On alpha-helices terminated by glycine. 2. Recognition by sequence patterns.
Consensus sequence patterns were constructed to describe helix ends with a characteristic conformation caused by specific three-center hydrogen bonds. This special type of hydrogen bond pattern comprises about one third of all helices and mostly contains glycine with a positive torsion angle phi at the helix ends. After a simple clustering procedure 6 resulting consensus sequence patterns were able to identify 501 out of 575 helix ends in the Brookhaven Protein Data Bank, showing the above-mentioned features. The patterns did not detect any false segment, but numerous sequence segments not identified by structural criteria were recognized. It is likely that they are indeed helices terminated by glycine with a positive torsion angle phi.
Bork
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Zentralinstitut für Molekularbiologie, Berlin-Buch, Germany.
Preissner
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D000595:Amino Acid Sequence; D016208:Databases, Factual; D004798:Enzymes / Q000737:chemistry; D005998:Glycine; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry
D004798:Enzymes; D011506:Proteins; D005998:Glycine