Calculator Inputs
Example Data Table
| Example | Sequence | Length | pH | Calculated Net Charge |
|---|---|---|---|---|
| Acid-rich peptide | ACDEDE |
6 | 7.00 | -4.0595 |
| Basic peptide | KKRHHR |
6 | 7.40 | 4.0700 |
| Mixed peptide | MHCDEKRY |
8 | 6.50 | 0.2259 |
Formula Used
The calculator applies the Henderson-Hasselbalch relationship to each ionizable group. Basic groups contribute positive fractional charge, while acidic groups contribute negative fractional charge.
Basic groups: Charge = count / (1 + 10(pH - pKa))
Acidic groups: Charge = -count / (1 + 10(pKa - pH))
Net charge: Sum of all basic and acidic group contributions, including both termini.
The estimated isoelectric point is found numerically by locating the pH where net charge approaches zero across the 0 to 14 range.
How to Use This Calculator
- Enter a protein name for labeling your result.
- Paste the amino acid sequence or a FASTA block.
- Set the working pH for the net charge calculation.
- Adjust pKa values when your experiment requires custom assumptions.
- Define graph range and step to control curve detail.
- Click Calculate Net Charge to display metrics, contributions, and the titration plot.
- Use the export buttons to save current results as CSV or PDF.
FAQs
1. How does this calculator determine protein net charge?
It counts ionizable residues, adds terminal groups, and applies Henderson-Hasselbalch equations at the selected pH. Each group contributes a fractional positive or negative value.
2. Which amino acids affect net charge most directly?
Asp, Glu, Cys, Tyr, His, Lys, and Arg contribute side-chain charge changes. The N-terminus and C-terminus also matter, especially for short peptides.
3. Why does pH strongly change the result?
pH controls protonation and deprotonation. At low pH, proteins tend to gain positive charge. At high pH, acidic groups dominate and net charge usually decreases.
4. What is the estimated pI value?
The estimated pI is the pH where the calculated net charge approaches zero. It is useful for screening, but experimental values may differ because local environments shift pKa values.
5. Can I use custom pKa values?
Yes. This file includes editable pKa fields for all common ionizable groups and both termini. That helps when you need literature-specific or experimental assumptions.
6. Does sequence length alone predict charge?
No. Charge depends on the number of ionizable residues, terminal groups, pH, and pKa assumptions. A long neutral sequence can have lower charge than a short basic peptide.
7. Why might lab measurements differ from this output?
Real proteins fold, bind ligands, form salt bridges, and experience local microenvironments. Those effects alter apparent pKa values and can shift net charge from simple theoretical estimates.
8. Is this tool suitable for peptides and proteins?
Yes. It works well for peptides, fragments, and full protein sequences entered in one-letter code. Termini become especially important for very short sequences.