Prediction of β‐sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 × 20 table for evaluation of the effects of nearest‐neighbors on conformations of middle amino acids in proteins

The extraordinarily large number of immunoglobulins renders them an intriguing class of molecules for attempts to predict their conformations. The predictive method applied, using a 20 × 20 table of the observed effects of nearest‐neighboring amino acids on the conformation (Φ,Ψ angles) of the middle residue in known proteins, indicates positions of tri‐peptides that tend to break α‐helices or regular β‐sheets. This 20 × 20 table is derived from data on 19 proteins, as compared with the earlier version based on 12 proteins, and includes a separate listing of residues of β‐turns that have helical Φ,Ψ values. Secondary conformations predicted by methods of Chou and Fasman, Lim and Burgess, Ponnuswamy, and Scheraga have also been compared; for all three methods, wrong predicitons of residues in β‐sheet conformation exceed correct ones. Better predictions are obtained when there is agreement with two or three of the methods. If there is consistent overprediction of β‐structure, as with the Chou and Fasman method, the use of the β‐sheet‐breaking tripeptides can improve pre‐dictability somewhat.