How to Use This Calculator
Type or paste the sequence in one-letter amino acid code, for example GHK, then click Calculate. The calculator ignores spaces and line breaks, so a sequence copied across several lines works. The result shows the sequence length, the average molecular weight in daltons, the net charge at pH 7.0 and the count and percentage of each amino acid.
How the Net Charge Is Worked Out
Net charge depends on pH, so this calculator reports it at pH 7.0. It adds up the charge on the free N-terminus and the basic side chains of lysine, arginine and histidine, and subtracts the charge on the free C-terminus and the acidic side chains of aspartate, glutamate, cysteine and tyrosine, each from its pKa using the Henderson-Hasselbalch relation with the EMBOSS pKa set. Because the method and the pH are fixed and stated, the number is reproducible; a tool that uses a different pKa set or pH can report a slightly different value.
Average Residue Masses Used for Polypeptide Molecular Weight
The molecular weight is the sum of the average residue masses in the sequence plus one water (18.02). The table lists the residue mass for each of the 20 standard amino acids, in daltons.
| Amino acid | Code | Residue mass (Da) |
|---|---|---|
| Glycine | G | 57.05 |
| Alanine | A | 71.08 |
| Serine | S | 87.08 |
| Proline | P | 97.12 |
| Valine | V | 99.13 |
| Threonine | T | 101.10 |
| Cysteine | C | 103.14 |
| Leucine | L | 113.16 |
| Isoleucine | I | 113.16 |
| Asparagine | N | 114.10 |
| Aspartic acid | D | 115.09 |
| Glutamine | Q | 128.13 |
| Lysine | K | 128.17 |
| Glutamic acid | E | 129.12 |
| Methionine | M | 131.19 |
| Histidine | H | 137.14 |
| Phenylalanine | F | 147.18 |
| Arginine | R | 156.19 |
| Tyrosine | Y | 163.18 |
| Tryptophan | W | 186.21 |
Example: the sequence GAS is 57.05 + 71.08 + 87.08 = 215.21, and 215.21 + 18.02 = 233.23 Da. Values are rounded to two decimals, so another tool may differ in the last digit.
Where This Fits Alongside Other Research Tools
The Molecular Weight Calculator covers the weight on its own. This page adds the net charge and the amino acid composition for the same sequence, so you can read all three at once.
Who Should Use This
Researchers who have an amino acid sequence and want its molecular weight, net charge and composition in one place, in one-letter code.
What This Calculator Does
The Polypeptide Calculator reads a one-letter amino acid sequence and returns the sequence length, the average molecular weight in daltons, the net charge at pH 7.0 computed with the EMBOSS pKa set, and the count and percentage of each amino acid.
Formula Used
Molecular weight (Da) = sum of average residue masses + 18.01528 (one water for the free termini)Net charge at pH 7.0 = [N-terminus and K, R, H positive terms] + [C-terminus and D, E, C, Y negative terms], each from its pKa by the Henderson-Hasselbalch relationComposition = count of each amino acid, and that count as a percentage of the sequence lengthExample Calculation
Limitations
This is a sequence-property calculator, not guidance on what to use. It assumes a linear peptide with free N- and C-termini and the 20 standard amino acids, and it does not account for modifications, disulfide bonds, blocked termini or non-standard residues. Net charge is reported at pH 7.0 with one standard pKa set; a different pH or pKa set gives a different value.
Frequently Asked Questions
What does the net charge at pH 7 mean?
It is the overall charge the peptide carries at pH 7.0, adding the positive charge on the N-terminus and the lysine, arginine and histidine side chains and subtracting the negative charge on the C-terminus and the aspartate, glutamate, cysteine and tyrosine side chains. GHK, for example, has a net charge of +1.22 at pH 7.0.
Why does another tool give a different net charge?
Net charge depends on the pH and the pKa values used. This calculator fixes the pH at 7.0 and uses the EMBOSS pKa set, and states both, so the number is reproducible. A tool that uses a different pH or a different pKa set can report a slightly different charge for the same sequence.
Which amino acid codes can I paste?
The 20 standard amino acids in one-letter code: A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y and V. Spaces and line breaks are ignored. The ambiguous letters B, J, O, U, X and Z and any other character are not accepted, and the calculator will tell you which characters it could not read.
Is the molecular weight the average or the monoisotopic mass?
It is the average molecular weight, the mass used for most peptide ordering and handling, from the average residue masses plus one water for the free termini. It matches the Molecular Weight Calculator on this site for the same sequence.
How do I calculate the molecular weight of a polypeptide?
Add the average residue mass of every amino acid in the sequence, then add one water (18.02) for the free N-terminus and C-terminus. For example, GG is 57.05 + 57.05 + 18.02 = 132.12 Da. Longer sequences use the same sum, just with more residues. Paste the sequence in one-letter code and the calculator ignores spaces and line breaks and returns the molecular weight for you.
How do I convert the mass of a peptide to nmol?
Divide the mass in mg by the molecular weight in Da, then multiply by 1,000,000 to get nmol. For example, 1 mg of a peptide with a molecular weight of 1,000 Da is 1 / 1,000 x 1,000,000 = 1,000 nmol. Use the molecular weight from the calculator above as the divisor. This is arithmetic only.