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We investigated the correlation between the Shannon information entropy, ‘sequence entropy’, with respect to the local flexibility of native globular proteins as described by inverse packing density. These are determined at each residue position for a total set of 130 query proteins, where sequence entropies are calculated from each set of aligned residues. For the accompanying aggregate set of 130 alignments, a strong linear correlation is observed between the calculated sequence entropy and the corresponding inverse packing density determined at an associated residue position. This region of linearity spans the range of Cα packing densities from 12 to 25 amino acids within a sphere of 9 Å radius. Three different hydrophobicity scales all mimic the behavior of the sequence entropies. This confirms the idea that the ability to accommodate mutations is strongly dependent on the available space and on the propensity for each amino acid type to be buried. Future applications of these types of methods may prove useful in identifying both core and flexible residues within a protein.


This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Protein Engineering following peer review. The definitive publisher-authenticated version "Protein sequence entropy is closely related to packing density and hydrophobicity. Protein Engineering, Design and Selection (February 2005) 18 (2): 59-64." is available online at: