Educational resource
1-letter vs 3-letter codes
Both alphabets describe the same twenty proteinogenic residues. They are interchangeable for those residues — but they are used for different jobs in literature, software, and on this site.
One-letter codes
One-letter codes were recommended by the IUPAC-IUB Commission on Biochemical Nomenclature (1968, with later clarifications). They are the search alphabet of Peptide Sequence Database and the default in FASTA, UniProt, GenBank protein features, and most proteomics pipelines.
Advantages: compact typing, easy substring search, short directory cards, and consistent machine parsing.
Example — oxytocin core: CYIQNCPLG.
Limitation: a single letter cannot encode D-stereochemistry, N-methylation, side-chain lipids, or non-canonical amino acids without additional rules.
Three-letter codes
Three-letter codes (Ala, Cys, Asp, …) remain the default in synthetic peptide chemistry, many pharmacopeial monographs, and spoken laboratory communication. They are easier to proofread when sequences include modifications.
Example — oxytocin display: Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2.
Display notation on this site prefers three-letter (or full residue-name) form whenever a position is not a plain L-proteinogenic residue.
Side-by-side examples
| Peptide | 1-letter (search) | Typical display |
|---|---|---|
| Oxytocin | CYIQNCPLG |
Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2 |
| Angiotensin II | DRVYIHPF |
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe |
| TRH | EHP (stand-in) |
pGlu-His-Pro-NH2 |
For TRH, the 1-letter field may still use E as a stand-in for pyroglutamate; the display field is authoritative for the true N-terminus.
Mixing alphabets
Hybrid strings such as dF-PRP… are intentional on some records: the D-residue is flagged, while neighboring standard residues stay in 1-letter form for search density. Do not assume lowercase letters always mean D-residues in external files — some DNA tools use lowercase for other reasons. On this site, a leading d or D- attached to a residue name indicates D-stereochemistry.
Lossless vs lossy conversion
Converting among the twenty standard residues is lossless in either direction. Conversion is lossy for:
Xplaceholders- lipidated lysines and other side-chain adducts
- Aib, ornithine, MeBmt, and other non-canonical residues
- pyroglutamate versus Glu/Gln
- amino alcohols and ethylamides at the C-terminus
Those details belong in display notation and modifications, not in a naïve 3-to-1 lookup table.
Recommendation
Search with 1-letter fragments. Read and cite with display notation. Filter unusual chemistry with modification tags. Verify registry identity with CAS and PubChem.