Amino Acid pKa Values and Isoelectric Point (pI)
Seven amino-acid side chainsare ionizable, and so are the protein's N-terminus and C-terminus. Each has a characteristic pKa— the pH at which it is half charged. Together these groups set a protein's net charge at any pH and its isoelectric point (pI). The values below are the EMBOSS set used by the SeqBench Protein Properties tool.
| Group | Residue | pKa | Charged form | Type |
|---|---|---|---|---|
| N-terminus (α-amino) | any | 8.6 | +1 when protonated (below pKa) | Basic (terminus) |
| C-terminus (α-carboxyl) | any | 3.6 | −1 when deprotonated (above pKa) | Acidic (terminus) |
| side-chain COOH | Aspartate (D, Asp) | 3.9 | −1 above pKa | Acidic |
| side-chain COOH | Glutamate (E, Glu) | 4.1 | −1 above pKa | Acidic |
| imidazole | Histidine (H, His) | 6.5 | +1 below pKa | Basic |
| thiol | Cysteine (C, Cys) | 8.5 | −1 above pKa | Acidic (thiolate) |
| phenol | Tyrosine (Y, Tyr) | 10.1 | −1 above pKa | Acidic (phenolate) |
| ε-amino | Lysine (K, Lys) | 10.8 | +1 below pKa | Basic |
| guanidinium | Arginine (R, Arg) | 12.5 | +1 below pKa | Basic |
Only these 7 side chains are ionizable; the other 13 amino acids have non-ionizable (neutral) side chains. pKa values are read from the SeqBench Protein Properties tool so this table and the tool always match.
Which amino acids are ionizable
Seven side chains can gain or lose a proton: the acidic carboxyls of aspartate (D) and glutamate (E), the cysteine (C) thiol, the tyrosine (Y) phenol, and the basic side chains of histidine (H), lysine (K) and arginine (R). The chain ends — the N-terminal α-amino and C-terminal α-carboxyl groups — are ionizable too. The remaining 13 amino acids have non-ionizable side chains and stay neutral across the normal pH range.
Acidic vs basic side chains
Acidic groups (D, E, C, Y) are neutral when protonated and carry a −1 charge above their pKa, once deprotonated. Basic groups (K, R, H) carry a +1 charge below their pKa, while protonated, and become neutral above it. The transition is not a switch but a curve: the Henderson–Hasselbalch relation governs the fraction of each group that is charged at a given pH, so a group within a pH unit of its pKa is only partly charged.
Isoelectric point (pI)
The isoelectric point (pI)is the pH at which a protein's net charge is zero — the positive contributions from the N-terminus, His, Lys and Arg exactly cancel the negative contributions from the C-terminus, Asp, Glu, Cys and Tyr. It is computed by summing the charge over all ionizable groups in the sequence across pH. SeqBench computes pI by bisection on that net-charge curve, narrowing in on the pH where the total charge crosses zero.
A note on pKa values
Published side-chain pKa values vary by source and method — EMBOSS, Lehninger, Sillero and others differ by a few tenths of a pH unit. The set shown here is the EMBOSS set used by the SeqBench Protein Properties tool, chosen so this reference and the tool always agree. Verify the set your downstream software uses if you need to compare results exactly.
Frequently asked questions
What is a pKa?
A pKa is the pH at which an ionizable group is half protonated and half deprotonated. Below its pKa a group is mostly protonated; above its pKa it is mostly deprotonated. The Henderson–Hasselbalch equation gives the exact fraction charged at any pH.
Which amino acids are charged?
Only seven of the twenty amino acids have an ionizable side chain: aspartate (D), glutamate (E), cysteine (C) and tyrosine (Y) can carry a negative charge, while histidine (H), lysine (K) and arginine (R) can carry a positive charge. The other thirteen have non-ionizable, neutral side chains. The N-terminus and C-terminus of the chain are also ionizable.
How is the isoelectric point calculated?
The isoelectric point (pI) is the pH at which a protein's net charge is zero. It is found by summing the charge contributed by every ionizable group — the two termini plus each acidic and basic side chain — across pH, then locating the pH where the positive and negative contributions cancel. SeqBench finds it by bisection on the net-charge curve.
Why do different sources give different pKa values?
Side-chain pKa values depend on the measurement method and the model used, so published sets (EMBOSS, Lehninger, Sillero and others) differ by a few tenths of a pH unit. The values here are the EMBOSS set used by the SeqBench Protein Properties tool, so the reference and the tool agree.
What charge does histidine carry at pH 7?
Histidine's imidazole has a pKa of 6.5, just below pH 7, so at pH 7 it is mostly neutral with only a small protonated (positively charged) fraction. This is why histidine is the residue whose charge changes most over physiological pH.
See also
Sources
- 1EMBOSS: iep — application documentation (contains the Epk.dat amino acid pK table)EMBOSS (European Molecular Biology Open Software Suite), release 6.6 · 2013Every number in the page's pKa table, exactly. Fetched, and the page's 'Data files' section prints the table verbatim: Amino 8.6, Carboxyl 3.6, C 8.5, D 3.9, E 4.1, H 6.5, K 10.8, R 12.5, Y 10.1 — a 9/9 match with the PKA object in src/lib/bio/protein.ts (nTerm 8.6, cTerm 3.6, K 10.8, R 12.5, H 6.5, D 3.9, E 4.1, C 8.5, Y 10.1) that the ROWS array renders. Also backs the page's repeated claim that this is 'the EMBOSS set', and the FAQ line 'Histidine's imidazole has a pKa of 6.5'. Important provenance note: this manual's own References section reads 'References: None' — EMBOSS publishes no literature source for Epk.dat, so the data file IS the primary citation for this particular set. Do not attribute these nine values to a journal paper.
- 2EMBOSS: The European Molecular Biology Open Software SuiteRice P, Longden I, Bleasby A · Trends in Genetics 16(6):276-277 (PMID 10827456) · 2000Provenance only — the software-package citation for EMBOSS, i.e. what 'the EMBOSS set' refers to in the header paragraph and the 'A note on pKa values' section. It does NOT contain the pKa numbers themselves; cite it beside the iep documentation, never instead of it. Record verified via the PubMed E-utilities (DOI 10.1016/S0168-9525(00)02024-2).
Related tools and references
Nearby reference tables
One-letter and three-letter amino acid codes with key properties.
Common affinity, epitope and solubility protein tags with amino acid sequences, mass, purification/detection and protease cleavage.
Kyte-Doolittle, Hopp-Woods and Eisenberg values for all 20 amino acids, with the window sizes and transmembrane threshold each scale is read with.