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The Automated Protein Structure Analysis (APSA) method is used for theclassification of supersecondary structures. Basis for the classification isthe encoding of three-dimensional (3D) residue conformations into a 16-lettercode (3D-1D projection). It is shown that the letter code of the protein makesit possible to reconstruct its overall shape without ambiguity (1D-3Dtranslation). Accordingly, the letter code is used for the development ofclassification rules that distinguish supersecondary structures by theproperties of their turns and the orientation of the flanking helix or strandstructures. The orientations of turn and flanking structures are collected inan octant system that helps to specify 196 supersecondary groups for(alpha,alpha)-, (alpha,beta)-, (beta,alpha)-, (beta,beta)-class. 391 proteinchains leading to 2499 super secondary structures were analyzed. Frequentlyoccurring super secondary structures are identified with the help of the octantclassification system and explained on the basis of their letter andclassification codes.

Classification of Supersecondary Structures in Proteins Using the Automated Protein Structure Analysis Method