Identification of secondary structures in globular proteins ‐ a new algorithm*

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Abstract
A new algorithm was developed for identifying helices, extended structures, and bends from the positions of the .alpha.-C atoms using the virtual bond approach. The parameters used are 2 virtual bond angles (.delta.1 and .delta.2), the virtual dihedral angle (.theta.), and the distance (D) between the terminal .alpha.-C atoms of the tripeptide. The criteria for classification were worked out by model building as well as from proteins whose complete secondary structures are known. These criteria are as follows: .theta. .ltoreq. 60.degree. and (.delta.1 + .delta.2) .ltoreq. 230.degree. for a bend, for a helix, successive .theta. should not differ by more than 30.degree., and for an extended structure, the cumulative deviation of the above parameters should not vary by more than 20% from the ideal extended chain. The method developed was applied successfully to 3 proteins wherein the coordinates of .alpha.-C atoms alone are known and a complete mapping of the secondary structures was obtained. One interesting observation is that the percentage of residues not taking part in helices, extended structures, and bends is very small.sbd.of the order of 4%.