N cap explained

The term N cap (N-cap, Ncap) describes an amino acid in a particular position within a protein or polypeptide.^{[1] [2] [3] [4] [5] [6]} 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

References

1. Richardson. JM. Richardson DC . Amino acid preferences for specific locations at the ends of alpha-helices. Science. 1988. 240. 4859. 1648–1652. 10.1126/science.3381086. 3381086. 1988Sci...240.1648R. 38467101.
2. Presta. LG. Rose GD . Helix Caps. Science. 1988. 240. 4859. 1632–1641. 10.1126/science.2837824. 2837824. 1988Sci...240.1632P.
3. Doig. AJ. MacArthur MW . Structures of N-termini of helices in proteins. Protein Science. 1997. 6. 1. 147–155. 10.1002/pro.5560060117. 9007987. 2143508.
4. Aurora. R. Rose GD . Helix Capping. Protein Science. 1998. 7. 1. 21–38. 10.1002/pro.5560070103. 9514257. 2143812.
5. Gunasekaran. K. Nagarajam HA . Stereochemical punctuation marks in protein structure. Journal of Molecular Biology. 1998. 275. 5. 917–932. 10.1006/jmbi.1997.1505. 9480777.
6. Leader. DP. Milner-White EJ . The structure of the ends of helices in globular proteins. Proteins. 2011. 79. 3. 1010–1019. 10.1002/prot.22942. 21287629. 22240314.