Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
Lobanov M.Y. Pereyaslavets L.B. Likhachev I.V. Matkarimov B.T. Galzitskaya O.V.
January 2021Elsevier B.V.
Computational and Structural Biotechnology Journal
2021#195960 - 5968 pp.
The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic residues were analyzed for 511 282 pairs in 35 493 protein structures sharing less than 50% identity. Pairs with a parallel arrangement of aromatic residues made up 6.2% of all possible ones, which was twice as much as expected. Pairs with a perpendicular arrangement of aromatic residues made up 25%. We demonstrate that the most favorable arrangement was at an angle of 60° between the interacting aromatic residues. Among all possible aromatic pairs, the His-His pair was twice as frequent as expected, and the His-Phe pair was less frequent than expected. A server (CARP – Contacts of Aromatic Residues in Proteins) has been created for calculating essential structural features of interacting aromatic residues in proteins: http://bioproteom.protres.ru/arom_q_prog/.
Aromatic residues , Conformation , Exhaustive enumeration , Identity , Protein Data Bank , Server , Stacking
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Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Moscow Region, Russian Federation
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, 142290, Moscow Region, Russian Federation
National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290, Moscow Region, Russian Federation
Institute of Protein Research
Institute of Mathematical Problems of Biology
National Laboratory Astana
Institute of Theoretical and Experimental Biophysics
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