A NEW-TYPE OF PHI,PSI-REPRESENTATION OF THE PROTEIN TERTIARY STRUCTURE AND THE ANALYSIS OF THE AMINO-ACID PREFERENCES FOR SPECIFIC LOCATIONS AT TYPE-II BETA-TURN BY USING 8000 POSSIBLE KINDS OF AMINO-ACID-RESIDUES

phi, psi Representations of three-dimensional structures of 125 globul ar proteins were depicted for analyzing conformational details in thei r secondary and tertiary structures. They can be drawn in the form of a two-dimensional diagram. The new type of representation of the prote in 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 ho mologous proteins. The precise or broad similarity between the pattern s of proteins classified into the same family is obvious. This represe ntation is also useful in readily recognizing all of the secondary str uctures as one progresses along the chain. Complicated three-dimension al structures of 125 globular proteins are easily recognized to be bui lt up from only four secondary structures: helix, beta-strand, beta-tu rn, and unordered structure. A combination of intersegments hydrogen b onds among beta-strands was also shown in the diagram. In order to dem onstrate the usefulness of the diagram, 195 type-II beta-turns were ex tracted from 125 proteins using the new type of two-dimensional phi, p si diagrams. Their amino acid sequences were surveyed so as better to understand amino acid preferences previously observed. For their analy sis, a normalized preference (NP) value of an amino acid residue at a particular position of the secondary structure is defined as the ratio of the average percentage composition at the position based on averag e percentage composition at large. The statistical significance of the NP-value used in this study is more simple and clearer than that of t he d-test based on a normal distribution, which was used in the previo us study. It is clearly shown that a high NP-value (5.0) of a single P residue for the position i+1 of the type-II beta-turn is an average p reference of a variety of P residues in the middle of triplets consist ing of consecutive amino acid residues. The NP-values of P residues, i n the middle of 25 particular triplets are outstandingly high. Out of 400 possible P residues 322 kinds of P residues were found in 125 prot eins. A remarkable high NP-value (8.8) of a single G residue for the p osition i+2 is also an average preference of G residues in the middle of various triplets.