Peptide sequence calculator
Enter a peptide sequence in one-letter amino acid code to compute its length, average molecular weight, theoretical isoelectric point (pI), net charge at pH 7.4, and grand average of hydropathy (GRAVY). Calculations run in the browser; nothing is sent to a server.
How the calculation works
Average molecular weight. Each residue contributes its average residue mass (the amino acid mass minus one water molecule). One water molecule (18.015 Da) is added back for the free N- and C-termini: MW = Σ residue masses + 18.015.
Net charge. For each ionizable group the Henderson–Hasselbalch equation gives the fractional charge. Basic groups (N-terminus, K, R, H) contribute +1 / (1 + 10pH − pKa); acidic groups (C-terminus, D, E, C, Y) contribute −1 / (1 + 10pKa − pH). The pKa values used are N-term 8.6, C-term 3.6, K 10.8, R 12.5, H 6.5, D 3.9, E 4.1, C 8.5, Y 10.1.
Isoelectric point. The pI is the pH at which the computed net charge is zero. It is found by bisection between pH 0 and 14.
GRAVY. The sum of Kyte–Doolittle hydropathy values divided by the number of residues.
Worked example
The 15-residue sequence GEPPPGKPADDAGLV gives an average molecular weight of 1419.55 Da, a theoretical pI of 3.88, a net charge of -2.06 at pH 7.4, and a GRAVY score of -0.693. These values are computed by the same code that runs in the calculator above.
Limitations
- Only the 20 standard amino acids are supported.
- D-amino acids, non-natural residues, and modified peptides (acetylated, amidated, lipidated, cyclized, PEGylated) are not supported; results for such peptides would be wrong.
- pI and net charge are theoretical values based on one pKa set; other tables give different results.
- Average molecular weight is not the same as a monoisotopic mass measured by mass spectrometry.
- Disulfide bonds are not modelled; each bond would reduce the mass by about 2 Da.
Frequently asked questions
Why does the calculated molecular weight differ from a mass spectrometry result?
This tool reports the average molecular weight from average residue masses. Mass spectrometry often reports the monoisotopic mass, and real samples can carry counter-ions, salts, or modifications. Differences of one dalton or more are common.
Which amino acids are supported?
Only the 20 standard amino acids in one-letter code. D-amino acids, non-natural residues, and modifications such as acetylation, amidation, lipidation, PEGylation, or cyclization are not supported, and the tool rejects unknown letters.
How accurate is the isoelectric point?
The pI is a theoretical value computed from a single published set of pKa values. Different pKa tables give different results, and folding, neighbouring residues, and modifications shift real values. It is an estimate for comparison, not a measured property.
What does a positive or negative GRAVY score mean?
GRAVY is the average Kyte-Doolittle hydropathy of all residues. Positive values indicate a more hydrophobic sequence and negative values a more hydrophilic sequence. It is a simple index and does not predict solubility on its own.