Amino acid codes

A residue is an amino acid as it sits inside a chain. Each peptide bond releases one molecule of water, so a residue weighs one water less than the free amino acid. To find a peptide's mass, add the residue masses of its sequence, then add one water for the two free ends: 18.01056 Da monoisotopic, 18.01524 Da average.

KPV is a tripeptide in our research range. Its sequence is Lys-Pro-Val.

A mass spectrometer would show the singly protonated ion, [M+H]⁺, at 342.22669 + 1.00728 = 343.23397. The peptide calculator does the same sum for any sequence.

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, for molarity and for large molecules.

Average masses depend on the atomic weights used, and these have been revised over the years. The values here are ExPASy's. Other tables can differ in the third or fourth decimal place, most of all for the two sulfur-containing residues, cysteine and methionine. Always compare like with like.

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

That is why a certificate gives the sequence as well as the mass. The mass confirms a sequence; it does not reveal one.

Several amino acids share an initial, so some one-letter codes were assigned differently. These are memory aids, not the official reasoning: F for phenylalanine (as in "fenylalanine"), R for arginine ("aRginine"), Y for tyrosine ("tYrosine"), W for tryptophan (the double ring drawn as a W), N for asparagine ("asparagiNe"), Q for glutamine ("Q-tamine"), D and E for the two acids, aspartic and glutamic, and K for lysine, next to L, which leucine already held.

Selenocysteine is the only residue on this page whose monoisotopic mass is larger than its average mass. The reason is selenium: its most abundant isotope, ⁸⁰Se, is heavier than its average atomic weight.

Twenty form the standard set used in the proteins of all living things. 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.

A sequence runs from the N-terminus on the left to the C-terminus on the right, in either code. KPV and Lys-Pro-Val are the same peptide; VPK is a different one with the same mass. What are peptides? explains the peptide bond and the shorthand for modified ends.

Each of our product pages gives the product's sequence, formula and mass. We supply businesses and institutions in Iraq, not individuals.