Amino acid codes

A residue is an amino acid as it sits inside a chain: one water lighter than the free amino acid, because each peptide bond gives off a water molecule. To get the mass of a peptide, add its residue masses and then add one water for the two free ends: 18.01056 Da monoisotopic, 18.01524 Da average.

Worked example, Gly-His-Lys (GHK), the peptide in copper tripeptide-1:

A mass spectrometer would show the singly protonated ion, [M+H]⁺, at 340.18589 + 1.00728 = 341.19317. Our peptide calculator does this sum for any sequence.

Common changes to the ends, calculated from the element masses:

The monoisotopic mass uses the most abundant isotope of each element (¹²C, ¹H, ¹⁴N, ¹⁶O, ³²S). It is what a high-resolution mass spectrometer sees for a small peptide. The average mass uses the natural mixture of isotopes. It is the figure for weighing, molarity and larger molecules.

Average masses depend on the atomic weights used, and these have been revised over the years. The values above are ExPASy's; other tables can differ in the third or fourth decimal place, most visibly for the two sulfur-containing residues, cysteine and methionine. Compare like with like.

• Leucine and isoleucine have the same formula and the same mass. Mass alone cannot tell them apart.
• Glutamine and lysine differ by 0.03638 Da (128.09496 against 128.05858). A low-resolution instrument shows them as one mass.

That is why a certificate states the sequence as well as the mass: the mass confirms the sequence, it does not reveal it.

Several amino acids share a first letter, so some codes come from elsewhere. Memory aids people use, not the official reasons: F for phenylalanine ("fenylalanine"), R for arginine ("aRginine"), Y for tyrosine ("tYrosine"), W for tryptophan (its double ring, as "W"), D and E for the two acids, aspartic and glutamic, N for asparagine ("asparagiNe"), Q for glutamine ("Q-tamine"), and K for lysine, the letter before L, which leucine took.

Twenty are the standard set used in the proteins of every living thing. Selenocysteine is counted as the 21st and pyrrolysine as the 22nd; some organisms build them into proteins through a special reading of the genetic code. Many more amino acids exist outside proteins, and synthetic peptides often contain them.

Sequences run from the N-terminus on the left to the C-terminus on the right, in either code. GHK and Gly-His-Lys are the same peptide; KHG is a different one with the same mass. What are peptides? explains the peptide bond and the shorthand for modified ends.

We supply peptides to businesses and institutions in Egypt, not to individuals. Each product page gives the product's sequence, formula and mass.