Protein
Protein parameters
Molecular weight, isoelectric point, extinction coefficient, GRAVY and aliphatic index from an amino acid sequence. Everything is computed in your browser.
Amino acid composition
The extinction coefficient comes from tryptophan, tyrosine and cystine counts. The cystine column assumes every cysteine forms a disulfide bond. Aliphatic index and GRAVY are relative measures for comparing proteins, not absolute stability predictions.
Formula
ε₂₈₀ = 5500 × Trp + 1490 × Tyr + 125 × cystines
- molecular weight
- the summed residue masses plus one molecule of water
- pI
- the pH at which the net charge crosses zero
- ε₂₈₀
- molar extinction coefficient at 280 nm
- GRAVY
- the mean Kyte-Doolittle hydropathy over the whole sequence
Worked example
The thirty-residue insulin B chain
- FVNQHLCGSHLVEALYLVCGERGFFYTPKT
- The residue masses are summed and 18.02 Da of water is added.
- This sequence has two tyrosines and no tryptophan: 2 × 1490 = 2980.
- Net charge is evaluated across the pH range and the zero crossing found by bisection.
Answer 3430 Da, pI 7.4, extinction 2980, GRAVY 0.22
Common mistakes
- Reading the cystine column for a protein held under reducing conditions. That column assumes every cysteine forms a disulfide; with DTT or 2-mercaptoethanol present, use the reduced figure.
- Trying to quantify a protein with no tryptophan and no tyrosine. Its extinction coefficient is near zero and A280 carries no information; use BCA or Bradford instead.
- Expecting the calculated pI to match the focusing point on a gel. The calculation sees only the ionisable side chains, not the folded structure, post-translational modifications or interactions.
- Reading GRAVY as a solubility prediction. It is a mean hydropathy for comparing proteins, not a forecast of whether yours will end up in inclusion bodies.
Frequently asked
What does the A280 of a 0.1 per cent solution mean?
The absorbance a 1 mg/ml solution of that protein would give over a 1 cm path. It is the extinction coefficient divided by the molecular weight, and it converts absorbance straight into mass concentration.
Why is there no instability index?
It needs a four-hundred-entry table of dipeptide weights that has not been reproduced here. The aliphatic index and GRAVY are given instead, both of which have simple, unambiguous formulas.
Should tags be included in the sequence?
If the final protein carries them, yes. A hexahistidine tag adds roughly 840 Da and pulls the pI upwards; leaving it out shifts both numbers.