An attempt to evaluate the influence of neighboring amino acids (n-1) and (n+1) on the backbone conformation of amino acid (n) in proteins. Use in predicting the three-dimensional structure of the polypeptide backbone of other proteins

From φ, ψ data on eleven proteins, a 20 × 20 × 20 Table of tripeptides has been computed to evaluate the influence of nearest neighbors (n ? 1) and (n + 1) on the φ, ψ angles of amino acid (n). From this Table, having removed values for horse cytochrome c and using the sequences of 18 cytochromes c and the procedure of Kabat &; Wu (1972), an attempt was made to select a set of φ, ψ angles for positions 2 to 103 of cytochrome c and compare them with the values obtained from the atomic co-ordinates. Agreement was good for 56, intermediate for 29 and poor for 17 residues. Eleven of the 17 with poor agreement were residues contacting the heme or adjacent to a contacting residue. Moreover, 6 of the 17 poor values were in regions of the φ, ψ plot for which no occurrences in the ten known proteins were reported, and for four others known values were minimal so that no basis for selection existed. Frequency distributions on the Ramachandran plot (Ramachandran &; Sasisekharan, 1968) of all φ, ψ values in the eleven known proteins are given as well as a contour plot for such frequencies. The uses and limitations of the procedure are discussed and the need for obtaining accurate estimates of errors in experimentally determined φ, ψ angles is emphasised.