The Influence of Nearest-Neighbor Amino Acids on the Conformation of the Middle Amino Acid in Proteins: Comparison of Predicted and Experimental Determination of β-Sheets in Concanavalin A

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Abstract
A 20 x 20 table of tripeptides has been compiled that may be used to locate beta-sheet breaking and alpha-helix breaking residues in proteins. It is based on the definition of an alpha-helical and a beta-sheet domain on the (varphi, Psi) map based on the occurrences of alpha-helices and beta-sheets in 12 known proteins whose sequence and three-dimensional structure have been determined. Each entry in the 20 x 20 table lists three numbers, the frequency of occurrences of the middle amino acid (n) in relation to its nearest neighbors (n - 1) and (n + 1) in the alpha-helical domain, the beta-sheet domain and outside these regions. The regions between two beta-sheet-breaking residues would be permissively beta-sheet regions. The sequence of concanavalin A has been examined in this manner and of the 13 beta-strands defined by x-ray crystallography, 10 were in agreement with the permissively beta-sheet regions and, in the remaining three, beta-sheet-breaking residues were the third in one, and the third, fourth, and fifth residues in another, and the sixth residue in the third from the beginning of the beta-strands. The findings provide strong support for the role of nearest-neighboring amino acids in determining secondary structure of proteins.

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