Charged Residue Fraction Calculator

The most consequential distinction on this page is between a count of residues that can carry a charge and the charge itself. The first is a whole number divided by a length. The second is signed, fractional, and a function of pH. A chain can be fifty percent charged by this count and be net positive, net negative, or very nearly neutral, depending entirely on which types are present. The net charge calculator returns the signed number, and the two answering different questions is not a defect in either.

The count is a proportion of the chain and carries no unit. It describes how much of the sequence is equipped for electrostatic interaction, which is a real and useful thing to know, and it says nothing about the direction of that interaction, its magnitude at any particular pH, or how the groups are arranged. Nothing in a count over positions can recover a sign, because the sign depends on which side chain types are present rather than on how many there are.

Histidine is counted here as one fully charged residue, and that is the largest single source of disagreement between this figure and the modelled charge. Its side chain pKa in the table used on this site sits at 6.0, and at a pH of 7 the fraction that is actually protonated is one divided by one plus ten to the power of one, which is about nine percent. A histidine therefore contributes one to this count and roughly 0.09 to a charge at neutral pH, and the gap between those two numbers is not small.

The asymmetry is worth stating plainly because it runs one way in the classification. No other residue counted as charged here is over-counted by as much as histidine, since the acidic and the strongly basic groups really are close to fully in one state across most of the working range. That is why a short acidic chain gives a count and a charge that agree reasonably well, while a chain relying on histidine does not. The guide to net charge and Henderson-Hasselbalch sets out the per group arithmetic, and the charge versus pH calculator shows how much a group sitting near its pKa can move.

Neither terminal group appears in this percentage, and for a short peptide that omission is large. A four residue chain with two acidic side chains is fifty percent charged by this count, while the molecule actually contains four ionisable groups: the two side chains plus one basic N terminus and one acidic C terminus. The true fraction of ionisable positions is therefore one hundred percent rather than fifty, and the whole discrepancy sits in the two ends.

The termini are also the easiest groups to remove and the largest that they are. Amidation or acetylation of an end removes a full charge, which on a short chain can be the difference between a comfortably soluble peptide and one with half the electrostatic support it appeared to have. The terminal modification calculator gives the mass change, and the arithmetic on the net charge page is where the consequence for charge is actually worked out, because both termini are counted there automatically.

Treated as one number among four, the charged fraction is most useful for locating a sequence between the two poles of the count-based view. A high charged fraction alongside a high polar fraction is a peptide held in water mainly by charge and by side chain hydrogen bonding. A high charged fraction alongside a low polar fraction is one whose behaviour in water is dominated by electrostatics with little cooperative hydrogen bonding, and those two have different implications for anything that has to bind a neutral surface.

The classes overlap by convention rather than cleanly, which is why the four percentages are not meant to sum to one hundred. Tyrosine belongs to three of them, histidine to the charged list in a form that overstates it, and the polar residue fraction calculator is the companion that fills in the hydrogen bonding side. Where a summary of the pH dependence is wanted rather than a count, the isoelectric point calculator returns the pH at which the charge this count cannot give you passes through zero.