Linde D. M.
Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 119832, Moscow, Russia, fax (7-095) 2450857, E-mail: dlinde@ru.oracle.com
We have analyzed the contacts between nonhomologous multisubunit proteins
and complexes from Brookhaven data bank. We have analyzed distribution
of amino acids in the contact area for 122 protein sequences and calculated
frequencies of amino acid residues contacts in ternary structure. The pair
of residues is considered as a contact if the minimum distance between
their atoms is less than 2.8 A. We have compared the calculated frequencies
of external contacts in protein complexes with contacts inside the tertiary
structure (internal contacts) extracted from Protein contacts atlas available
via Internet. The contacts CC, VV, WW, II, LL, FF occur more frequently
for both samples than expected on the random basis, but their frequency
in tertiary structure is higher. The pairs RN, RE, AV, CC, EK, IL, IF,
IV, LL, LF, LV are statistically more frequent comparing to the average
values in both samples.
The most/less frequent contacts are the same in tertiary and ternary
structure for 16 cases from 32 possible. There are no cases where statistically
frequent contact for one sample is rare for another. The most preferable
contacts in both samples are contacts between hydrophobic amino acids or
between polar amino acids. Pairings between individual amino acid residues
are also very frequent. The size of amino acid residue plays an important
role in forming the sample. The role of large aromatic residues in protein
contacts is discussed.