Peptide Property Calculator
Comprehensive peptide property calculator: molecular weight, isoelectric point, net charge at pH, Kyte-Doolittle hydrophobicity, molar extinction coefficient, and in vivo half-life estimate.
Formulas
Molecular Weight
MW = Σ(MW_residue) − (n−1) × 18.015
Sum residue weights, subtract water lost per peptide bond. For disulfide bonds, subtract 2.016 Da per bond.
Isoelectric Point
pI = (pKa1 + pKa2) / 2
For peptides with multiple ionizable groups, the pI is the pH where the average charge equals zero, calculated from flanking pKa values.
Net Charge
Charge = Σ [1 / (1 + 10^(pKa − pH))] for acids; Σ [1 / (1 + 10^(pH − pKa))] for bases
Henderson-Hasselbalch equation applied to each ionizable group. N-terminus and Lys are basic; C-terminus, Asp, Glu, His, Cys, Tyr are acidic.
Kyte-Doolittle Hydrophobicity
KD = Σ(KD_residue) / n
Sum the Kyte-Doolittle hydrophobicity values for each residue and divide by the number of residues. Positive = hydrophobic; negative = hydrophilic.
Extinction Coefficient
ε₂₈₀ = (nTrp × 5500) + (nTyr × 1490) + (nCys × 125)
Pace method. Trp contributes most to absorbance at 280 nm, followed by Tyr. Cystine (disulfide-bonded Cys) contributes minimally.
Half-Life Estimate
t₁/₂ ≈ f(N-term, length, charge, hydrophobicity)
Empirical estimate based on N-terminal residue stability, peptide length, charge distribution, and protease susceptibility. N-terminal Gln/Asp cyclize; N-terminal Pro/Ala/Val stabilize.
Example Calculations
Glutathione (GSH)
Gly-Ser-His (GSH)
MW: 75.03 + 105.09 + 155.16 − 2×18.015 = 299.30 Da
pI: ~7.5 (His imidazole) | Charge at pH 7.4: ~0
Hydrophobicity: −0.72 (hydrophilic)
Oxytocin
CYIQNCPLG (disulfide-bonded)
MW: 1007.19 − 2.016 (1 SS bond) = 1005.18 Da
pI: ~7.8 | Charge at pH 7.4: ~0
Hydrophobicity: +0.18 (slightly hydrophobic)
BPC-157 (fragment)
GEPPPGKPADDAGLV
MW: 15 residues, rich in Pro and Gly
Net charge at pH 7.4: −1 (Asp residues)
Hydrophobicity: +0.12 (balanced)
Semaglutide (fragment)
31-aa GLP-1 analog
MW: ~4,114 Da (peptide only, no fatty acid)
Extinction coeff: ~7,000 M⁻¹cm⁻¹ (1 Trp)
Hydrophobicity: modified by fatty acylation
Amino Acid Properties Reference
| AA | MW (Da) | pKa | KD |
|---|---|---|---|
| G | 75.03 | — | −0.4 |
| A | 89.09 | — | 1.8 |
| V | 117.15 | — | 4.2 |
| L | 131.17 | — | 3.8 |
| I | 131.17 | — | 4.5 |
| P | 115.13 | — | −1.6 |
| F | 165.19 | — | 2.8 |
| W | 204.23 | — | −0.9 |
| M | 149.21 | — | 1.9 |
| S | 105.09 | — | −0.8 |
| T | 119.12 | — | −0.7 |
| C | 121.16 | 8.18 | 2.5 |
| Y | 181.19 | 10.07 | −1.3 |
| H | 155.16 | 6.00 | −3.2 |
| D | 133.10 | 3.65 | −3.5 |
| E | 147.13 | 4.25 | −3.5 |
| N | 132.12 | — | −3.5 |
| Q | 146.15 | — | −3.5 |
| K | 146.19 | 10.53 | −3.9 |
| R | 174.20 | 12.48 | −4.5 |
Frequently Asked Questions
How do you calculate the molecular weight of a peptide?
Sum the residue molecular weights of each amino acid in the sequence, then subtract 18.015 Da for each peptide bond (n−1 bonds for n residues). For disulfide bonds, subtract 2.016 Da per bond. For example, for GSH: 75.03 + 105.09 + 155.16 − 2×18.015 = 299.30 Da.
What is the isoelectric point of a peptide?
The isoelectric point (pI) is the pH at which the peptide carries zero net charge. It is calculated from the pKa values of ionizable groups using the Henderson-Hasselbalch equation. For peptides with a single ionizable group, pI = pKa. For multiple groups, it is the pH midway between the two pKa values flanking the neutral species.
How is hydrophobicity calculated using the Kyte-Doolittle scale?
The Kyte-Doolittle hydrophobicity index sums the hydrophobicity value of each amino acid residue and divides by the number of residues. Positive values indicate hydrophobic peptides that tend to aggregate or insert into membranes. Negative values indicate hydrophilic peptides with good aqueous solubility.
What is the extinction coefficient of a peptide?
The molar extinction coefficient at 280 nm (ε₂₈₀) is calculated from the number of tryptophan, tyrosine, and disulfide-bonded cysteine residues using the Pace method: ε₂₈₀ = (nTrp × 5500) + (nTyr × 1490) + (nCystine × 125) M⁻¹cm⁻¹. This enables concentration determination via UV spectroscopy.
How is peptide half-life estimated?
In vivo serum half-life is estimated using empirical rules based on N-terminal residue identity (N-terminal Gln and Asp cyclize rapidly, reducing half-life; Pro, Ala, and Val are stabilizing), peptide length, charge distribution, and hydrophobicity. Short peptides (<10 aa) generally have half-lives of 2–15 minutes. N-terminal modifications (acetylation, D-amino acids) can dramatically extend half-life.