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. 1973 May;70(5):1473–1477. doi: 10.1073/pnas.70.5.1473

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

Elvin A Kabat 1,2,3,4,5,6, T T Wu 1,2,3,4,5,6
PMCID: PMC433522  PMID: 4514316

Abstract

A 20 × 20 table of tripeptides has been compiled that may be used to locate β-sheet breaking and α-helix breaking residues in proteins. It is based on the definition of an α-helical and a β-sheet domain on the (ϕ, Ψ) map based on the occurrences of α-helices and β-sheets in 12 known proteins whose sequence and three-dimensional structure have been determined. Each entry in the 20 × 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 α-helical domain, the β-sheet domain and outside these regions. The regions between two β-sheet-breaking residues would be permissively β-sheet regions. The sequence of concanavalin A has been examined in this manner and of the 13 β-strands defined by x-ray crystallography, 10 were in agreement with the permissively β-sheet regions and, in the remaining three, β-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 β-strands. The findings provide strong support for the role of nearest-neighboring amino acids in determining secondary structure of proteins.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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