Sequence Analysis
Protein Parameters Calculator
Molecular weight, isoelectric point, extinction coefficient and amino acid composition from a sequence.
An example is loaded. Click here and it clears.
Examples:
sp|P00698|LYSC_CHICK
- Length
- 147 aa
- Molecular weight
- 16238.70 Da
- Theoretical pI
- 9.37
- Net charge at pH 7
- +8.76
- Aliphatic index
- 81.70
- GRAVY
- -0.150
The pI is the pH at which the net charge is exactly zero, solved on the published Bjellqvist pK scale. ExPASy ProtParam reports a value about 0.01 lower, because it varies the terminal pK with the residue at that terminus and reports a step rather than the crossing.
Absorbance at 280 nm
Cysteines reduced
- Extinction coefficient
- 37,470
- Abs 0.1% (1 g/L)
- 2.307
All cysteines paired
- Extinction coefficient
- 37,970
- Abs 0.1% (1 g/L)
- 2.338
Which column applies depends on your buffer, not on the sequence. In a reducing buffer use the left one. The difference is 125 per disulphide bond.
Amino acid composition
| Residue | Count | % | Share of the chain |
|---|---|---|---|
| A Ala | 14 | 9.5 | |
| C Cys | 9 | 6.1 | |
| D Asp | 7 | 4.8 | |
| E Glu | 2 | 1.4 | |
| F Phe | 4 | 2.7 | |
| G Gly | 13 | 8.8 | |
| H His | 1 | 0.7 | |
| I Ile | 7 | 4.8 | |
| K Lys | 6 | 4.1 | |
| L Leu | 15 | 10.2 | |
| M Met | 3 | 2.0 | |
| N Asn | 14 | 9.5 | |
| P Pro | 3 | 2.0 | |
| Q Gln | 3 | 2.0 | |
| R Arg | 12 | 8.2 | |
| S Ser | 11 | 7.5 | |
| T Thr | 7 | 4.8 | |
| V Val | 7 | 4.8 | |
| W Trp | 6 | 4.1 | |
| Y Tyr | 3 | 2.0 | |
| Total | 147 | 100.0 |
How to use
- Paste a protein sequence in one-letter code, plain or as FASTA. Digits, spaces and line breaks are ignored, so numbered output pastes in as it is.
- Read the figures. Molecular weight and composition are arithmetic; the isoelectric point is solved for the pH where the net charge crosses zero.
- For a concentration, take the extinction coefficient from the column that matches your buffer, then divide the measured A280 by it.
Worth knowing
- The extinction coefficient has two values because cysteines behave differently depending on whether they are paired. Only a disulphide bond absorbs at 280 nm, at 125 per bond; a free cysteine contributes nothing. Reading the wrong column is a small error on most proteins and a large one on a cysteine-rich one.
- The isoelectric point is computed from the sequence alone. It ignores folding, bound ligands and post-translational modifications, all of which move the real value. It is a starting point for choosing a buffer, not a measurement.
- Molecular weight here is the average mass, which is what a protein table means and what mass spectrometry reports as the deconvoluted average. It is not the monoisotopic mass.
- A chain with no tryptophan, no tyrosine and no disulphide bond cannot be quantified at 280 nm. The tool says so instead of printing a zero, because a zero looks like a measurement.
Frequently asked questions
Two reasons, both small. ProtParam varies the pK of each terminus with the residue that sits there, which the published table cannot express; and it reports a stepped value rather than solving for the crossing, so its answer sits just short of the pH where the charge is actually zero. On three reference proteins the gap was 0.01 in each case.
The residue masses here are derived from the IUPAC 2021 abridged standard atomic weights, which carry four or five significant figures. Over hundreds of residues that accumulates to a few parts per million. On a 607-residue protein it came to 0.16 Da.
They are ambiguity codes, not amino acids, and none of them has a single mass. Skipping them would quietly shorten the chain and change every figure divided by its length, so the tool stops and names the character instead.
Extinction coefficients from Pace et al. (1995) with Edelhoch (1967); the pK scale from Bjellqvist et al., as tabulated by Kozlowski (2016); hydropathy from Kyte and Doolittle (1982); the aliphatic index from Ikai (1980). Residue masses come from the IUPAC 2021 standard atomic weights this site already uses.
Other sequence tools
- DNA to Protein Translation — Six-frame translation and open reading frames, in any NCBI genetic code.
- GC Content Calculator — GC and AT content, skew, and GC along the sequence.
- Primer Tm Calculator — Melting temperature by the nearest-neighbour model