An amino acid residue is the part of an amino acid that remains once it is built into a peptide. Joining two amino acids removes the elements of one water, so every unit in the chain is a residue, and a residue weighs about 18 grams per mole less than the free amino acid it came from.
- An amino acid residue is what remains of an amino acid after it joins a peptide and the elements of water are removed.
- Every unit in a peptide chain is a residue, and chain length is counted in residues.
- A residue's mass is its amino acid's mass minus one water: 18.0106 monoisotopic, 18.015 average.
- A linear peptide's mass equals the sum of its residue masses plus one water.
- Residues are numbered from the N-terminus, and all but the C-terminal residue take a -yl ending in a peptide name.
What a residue is
Snap two plastic building bricks together and each one loses a little knob where they meet. Nothing else about the bricks changes, but neither is quite the loose brick it was before. An amino acid inside a peptide is in the same position. Chemists call what is left of it a residue.
The IUPAC-IUB rules for amino acid and peptide nomenclature put it in one sentence: when two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. The same rules add that all units of a peptide chain are therefore residues. A free glycine molecule sitting in a bottle is an amino acid. The glycine inside a peptide is a glycine residue.
That is why peptide papers count length in residues. A pentapeptide has five residues. A sequence written as Tyr-Gly-Gly-Phe-Leu lists five residues from left to right, and the numbering of positions in the chain, residue 1, residue 2 and so on, starts at the amine end.
The word also turns up outside peptide chemistry, which can confuse people new to the lab. In an analytical context "residue" can mean leftover material, such as residual solvent. In sequence work it only ever means one of the units that make up the chain.
- Start with a free amino acid
- Its carboxyl meets the next amine
- One water leaves
- What remains is a residue
- Peptide mass is residues plus one water
Which atoms does a residue lose?
A residue loses the elements of one water: a hydrogen from one end and a hydroxyl from the other. Every standard amino acid carries an amine group and a carboxyl group on the same alpha carbon, plus a side chain. When a peptide bond forms, the carboxyl group of one amino acid reacts with the amine group of the next. A hydroxyl leaves from the carboxyl and a hydrogen leaves from the amine, and together they make one water molecule.
The IUPAC text spells out the three shapes a residue can take depending on its place in the chain:
- N-terminal residue: keeps its free amine but has lost the hydroxyl of its carboxyl group, written NH2-CHR-CO-.
- Internal residue: has lost both, written -NH-CHR-CO-. Most residues in a long chain look like this.
- C-terminal residue: keeps its free carboxyl but has lost a hydrogen from its amine, written -NH-CHR-COOH.
The side chain, the R in those formulas, is untouched in an ordinary peptide bond. A serine residue still has its hydroxyl and a cysteine residue still has its thiol. Our guide to the R group covers those side chains in detail.
There is one exception worth knowing. Lysine has a second amine and aspartic and glutamic acid have a second carboxyl, so they can form bonds through the side chain instead of the backbone. The IUPAC rules call these isopeptide bonds and note that such residues may not match the formulas above. The Lys-Ala isopeptide bond page walks through one.
Residue mass versus free amino acid mass
Because each peptide bond removes one water, a residue weighs less than its parent amino acid by the mass of that water. PubChem lists water at a monoisotopic mass of 18.0106 and an average molecular weight of 18.015. Subtracting it from the PubChem values for a few amino acids gives their residue masses:
| Amino acid | Free monoisotopic mass | Residue monoisotopic mass | Free average MW | Residue average MW |
|---|---|---|---|---|
| Glycine (C2H5NO2) | 75.0320 | 57.0215 | 75.07 | 57.06 |
| L-Alanine (C3H7NO2) | 89.0477 | 71.0371 | 89.09 | 71.08 |
| L-Serine (C3H7NO3) | 105.0426 | 87.0320 | 105.09 | 87.08 |
| L-Cysteine (C3H7NO2S) | 121.0197 | 103.0092 | 121.16 | 103.15 |
The formula changes the same way. Glycine is C2H5NO2; the glycine residue is C2H3NO, two hydrogens and one oxygen lighter. Every residue in the table follows that pattern.
Monoisotopic and average masses answer different questions. The monoisotopic value uses the most common isotope of each element and is what a high-resolution mass spectrometer compares against. The average value reflects natural isotope mixtures and is what you use when weighing powder. A certificate or method should say which one it quotes.
How do you get a peptide's mass from its residues?
Add the residue masses, then add one water for the two ends. A linear peptide's mass is the sum of its residue masses plus one water, because the chain as a whole still carries one free amine hydrogen at the N-terminus and one free hydroxyl at the C-terminus. Those two end pieces add up to exactly one water.
