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

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