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Amino Acid Composition Calculator

Count the amino acids in a protein or peptide, and calculate its GRAVY, aliphatic index and the share of basic, acidic, aromatic and sulfur-containing residues.

Formula

GRAVY=∑hKDL\mathrm{GRAVY} = \dfrac{\sum h_{\mathrm{KD}}}{L}
aliphatic index=XAla+2.9 XVal+3.9 (XIle+XLeu)\text{aliphatic index} = X_{\mathrm{Ala}} + 2.9\,X_{\mathrm{Val}} + 3.9\,(X_{\mathrm{Ile}} + X_{\mathrm{Leu}})
share=countL×100\text{share} = \dfrac{\text{count}}{L}\times 100
XX
mole percent of the residue in the sequence
hydropathy\text{hydropathy}
a scale of each amino acid's tendency to be in a hydrophobic environment

How it works

The composition of a protein says a lot about it before its structure is known. A positive GRAVY means the residues are on average hydrophobic, as in membrane proteins, and a negative one that they are hydrophilic, as in most soluble proteins. The aliphatic index, which weights alanine, valine, isoleucine and leucine, was proposed as a measure of the thermostability of globular proteins.

The counts of charged, aromatic and sulfur-containing residues help plan an experiment: aromatic residues set the absorbance at 280 nm, cysteines can form disulfides, and the balance of basic and acidic residues bears on the isoelectric point.

Worked example

Glucagon, HSQGTFTSDYSKYLDSRRAQDFVQWLMNT (29 residues).

  1. GRAVY = the sum of 29 Kyte-Doolittle values / 29 = −0.990.
  2. Aliphatic index = X(Ala) + 2.9 X(Val) + 3.9 (X(Ile) + X(Leu)) = 40.3.
  3. Basic residues (K, R): 3 of 29 = 10.3%; aromatic (F, W, Y): 5 of 29 = 17.2%.

A hydrophilic peptide (GRAVY −0.99) with a low aliphatic index of 40.3.

These are the values the calculator opens with, so you can check its output against this example.

Assumptions

  • The 20 standard amino acids. Other letters are not accepted.
  • GRAVY and the aliphatic index are summaries of the whole sequence and do not show where hydrophobic stretches lie.

Common mistakes

  • Reading a GRAVY value as a solubility prediction. It is a rough guide, and solubility depends on the fold, charge and conditions.
  • Applying the aliphatic index to a peptide or to an unfolded or membrane protein, where it was not validated.
  • Comparing values from a sequence that includes a signal peptide with one that does not.

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