Notes

This page describes the technical details of our Peptide Property Calculator.

Calculating the molecular weight

The molecular weight M of a peptide may be estimated by calculating

The equation for the molecular weight of a peptide.

where Ni are the number, and Mi the average residue molecular weights, of the amino acids. MN + MC are added to the total in order to account for the termini: H at the N-terminus and OH at the C-terminus. Of course, if the termini are modified, these additions are replaced by those of the modifiers.
The resulting molecular weight depends on what values the algorithm uses. Innovagen's Peptide Property Calculator uses the following values:


A, Ala 71.0788 C, Cys 103.1448 D, Asp 115.0886 E, Glu 129.1155
F, Phe 147.1766 G, Gly 57.052 H, His 137.1412 I, Ile 113.1595
K, Lys 128.1742 L, Leu 113.1595 M, Met 131.1986 N, Asn 114.1039
P, Pro 97.1167 Q, Gln 128.1308 R, Arg 156.1876 S, Ser 87.0782
T, Thr 101.1051 V, Val 99.1326 W, Trp 186.2133 Y, Tyr 163.1760
 
H 1.0079 OH 17.0073 pS, pSer 167.0581
Ac 43.0452 NH2 16.0226 pT, pThr 181.0850
Biotin 227.3013 pY, pTyr 243.1559

Calculating the net charge

The net charge Z of a peptide at a certain pH can be estimated by calculating

The equation for the net charge of a peptide.

where Ni are the number, and pKai the pKa values, of the N-terminus and the side chains of Arginine, Lysine, and Histidine. The j-index pertain to the C-terminus and the Aspartic Acid, Glutamic Acid, Cysteine, Tyrosine amino acids.

Innovagen's Peptide Property Calculator calculates the net charge for all pH values of 0.1 to 14 in increments of 0.1, and plots these producing a titration curve.

This algorithm has its limitations:

Finally, the resulting net charge depends on what pKa values the algorithm uses. Innovagen's Peptide Property Calculator uses the following values:


(NH2-) 9.69 (-COOH) 2.34
K, Lys 10.5 D, Asp 3.86
R, Arg 12.4 E, Glu 4.25
H, His 6.00 C, Cys 8.33
    Y, Tyr 10.0
 
A. Lehninger

Calculating the isoelectric point, pI

The isoelectric point, pI, is the pH at which the net charge of the peptide is zero. Innovagen's Peptide Property Calculator first calculates the net charge for pH 7.0. If the charge is > 0 the next pH to check is 7 + 3.5, if the charge is < 0 then pH 7 - 3.5 is checked. This is repeated, using increments/decrements half the size of the previous, until the charge found equals 0, or is sufficiently close to 0.

Hydrophilicity

Innovagen's Peptide Property Calculator plots the hydrophilicty for each amino acid in the peptide sequence in a bar graph. The average hydrophilicity is calculated and the ratio of hydrophilic residues to total number of amino acids is reported. The results depend on what index is used. Innovagen's Peptide Property Calculator uses the following values:


A, Ala -0.5 C, Cys -1 D, Asp 3 E, Glu 3
F, Phe -2.5 G, Gly 0 H, His -0.5 I, Ile -1.8
K, Lys 3 L, Leu -1.8 M, Met -1.3 N, Asn 0.2
P, Pro 0 Q, Gln 0.2 R, Arg 3 S, Ser 0.3
T, Thr -0.4 V, Val -1.5 W, Trp -3.4 Y, Tyr -2.3
 
Hopp & Woods


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