Amino acid pKa chart.

pKa values and isoelectric points.

Values for the free amino acids in water at 25 °C, from the standard reference tables. pKa₁ is the α-carboxyl group, pKa₂ the α-amino group. The last column is computed from the side-chain pKa with the Henderson-Hasselbalch equation at pH 7.0; the amino and carboxyl groups of a free amino acid are left out of it because inside a peptide only the two terminal groups remain.

Half charged, half not.

The pKa of a group is the pH at which half of the molecules carry a proton on that group and half do not. One pH unit below the pKa about 91 percent are protonated; one unit above, about 9 percent. The fraction follows the Henderson-Hasselbalch relation: for a base such as a lysine side chain the protonated (charged) share is 1 / (1 + 10^{pH − pKa}), and for an acid such as an aspartate side chain the deprotonated (charged) share is 1 / (1 + 10^{pKa − pH}).

So at pH 7 lysine and arginine side chains are almost fully positive, aspartate and glutamate almost fully negative, and histidine, with a pKa close to 7, sits in between: roughly a quarter of histidine side chains carry a charge at that pH, which is why it responds to small pH changes and shows up so often in enzyme active sites. Cysteine and tyrosine side chains stay neutral until the pH climbs toward 8.5 and 10.

Where the net charge is zero.

The isoelectric point, pI, is the pH at which an amino acid carries no net charge. For the thirteen with a non-ionizable side chain it is the average of pKa₁ and pKa₂, close to 6. For the acidic pair it is the average of the two acid pKa values (aspartic acid 2.85, glutamic acid 3.15), and for lysine and arginine the average of the two basic ones (9.60 and 10.76). Histidine lands at 7.60.

A peptide's pI follows the same logic with more groups: the pH where the positive charges on the N-terminus, lysine, arginine and histidine balance the negative charges on the C-terminus, aspartate, glutamate and, at high pH, cysteine and tyrosine. The molecular weight calculator solves that balance for any sequence and reports the net charge at pH 7 and the pI.

Free amino acids vs residues in a chain.

Two things move the numbers. First, measurement: values for free amino acids come from titrations at a stated temperature and ionic strength, and different compilations report slightly different results, usually within 0.1 to 0.3 units. Second, context: inside a peptide the α-carboxyl and α-amino groups of every interior residue are tied up in peptide bonds, so only the two terminal groups ionize, and their pKa values shift because a neighbouring peptide bond pulls electron density away. Peptide calculators therefore use residue sets fitted to proteins rather than the free-amino-acid values above.

This is the EMBOSS residue set, used by the molecular weight calculator. Other published sets (Bjellqvist, Lehninger, Sillero, IPC) differ by a few tenths; the IPC study compared them and found no single set best for every sequence. Folded structure moves individual side chains further still, by whole pH units in buried or salt-bridged positions.

Counting charges by eye.

To estimate a peptide's net charge at pH 7, add +1 for the free N-terminus and for each lysine and arginine, add about +0.3 per histidine, and subtract 1 for the free C-terminus and for each aspartate and glutamate. An N-terminal acetyl removes the +1 of the N-terminus; a C-terminal amide removes the −1 of the C-terminus. BPC-157 (GEPPPGKPADDAGLV) has one lysine and three acidic residues, so it sits at about −2 at neutral pH; MOTS-c (MRWQEMGYIFYPRKLR) has three arginines and one lysine against two glutamates, so about +3. The sequence notation guide explains the codes, the amino acid chart lists formulas and masses, and the N-terminus vs C-terminus guide covers the two ends and their caps.

Specs and storage by compound.