remain conserved during evolution due to their important role. In the present study, a general theoretical framework is provided for estimating interresidue distances from residue hydrophobicity and conservation deduced from multiple alignments. While the accurate prediction of individual distances by statistical procedures is theoretically impossible, the method is able to match the distribution of predicted distances to a prescribed distribution with good accuracy.
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