Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure

The degree of similarity in the three-dimensional structures of two proteins can be examined by comparing the patterns of hydrophobicity found in their amino acid sequences. Each type of amino acid residue is assigned a numerical hydrophobicity, and the correlation coefficient r H is computed between all pairs of residues in the two sequences. In tests on sequences from two properly aligned proteins of similar three-dimensional structure, r H is found in the range 0.3 to 0.7. Improperly aligned sequences or unrelated sequences give r H near zero. By considering the observed frequency of amino acid replacements among related structures, a set of optimal matching hydrophobicities (OMHs) was derived. With this set of OMHs, significant correlation coefficients are calculated for similar three-dimensional structures, even though the two sequences contain few identical residues. An example is the two similar folding domains of rhodanese ( r H = 0.5). Predictions are made of similar three-dimensional structures for the alpha and beta chains of the various phycobiliproteins, and for delta hemolysin and melittin.