Sequences are written to a convention set by the IUPAC-IUB Joint Commission on Biochemical Nomenclature. Reading them correctly matters: a reversed or mistyped sequence gives a different molecule, even when its mass is identical.
Direction: N-terminus to C-terminus
Sequences are always written from the free amino end (N-terminus) on the left to the free carboxyl end (C-terminus) on the right. GHK means glycine carries the free amine and lysine carries the free acid. KHG has the same composition and mass, but it is a different peptide.
Three-letter codes
Three-letter codes are joined by hyphens, which stand for peptide bonds: Gly-His-Lys. Terminal groups are written explicitly when it matters. H- marks the free amine, -OH the free acid, Ac- an acetylated N-terminus and -NH2 a C-terminal amide. So Ac-Gly-His-Lys-NH2 is a capped tripeptide.
One-letter codes
One-letter codes are compact and are the norm in databases and long sequences: GEPPPGKPADDAGLV. They are usually written without separators, often in blocks of ten for readability.
| Amino acid | 3-letter | 1-letter | Amino acid | 3-letter | 1-letter |
|---|---|---|---|---|---|
| Alanine | Ala |
A |
Leucine | Leu |
L |
| Arginine | Arg |
R |
Lysine | Lys |
K |
| Asparagine | Asn |
N |
Methionine | Met |
M |
| Aspartic acid | Asp |
D |
Phenylalanine | Phe |
F |
| Cysteine | Cys |
C |
Proline | Pro |
P |
| Glutamic acid | Glu |
E |
Serine | Ser |
S |
| Glutamine | Gln |
Q |
Threonine | Thr |
T |
| Glycine | Gly |
G |
Tryptophan | Trp |
W |
| Histidine | His |
H |
Tyrosine | Tyr |
Y |
| Isoleucine | Ile |
I |
Valine | Val |
V |
Codes that cause trouble
- Ambiguity codes.
B(Asx: Asp or Asn),Z(Glx: Glu or Gln) andX(any) appear in sequencing results, but they have no single formula. The calculators reject them rather than guess. - Look-alike letters.
Dis aspartic acid andEis glutamic acid.NandQare their amides, andKis lysine, not potassium. Mixing these up is the most common transcription error. - Leucine and isoleucine have identical formulas and masses, so mass alone cannot tell them apart.
- Stereochemistry. Some authors mark D-amino acids with a
D-prefix or lower-case letters. D- and L-forms have the same mass, but they are different molecules. Record them explicitly. - Selenocysteine (U) and pyrrolysine (O) are genuine amino acids, but they are outside the 20 standard residues handled here.
Length, bonds and a quick size check
A linear peptide of n residues has n − 1 peptide bonds. The average residue mass across proteins is about 110 g/mol, so n × 110 is a quick sanity check against a calculated molecular weight. Short peptides rich in glycine or alanine will come in lighter, and those rich in Trp, Tyr or Arg heavier.
Worked example
Gly-Glu-Pro-Pro-Pro-Gly-Lys-Pro-Ala-Asp-Asp-Ala-Gly-Leu-Val converts to GEPPPGKPADDAGLV: 15 residues and 14 peptide bonds. The size estimate is 15 × 110 ≈ 1650 g/mol. The exact average mass is 1419.56 g/mol, lighter because the sequence is rich in small residues (Gly, Ala, Pro).