Amino-acid composition

How much of each residue the protein is made of — with the atomic composition, and the absences a bar chart hides.

What it doesCopy Anchor Link

Composition is where several practical questions are answered at once, and most of them are answered by an absence. No tryptophan and no tyrosine means the extinction coefficient at 280 nm is close to zero and you cannot measure the concentration that way. No cysteine means no disulfides and no maleimide chemistry. A very high proportion of one residue is the signature of a low-complexity region.

Each residue's count and its share of the length are given, alongside the derived atomic composition and the molecular formula. Absences are stated in words rather than left as bars that happen to be at zero among eighteen that are not — which is the one thing a bar chart is worst at showing.

Percentages are of the total length, so a sequence containing non-standard or ambiguous residues sums to under 100. That is deliberate: the alternative is renormalising over the residues we could identify, which quietly reports a composition for a sequence you do not have.

When you'd use thisCopy Anchor Link

• Before measuring concentration by absorbance. The extinction coefficient is a function of tryptophan, tyrosine and cystine content, and a protein short of all three cannot be quantified at 280 nm.
• Before choosing a labelling chemistry. Cysteine and lysine counts decide whether a thiol- or amine-reactive label will be specific or will hit twenty sites.
• When a construct behaves oddly. An unusual proline, glycine or charged-residue content explains a lot of anomalous migration and anomalous solubility.
• To sanity-check a translation. A composition unlike any real protein usually means the reading frame or the genetic code is wrong.

What this computesCopy Anchor Link

• The count and the percentage of each of the twenty standard residues, over the analysed target.
• Which residues are absent entirely, stated explicitly.
• The atomic composition and molecular formula — carbon, hydrogen, nitrogen, oxygen and sulfur — derived from the residue counts and the loss of water at each peptide bond.
• Molecular weight, from the same counts.
• Grouped totals where the group is what you act on: acidic, basic, polar and hydrophobic content.

What it does not doCopy Anchor Link

It counts the sequence you gave it. Post-translational modification, signal-peptide cleavage, and proteolytic processing all change the composition of the protein that actually exists, and none of them is inferred here. Non-standard residues are counted as themselves and are not folded into the twenty.