Triplet information in helix prediction applied to the analysis of super-secondary structures

It is seen that the strength of the helix prediction function seems to be improved as a whole, and leads to the reasonable explantation of the formation of supersecondary structures presented in the accompanying paper ( Nagano, 1977 ).

Abstract

The method of secondary structure prediction was presented by Nagano (1973) on the basis of doublet analysis and tested for two proteins, adenylate kinase and phage lysozyme, when they were newly solved by X-ray crystallography. The result for phage lysozyme has revealed that the prediction of a helix which is composed of helix-indifferent residues, e.g. the region 149 to 154 (Val-Ile-Thr-Thr-Phe-Arg) of phage lysozyme (Matthews & Remington, 1974), would be very difficult by the methods based on either singlet or doublet information unless the helical wheel effect (Schiffer & Edmundson, 1967) or some triplet information was included. After such modifications have been made, it may be seen that the percentage of correct residues in helix prediction is not noticeably improved but that the strength of the helix prediction function seems to be improved as a whole, and leads to the reasonable explantation of the formation of supersecondary structures presented in the accompanying paper (Nagano, 1977). The percentages of agreement between prediction and observation for 36 proteins used in the present analysis are listed in Table 1. For the threshold values used for the analysis of super-secondary structures, the values of %res.cor. (Nagano, 1973, Nagano, 1974) and correlation coefficients C (Matthews, 1975) are as follows: 78·9% (C=0·528) for helix; 70·7% (C=0·396) for loop or β-turn; 80·8% (C=0·519) for β-structure.