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.

About one third of all helices is terminated by residues with a positive torsion angle phi. 74% of them are glycines. This strong propensity can be explained by typical bifurcated three-center hydrogen bonds which are only compatible with a positive torsion angle phi, causing helix termination. An algorithm was developed to identify these structural features in alpha-helices. 158 out of 456 helices in 79 different well-refined protein structures examined in our analysis were found to have a glycine with this special conformation which have been conserved remarkably during evolution.

On the basis of 8 tryptophan synthase beta subunits (EC 4.2.1.20) consensus patterns were constructed comprising two conserved motifs. Screening of the SWISSPROT protein sequence database with these patterns indicates similarities with O-acetylserine sulfhydrolases (EC 4.2.99.8), threonine synthases (EC 4.2.99.2), L- and D-serine dehydratases (EC 4.2.1.13/EC 4.2.1.14) and threonine dehydratases (EC 4.2.1.16). Using multiple alignment procedures the similar regions could be extended. In connection with their pyridoxal-phosphate-binding-capacity and their positions in biochemical pathways evolutionary relationships among these enzymes are discussed.