The clustering of protein structures from the Protein Data Bank (PDB) was performed. The analysis of the conformation of interacting aromatic residues was carried out for 511 282 pairs in 35 493 protein structures with 50% identity. In proteins, pairs with parallel arrangement of aromatic residues make up 6.2% of all possible ones, which is twice as much as expected, pairs with perpendicular arrangement of aromatic residues make up 25%. We have demonstrated that 60° is the most favorable arrangement of aromatic residues in pairs, as in proteins, and for an exhaustive enumeration of all conformations of aromatic residues in pairs. Among all possible aromatic pairs, the His-His pair is found in proteins twice as often as the expected frequency of the pairs, and the His-Phe pair turned out to be less than expected one. A server (CARP – Contacts of Aromatic Residues in Proteins) has been created for calculating the general parameters/properties of interacting aromatic residues in globular proteins http://bioproteom.protres.ru/arom_q_prog/.

Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. In turn, their amino acid composition remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage.