How to use the table
Tap a column heading to sort by it, again to reverse. The chips filter the twenty standard amino acids by side-chain class or show only the essential ones. On a phone the table scrolls sideways with the name column fixed. To convert a sequence between the one-letter and three-letter codes, use the one-to-three andthree-to-one converters; to see which codons encode each amino acid, see the codon table.
The columns explained
- Residue mass is the average mass an amino acid contributes inside a peptide: its molecular weight minus one water lost in forming the peptide bond. Sum the residues and add 18.015 Da for a peptide's average mass. Mono is the same for the most abundant isotopes, the value mass spectrometry reports. Thepeptide molecular weight andprotein molecular weight tools do the sum.
- MW is the molecular weight of the free amino acid, the number on the bottle.
- pI is the isoelectric point of the free amino acid, the pH at which it carries no net charge. A protein's pI depends on all its ionisable residues; calculate it with theisoelectric point tool.
- pKa side is the pKa of the side chain for the seven residues that ionise: Asp, Glu, His, Cys, Tyr, Lys and Arg. The values are the commonly tabulated ones for the free amino acid; within a folded protein they can shift by a unit or more.
- Hydropathy is the Kyte–Doolittle index, positive for hydrophobic side chains and negative for hydrophilic ones. The GRAVY calculator averages it over a sequence.
- Codons is how many of the 61 sense codons encode the amino acid in the standard genetic code.
Side-chain classes
Nonpolar aliphatic residues (Ala, Val, Leu, Ile, Met) are hydrophobic and fill the protein core. Aromatic residues (Phe, Tyr, Trp) are bulky, mostly hydrophobic, and absorb ultraviolet light at 280 nm, which is what the extinction coefficient depends on. Polar uncharged residues (Ser, Thr, Asn, Gln, Cys) form hydrogen bonds and sit at the surface or in active sites; Ser and Thr are the usual sites of phosphorylation and Cys forms disulfide bonds. Positively charged (Lys, Arg, His) andnegatively charged (Asp, Glu) residues form salt bridges and make proteins soluble.Glycine and proline are special cases: glycine has no side chain and is the most flexible residue, proline's side chain closes on its own backbone nitrogen and breaks helices.
Essential amino acids
Humans cannot synthesise nine of the twenty, so they must come from the diet: His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val, the residues ticked in the table. Arginine is conditionally essential in infancy and illness. The remaining eleven are made from intermediates of central metabolism.
Frequently asked questions
What are the 20 amino acids and their one-letter codes?
Alanine A, arginine R, asparagine N, aspartic acid D, cysteine C, glutamine Q, glutamic acid E, glycine G, histidine H, isoleucine I, leucine L, lysine K, methionine M, phenylalanine F, proline P, serine S, threonine T, tryptophan W, tyrosine Y and valine V. The letters that are not initials come from sound or convention: F for phenylalanine, W for tryptophan (double ring), K for lysine, Q for glutamine, E for glutamate, N for asparagine, D for aspartate, Y for tyrosine.
What is the difference between residue mass and molecular weight?
The molecular weight is the mass of the free amino acid. When amino acids join in a peptide bond a molecule of water, 18.015 Da, is lost, so the mass each contributes to a protein, its residue mass, is the free mass minus water. Add residue masses and one water to get a peptide mass.
Which amino acids are essential?
Nine cannot be made by the human body and must come from food: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Arginine is sometimes listed as conditionally essential.
What does the hydropathy index mean?
The Kyte–Doolittle scale scores how strongly each side chain prefers a hydrophobic environment: positive values such as isoleucine 4.5 are hydrophobic and tend to be buried or in membranes, negative values such as arginine −4.5 are hydrophilic and sit on the surface. Averaged over a window it predicts transmembrane segments.
Why do only some amino acids have a side-chain pKa?
Only seven side chains gain or lose a proton at physiological pH ranges: aspartate, glutamate, histidine, cysteine, tyrosine, lysine and arginine. Their pKa values decide the charge of a protein at a given pH, and with the terminal groups they set its isoelectric point.