N cap

{{Short description|Amino acid}}

The term N cap (N-cap, Ncap) describes an amino acid in a particular position within a protein or polypeptide.{{cite journal|last=Richardson|first=JM|author2=Richardson DC |title=Amino acid preferences for specific locations at the ends of alpha-helices|journal=Science|year=1988|volume=240|issue=4859|pages=1648–1652|doi= 10.1126/science.3381086|pmid=3381086|bibcode=1988Sci...240.1648R|s2cid=38467101}}{{cite journal|last=Presta|first=LG|author2=Rose GD |title=Helix Caps|journal=Science|year=1988|volume=240|issue=4859|pages=1632–1641|doi= 10.1126/science.2837824|pmid=2837824|bibcode=1988Sci...240.1632P}}{{cite journal|last=Doig|first=AJ|author2=MacArthur MW |title=Structures of N-termini of helices in proteins|journal=Protein Science|year=1997|volume=6|issue=1|pages=147–155|doi= 10.1002/pro.5560060117|pmid=9007987|pmc=2143508}}{{cite journal|last=Aurora|first=R|author2=Rose GD |title=Helix Capping|journal=Protein Science|year=1998|volume=7|issue=1|pages=21–38|doi= 10.1002/pro.5560070103|pmid=9514257|pmc=2143812}}{{cite journal|last=Gunasekaran|first=K|author2=Nagarajam HA |title=Stereochemical punctuation marks in protein structure|journal=Journal of Molecular Biology|year=1998|volume=275|issue=5|pages=917–932|doi= 10.1006/jmbi.1997.1505|pmid=9480777|url=http://repository.ias.ac.in/4151/1/320.pdf}}{{cite journal|last=Leader|first=DP|author2=Milner-White EJ |title=The structure of the ends of helices in globular proteins|journal=Proteins|year=2011|volume=79|issue=3|pages=1010–1019|doi= 10.1002/prot.22942|pmid=21287629|s2cid=22240314}} The N cap residue of an alpha helix is the first amino acid residue at the N terminus of the helix. More precisely, it is defined as the first residue (i) whose CO group is hydrogen-bonded to the NH group of residue i+4 (or sometimes residue i+3). Because of this it is sometimes also described as the residue prior to the helix.

Capping motifs are those often found at the N cap. Asx turns, ST turns, and asx motifs are often found at such situations, with the asx or serine or threonine residue at the N cap.

The C cap is the corresponding amino acid residue at the other end of the helix