Amino Acid Sequence Analyzer
Composition, net charge at any pH, isoelectric point, GRAVY hydropathy and extinction coefficient for a peptide sequence.
Net charge
Working
About this tool
The analyzer reads a peptide sequence and reports the properties researchers check before working with it: amino-acid composition, estimated net charge at a chosen pH, isoelectric point (pI), Kyte–Doolittle GRAVY score and the molar extinction coefficient at 280 nm.
How to use it
- Enter the sequence in one- or three-letter notation.
- Set the pH you want the net charge for (7.4 by default) and the terminal groups.
- Enter the number of disulfide bonds so cystines are counted correctly in the extinction coefficient and charge.
Charge and pI are estimates from a fixed pKa set. Real values shift with neighbouring residues, temperature and ionic strength.
Formula f(x)
Net charge: Z = Σ Ni / (1 + 10pH − pKai) − Σ Nj / (1 + 10pKaj − pH) over basic groups (i: N-terminus, Lys, Arg, His) and acidic groups (j: C-terminus, Asp, Glu, Cys, Tyr). pKa values follow EMBOSS.
pI: the pH at which Z = 0, found by bisection.
GRAVY: mean Kyte–Doolittle hydropathy over all residues.
ε280: 5500·nTrp + 1490·nTyr + 125·ncystine M−1cm−1 (Pace et al.).
Worked example check your setup
GHK at pH 7.4 with free termini: the N-terminus and Lys are mostly protonated, His is mostly neutral and the C-terminus is ionised, giving a net charge of about +1. The estimated pI is about 9.7. GHK has no Trp or Tyr, so ε280 is 0 and it cannot be quantified by A280.