The term C cap (C-cap, Ccap) describes an

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

in a particular position within a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

polypeptide Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A p ...

.{{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 C cap residue of an

alpha helix The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues e ...

is the last

residue at the

C terminus The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...

of the helix. More precisely, it is defined as the last residue (i) whose NH group is

hydrogen-bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing ...

ed to the CO group of residue i-4 (or sometimes residue i-3). Because of this it is sometimes also described as the residue following the helix. Certain motifs occur commonly at or around the C cap, notably the

Schellman loop Schellman loops (also called Schellman motifs or paperclips) are commonly occurring structural features of proteins and polypeptides. Each has six amino acid residues (labelled residues ''i'' to ''i''+5) with two specific inter-mainchain hydrogen ...

and the

niche (protein structural motif) In the area of protein structural motifs, niches are three or four amino acid residue features in which main-chain CO groups are bridged by positively charged or δ+ groups. The δ+ groups include groups with two hydrogen bond donor atoms such as N ...

. The

N cap The term N cap (N-cap, Ncap) describes an amino acid in a particular position within a protein or polypeptide.{{cite journal, last=Leader, first=DP, author2=Milner-White EJ , title=The structure of the ends of helices in globular proteins, journal= ...

is the corresponding amino acid residue at the other end of the helix

References

Amino acids