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The hydrophobic core residues of proteins are more conserved than non-core residues due to the evolutionary constraints of side-chain packing in the core. The amount of conservation at each position in a multiple sequence alignment should therefore have some structural meaning. However, conservation is also a feature of active sites and interaction surfaces. Hence patterns of conservation may be associated with specific functions of highly related molecules and will not be `conserved' across larger evolutionary distances. A measure of conserved hydrophobicity, which combines per-residue conservation with hydrophobicity averaged for each residue in a multiple sequence alignment, should minimise some of these effects. This measure has been used previously in fold recognition[Taylor, 1997].