The CBE abbreviations list includes two different abbreviations for amino acids with two different meanings:
Follow manuscript for upper and lowercase and allow the author's definition.
The following abbreviations for amino acids do not have to be defined. One-letter codes are given in parentheses.
| alanine | Ala | (A) |
| arginine | Arg | (R) |
| asparagine | Asn | (N) |
| aspartic acid | Asp | (D) |
| cysteine | Cys | (C) |
| glutamic acid | Glu | (E) |
| glutamine | Gln | (Q) |
| glycine | Gly | (G) |
| histidine | His | (H) |
| isoleucine | Ile | (I) |
| leucine | Leu | (L) |
| lysine | Lys | (K) |
| methionine | Met | (M) |
| phenylalanine | Phe | (F) |
| proline | Pro | (P) |
| serine | Ser | (S) |
| threonine | Thr | (T) |
| tryptophan | Trp | (W) |
| tyrosine | Tyr | (Y) |
| valine | Val | (V) |
Other amino acids are known by their common names and have only 3-letter codes. These should always be defined:
| citrulline | Cit |
| homocysteine | Hey |
| hydroxyproline | Hyp |
| ornithine | Orn |
| thyroxine | Thx |
Single-letter abbreviations should only be used in tabular information or as part of sequences. In text, use the three-letter abbreviation or the full word instead. Do not mix single-letter and 3-letter amino acid abbreviations.
Amino acids with the prefix "nor-" are abbreviated with a capital "N" at the beginning of the standard 3-letter abbreviation. For example, norleucine is abbreviated "Nle".
Some exceptions:
A free amino group (NH2) may be placed on the left end of a sequence, and a free carboxyl group (COOH) on the right end of a sequence peptide.
NH2-Gly-Ile-Val-Glu-Gln-Cys-Cys-Ala-Ser-Val-Cys-Ser-Leu-Tyr-COOH
The same left-right convention applies to sequences using single-letter abbreviations.
NH2 is sometimes given as "N terminus;" COOH is sometimes given as "C terminus." Change to "NH2 terminus" and "COOH terminus," respectively.
When the NH2 group appears on the right of a sequence, it has a meaning different than an amino end. Do not change.An amino acid plus a number refers to the amino acid by codon number (if known) or by protein residue. The number may be superscripted or positioned on the line, as long as usage is consistent throughout the paper.
Arg506
Arg506→Gln
Arg506Gln
R506Q
or
Arg506
Arg506→Gln
Arg506Gln
R506Q
For substituted peptides in which a particular amino acid is replaced, superscript numbers are preferred, when the 3-letter amino acid abbreviation is used. For example, a citrulline substituted into the number 8 position of the peptide vasopression may be rewritten as "[Cit8]vasopressin". This may also be written as "[8-citrulline]vasopressin".
last edited 10/06/03