This page lists the data and conventions the calculators use. All tools share one calculation core, so a constant changed here changes everywhere at once.
Atomic masses
Average molecular weights use the conventional standard atomic weights published by IUPAC’s Commission on Isotopic Abundances and Atomic Weights (CIAAW): C 12.011, H 1.008, N 14.007, O 15.999, S 32.06.
Monoisotopic masses use the masses of the most abundant isotopes (NIST): 12C 12 exactly, 1H 1.007 825 032, 14N 14.003 074 005, 16O 15.994 914 620, 32S 31.972 071. The proton mass used for m/z values is 1.007 276 467 Da.
Amino-acid residues
Residue formulas are the amino acid minus H2O. A peptide’s formula is the sum of its residues plus one H2O, adjusted for terminal groups and disulfide bonds. The masses below are calculated from these formulas with the atomic masses above.
| Amino acid | Codes | Residue formula | Average mass | Monoisotopic | Kyte–Doolittle |
|---|---|---|---|---|---|
| Alanine | Ala / A | C3H5NO | 71.0790 | 71.03711 | +1.8 |
| Arginine | Arg / R | C6H12N4O | 156.1890 | 156.10111 | -4.5 |
| Asparagine | Asn / N | C4H6N2O2 | 114.1040 | 114.04293 | -3.5 |
| Aspartic acid | Asp / D | C4H5NO3 | 115.0880 | 115.02694 | -3.5 |
| Cysteine | Cys / C | C3H5NOS | 103.1390 | 103.00918 | +2.5 |
| Glutamic acid | Glu / E | C5H7NO3 | 129.1150 | 129.04259 | -3.5 |
| Glutamine | Gln / Q | C5H8N2O2 | 128.1310 | 128.05858 | -3.5 |
| Glycine | Gly / G | C2H3NO | 57.0520 | 57.02146 | -0.4 |
| Histidine | His / H | C6H7N3O | 137.1420 | 137.05891 | -3.2 |
| Isoleucine | Ile / I | C6H11NO | 113.1600 | 113.08406 | +4.5 |
| Leucine | Leu / L | C6H11NO | 113.1600 | 113.08406 | +3.8 |
| Lysine | Lys / K | C6H12N2O | 128.1750 | 128.09496 | -3.9 |
| Methionine | Met / M | C5H9NOS | 131.1930 | 131.04048 | +1.9 |
| Phenylalanine | Phe / F | C9H9NO | 147.1770 | 147.06841 | +2.8 |
| Proline | Pro / P | C5H7NO | 97.1170 | 97.05276 | -1.6 |
| Serine | Ser / S | C3H5NO2 | 87.0780 | 87.03203 | -0.8 |
| Threonine | Thr / T | C4H7NO2 | 101.1050 | 101.04768 | -0.7 |
| Tryptophan | Trp / W | C11H10N2O | 186.2140 | 186.07931 | -0.9 |
| Tyrosine | Tyr / Y | C9H9NO2 | 163.1760 | 163.06333 | -1.3 |
| Valine | Val / V | C5H9NO | 99.1330 | 99.06841 | +4.2 |
Charge, pI, hydropathy and absorbance
- pKa values (EMBOSS): N-terminus 8.6, C-terminus 3.6, Lys 10.8, Arg 12.5, His 6.5, Asp 3.9, Glu 4.1, Cys 8.5, Tyr 10.1. Net charge uses the Henderson–Hasselbalch equation, and pI is found by bisection to better than 0.01 pH units.
- Hydropathy: Kyte & Doolittle (1982) scale. GRAVY is the mean over all residues.
- Extinction coefficient at 280 nm: Pace et al. (1995): Trp 5500, Tyr 1490, cystine 125 M−1cm−1.
Units and constants
- Avogadro constant: 6.022 140 76 × 1023 mol−1 (exact, SI 2019).
- Kelvin to Celsius: t/°C = T/K − 273.15.
- Concentration: 1 mg/mL = 1 g/L; 1% w/v = 10 g/L. ppm is treated as mg/L, which assumes a dilute aqueous solution with a density near 1 g/mL.
- Dilution ratios: “1 : F” means an F-fold dilution (1 part in F parts total).
Rounding and display
Calculations run at full double precision. Results are rounded only for display, to four significant figures by default. Molecular weights are shown to two decimal places (average) and four (monoisotopic). Values outside 0.001–1 000 000 are shown in scientific notation, and each result is expressed in the unit that keeps the number readable.
How results are checked
The calculation core is tested against reference values before each release. These include GHK (C14H24N6O4, 340.38 g/mol average, 340.1859 Da monoisotopic), Leu-enkephalin YGGFL (555.63 g/mol), GEPPPGKPADDAGLV (C62H98N16O22, 1419.56 g/mol), and hand-worked molarity, dilution and unit conversions.
Limitations
- Only the 20 standard amino acids are supported. Ambiguity codes (B, Z, X) and non-standard residues are rejected rather than guessed.
- pI and net charge are estimates from a fixed pKa set. Measured values depend on sequence context and conditions.
- The calculators do not know the purity, salt form or water content of your material. Use the values on your certificate of analysis.
Corrections
Found a value that looks wrong? Report it with the tool, your inputs and the result you expected. Confirmed corrections are applied to the shared core and noted on this page.