Amino acid composition of parallel helix-helix interfaces.
Amino acids at helix-helix parallel interfaces influence arrangement of helices and interhelical angles. Parallel interfaces in 79 proteins were considered. Location of amino acids at the positions analogous to a and d in GCN4 leucine zipper nomenclature shows that certain combinations of amino acids characteristic for parallel packing occur more often than could be expected by chance. Repeating sequence combinations occur at a and d positions of parallel helix-helix interfaces with similar values of interhelical angles not only in homologous proteins but also within the same protein and in nonhomologous proteins. Within each group of observed combinations correlation exists between the size of amino acid and magnitude of the interhelical angle.
Kurochkina
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Department of Biophysics, The School of Theoretical Modeling, P.O. Box 15676, Chevy Chase, MD 20825, USA. info@schtm.org
D020816:Amino Acid Motifs / Q000235:genetics; D000596:Amino Acids / Q000032:analysis*; D000818:Animals; D016350:Leucine Zippers; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D000596:Amino Acids