A New Type of φ, ψ Representation of the Protein Tertiary Structure and the Analysis of the Amino Acid Preferences for Specific Locations at Type-II β-Turn by Using 8000 Possible Kinds of Amino Acid Residues

φ, ψ Representations of three-dimensional structures of 125 globular proteins were depicted for analyzing conformational details in their secondary and tertiary structures. They can be drawn in the form of a two-dimensional diagram. The new type of representation of the protein tertiary structure can be used as a stereotyped finger printing for 125 protein molecules. It is powerful for a precise comparison of the relationship of the primary, secondary, and tertiary structures of homologous proteins. The precise or broad similarity between the patterns of proteins classified into the same family is obvious. This representation is also useful in readily recognizing all of the secondary structures as one progresses along the chain. Complicated three-dimensional structures of 125 globular proteins are easily recognized to be built up from only four secondary structures: helix, β-strand, β-turn, and unordered structure. A combination of intersegments hydrogen bonds among β-strands was also shown in the diagram...