Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales.

Today there are several different experimental scales for the intrinsic alpha-helix as well as beta-strand propensities of the 20 amino acids obtained from the thermodynamic analysis of various model systems. These scales do not compare well with those extracted from statistical analysis of three-dimensional structure databases. Possible explanations for this could be the limited size of the databases used, the definitions of intrinsic propensities, or the theoretical approach. Here we report a statistical determination of alpha-helix and beta-strand propensities derived from the analysis of a database of 279 three-dimensional structures. Contrary to what has been generally done, we have considered a particular residue as in alpha-helix or beta-strand conformation by looking only at its dihedral angles (phi-psi matrices). Neither the identity nor the conformation of the surrounding residues in the amino acid sequence has been taken into consideration. Pseudoenergy empirical scales have been calculated from the statistical propensities. These scales agree very well with the experimental ones in relative and absolute terms. Moreover, its correlation with the average of the experimental scales for alpha-helix or beta-strand is as good as the correlations of the individual experimental scales with the average. These results show that by using a large enough database and a proper definition for the secondary structure propensities, it is possible to obtain a scale as good as any of experimental origin. Interestingly the phi-psi analysis of the Ramachandran plot suggests that the amino acids could have different beta-strand propensities in different subregions of the beta-strand area.