Amino acid residue

An amino acid residue is the portion of an amino acid incorporated into a polypeptide chain. For example, the A in the illustrative protein primary structure is an alanine residue, rather than a free alanine molecule floating beside the chain. Counting amino acid residues counts chain positions; repeated letters are separate positions. See IUPAC-IUB, section 3AA-16: symbols for amino-acid residues.

A tyrosine residue is an amino acid residue whose amino acid side chain can accept a phosphate group during receptor tyrosine kinase signaling. The conventional one-letter sequence symbol is $Y$.

A phosphotyrosine residue is a tyrosine residue modified by phosphorylation. Its location and surrounding protein primary structure help determine which SH2 domains can recognize it.

An amino acid side chain is the variable group attached to an amino acid alpha carbon, conventionally denoted $R$. For alanine it is $\mathrm{C}{\mathrm{H}}_3$: a carbon bonded to three hydrogen chemical atoms. In a beta strand, successive amino acid side chains alternate between the two faces in the idealized arrangement. See Clark, Douglas and Choi: amino-acid R groups.

The amino acid alpha carbon is the backbone carbon carrying the amino acid side chain in the usual protein amino acid residue. Marking successive amino acid alpha carbons is a useful way to trace a polypeptide chain, but omits intervening backbone chemical atoms. See Clark, Douglas and Choi: the central alpha carbon.

A glutamic acid residue is an amino acid residue represented by Glu or E in polypeptide sequence notation. GAA and GAG specify glutamic acid residues in the standard genetic code; the ribosome example uses GAA as its third codon. See Elzanowski and Ostell, NCBI: standard genetic code, table 1. The name denotes an incorporated chain position, as distinguished from a free amino acid molecule.