Leucine enkephalin, Tyr-Gly-Gly-Phe-Leu, makes a clean check. PubChem lists the free amino acids at these monoisotopic masses: tyrosine 181.0739, glycine 75.0320, phenylalanine 165.0790 and leucine 131.0946. Five amino acids joined in a line form four peptide bonds and release four waters. Adding the five free masses and subtracting four waters gives 555.2693. PubChem's own record for leucine enkephalin, formula C28H37N5O7, lists a monoisotopic mass of 555.2693. The two routes agree to the fourth decimal place.
The same logic explains a common beginner's error. If you add the free amino acid masses and forget the waters, a five-residue peptide comes out about 72 units too heavy. For a thirty-residue peptide the error grows past 500. Our guide to peptide molecular formula and weight covers the full calculation, including salts and terminal modifications.
Modifications change the sum. A C-terminal amide replaces the free carboxyl's hydroxyl with an amine group, and an N-terminal acetyl adds an acetyl group to the free amine. Each one shifts the total by a fixed amount, which is how a mass spectrum can show whether a modification is present. The residue masses themselves stay the same; only the end pieces change, so the correction is a single addition or subtraction at the end of the sum.
How residues are named and written
The nomenclature rules name residues from the trivial name of the amino acid, so you get a glycine residue or a lysine residue. For aspartic and glutamic acid the word acid is dropped, giving an aspartic residue and a glutamic residue.
Inside a full peptide name, every residue except the last takes a -yl ending. Glycine acylating alanine gives glycylalanine; the reverse order gives alanylglycine. Only the C-terminal residue keeps its full amino acid name. In the three-letter and one-letter shorthand, residues are written from the N-terminus on the left to the C-terminus on the right, which is the direction a peptide sequence is always read.
The rules also allow a residue's charge state to be named when it matters. A lysine residue carrying an extra proton can be called a lysinium residue, and a deprotonated aspartic residue an aspartate residue. Most papers skip this and let the pH of the solution imply it.
Residue numbers make it easy to point at one spot in a chain. The IUPAC example N5.4-methyloxytocin means a methyl group on nitrogen 5 of the residue at position 4 of oxytocin. Researchers use the plainer form in practice: Ser-15 or Cys-2, the residue type followed by its position.
Why do residues matter in the lab?
Residues matter because mass spectrometry reads peptides one residue mass at a time. When a peptide breaks apart inside a tandem instrument, neighboring fragment ions differ by the mass of one residue. Reading those gaps is how a sequence can be confirmed, and it is why software for peptide identification stores residue masses, not free amino acid masses. The LC-MS identity testing guide shows how that comparison is used in practice.
Residue counts also set expectations for purity work. A longer chain offers more places for a residue to be missing, doubled or modified during synthesis, and each of those errors shows up as a mass difference equal to one residue or one modification. When a certificate reports an observed mass beside a theoretical one, the theoretical figure was built from residue masses plus one water.
For our own vials, identity and purity results appear only once the certificate for that lot is published. The certificate index lists what is available.
FOR LABORATORY AND IN-VITRO RESEARCH USE ONLY. NOT FOR HUMAN OR ANIMAL CONSUMPTION.
Common questions
Is a residue the same as an amino acid?
Why is a residue 18 lighter than its amino acid?
How many residues does a peptide have?
What does N-terminal residue mean?
More science guides
Sources
- IUPAC-IUB JCBN, Nomenclature and Symbolism for Amino Acids and Peptides, 3AA-11 to 3AA-13. Definition of a peptide and peptide bond, amino-acid residues, N- and C-terminal residues, and how peptides are named.
- PubChem compound record: Glycine. Formula C2H5NO2 and monoisotopic and average masses.
- PubChem compound record: L-Alanine. Formula and masses used for the residue table.
- PubChem compound record: L-Serine. Formula and masses used for the residue table.
- PubChem compound record: L-Cysteine. Formula and masses used for the residue table.
- PubChem compound record: Water. Monoisotopic mass 18.0106 and molecular weight 18.015.
- PubChem compound record: Leucine enkephalin. Formula C28H37N5O7 and monoisotopic mass 555.2693 used in the worked check.
- PubChem compound record: L-Tyrosine. Monoisotopic mass used in the leucine enkephalin sum.
- PubChem compound record: L-Phenylalanine. Monoisotopic mass used in the leucine enkephalin sum.
- PubChem compound record: L-Leucine. Monoisotopic mass used in the leucine enkephalin sum.
