Paste a protein or peptide sequence to calculate its theoretical isoelectric point (pI), net charge at any pH, and a charge-versus-pH curve. Compare published pKa models, analyze FASTA records separately, and account for blocked termini.
The original and tagged construct are calculated side by side. No linker is added; paste a linker into the sequence when one is part of the construct.
Custom mode starts with EMBOSS values; any nonblank field overrides that group. Custom terminal values do not reproduce Bjellqvist residue-specific corrections.
| pH | Net charge |
|---|
| Group | Count | Type | Charge contribution |
|---|---|---|---|
| Total net charge | — | ||
The isoelectric point (pI) is the pH at which a protein or peptide has zero modeled net charge. Below its pI it is generally positive; above its pI it is generally negative. A theoretical pI helps with buffer selection, isoelectric focusing, solubility screening, and ion-exchange chromatography, but it is not an experimental measurement.
Proteins often aggregate more readily near their pI because electrostatic repulsion is reduced. For solubility screening, test buffers away from the predicted pI and verify experimentally.
At a working pH below pI, a protein is usually net positive and may bind a cation exchanger. Above pI it is usually net negative and may bind an anion exchanger. Surface charge and buffer ions also matter.
For each pH, the calculator sums Henderson–Hasselbalch fractional charges. It then locates the zero crossing by bisection on pH 0–14. A free terminus contributes once per sequence; a blocked terminus contributes zero.
n is the number of that residue or active terminus, pKa is the selected dissociation constant, and Q is net charge in elementary-charge units. Acidic groups are C-terminus, D, E, C and Y; basic groups are N-terminus, H, K and R.
| Method | N-term | C-term | C | D | E | H | K | R | Y | Extra modeling |
|---|---|---|---|---|---|---|---|---|---|---|
| EMBOSS | 8.6 | 3.6 | 8.5 | 3.9 | 4.1 | 6.5 | 10.8 | 12.5 | 10.1 | None |
| Bjellqvist | 7.5 | 3.55 | 9.0 | 4.05 | 4.45 | 5.98 | 10.0 | 12.0 | 10.0 | N-terminal A/M/S/P/T/V/E and C-terminal D/E corrections |
| IPC_protein | 9.094 | 2.869 | 7.555 | 3.872 | 4.412 | 5.637 | 9.052 | 11.840 | 10.850 | Optimized nine-parameter protein set |
| IPC_peptide | 9.564 | 2.383 | 8.297 | 3.887 | 4.317 | 6.018 | 10.517 | 12.503 | 10.071 | Optimized nine-parameter peptide set |
Bjellqvist terminal corrections used here: N-terminal A 7.59, M 7.00, S 6.93, P 8.36, T 6.82, V 7.44, E 7.70; C-terminal D 4.55 and E 4.75. Other terminal residues use the generic value.
Method: IPC_peptide. Ionizable groups: N-term 1, C-term 1, D 1, K 1.
Calculating example…
Below its pI the peptide is net positive; above its pI it is net negative. Its two termini are a substantial fraction of all ionizable groups, so blocking either end can move the estimate.
Method: IPC_protein. Ionizable side chains: calculating…
Calculating example…
At pH 7.4, above its predicted pI, GFP is expected to be net negative in this model. The published IPC 2.0 teaching example describes GFP as a well-studied protein with pI around 5.8.
Running published IPC reference cases…
The embedded checks use the reference sequence and expected IPC_protein, IPC_peptide, and EMBOSS outputs published with the IPC package documentation. They verify the calculation engine on page load; they do not validate experimental accuracy.
Use IPC_protein for sequences longer than 50 residues and IPC_peptide for sequences of 50 residues or fewer as a practical starting rule. Use EMBOSS or Bjellqvist when reproducing those specific workflows, and compare the full method range for sensitivity to the pKa model.
IPC_protein and IPC_peptide were optimized against different experimental datasets. Termini usually contribute more strongly to short peptides, while side-chain composition dominates larger proteins; the 50-residue recommendation used here is a transparent interface rule, not a biological boundary.
Calculators may use different pKa sets, terminal-residue corrections, numerical procedures, sequence handling, or machine-learning models. This page implements the published Bjellqvist-style pKa calculation and IPC 1.0 optimized pKa presets, not the deep-learning IPC 2.0 predictor.
N-terminal acetylation blocks the positive N-terminal group and C-terminal amidation blocks the negative C-terminal group. A disulfide removes the ionizable thiols of two cysteines; this calculator models terminal blocking explicitly but does not infer disulfide bonds.
Yes. Each FASTA record is parsed and calculated separately, shown in the batch table, and included in CSV export. Raw sequence without a FASTA header is treated as one record.
Only the 20 standard one-letter amino-acid codes are accepted. B, Z, X, U, O, J and other letters are reported with their positions and block calculation for that record rather than being silently removed.
In this sequence-only model, net charge is generally positive below the pI and negative above the pI. Close to the pI, low net charge can reduce electrostatic repulsion and may increase aggregation risk.
Uniform pKa models omit folded microenvironments, coupled ionization, salt, temperature, ligands and many post-translational modifications. Experimental pI can therefore differ substantially from a theoretical sequence estimate.
Yes. Sequence parsing, calculation, charting and CSV generation occur locally in your browser; sequences are not uploaded by this page.
