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Pep-Calc

Science Lab

Build a peptide. See the chemistry.

Pick amino acids, chain them together and watch the formula, mass and charge recalculate. Everything is computed from the sequence with published constants — an illustrative model, not a lab result.

Peptide builder

Type a sequence or tap residues. A is read from the amino (N) end to the carboxyl (C) end.

Model · ignores salts, metals & 3-D structure

Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg

Examples:

Tap to add a residue:

Modifications
H₂N––COOH

Each line between beads is a peptide bond. Colour shows the side-chain class. Tap a residue to inspect it.

Molecular formula

C₅₀H₇₃N₁₅O₁₁

Neutral form, no salt

Average mass

1060.21 g/mol

Use for weighing & molarity

Monoisotopic mass

1059.5614 Da

Use for mass spectrometry

Length

9 aa

8 peptide bonds

Net charge at pH 7

+1.98

Estimate (EMBOSS pKa set)

Isoelectric point

12.50

pH where net charge is 0

GRAVY

-1.044

Kyte–Doolittle hydropathy

Water released forming it

8 H₂O

One per peptide bond

Charge across pH

Drag the slider. Charge changes as acidic and basic groups gain or lose protons.

024678101214+3+2+10-1pH 7.4 (blood)

Composition

  • Nonpolar (hydrophobic) 4
  • Aromatic 2
  • Polar, uncharged 1
  • Acidic (− charge) 0
  • Basic (+ charge) 2
  • Pro3 · 33%
  • Phe2 · 22%
  • Arg2 · 22%
  • Gly1 · 11%
  • Ser1 · 11%

Hydropathy (GRAVY -1.04)

Water-loving −4.5Water-avoiding +4.5
Lab work? Use 1060.21 g/mol in the molarity calculator →Real material is often a salt (e.g. acetate or TFA), which weighs more. Check the certificate of analysis.

The 20 amino acids

Every peptide in nature is built from this alphabet. Side chains decide how each residue behaves: whether it avoids water, carries a charge or can form a bridge to another chain.

G

Amino acid

Glycine Gly · G

A single hydrogen — the smallest side chain, which makes glycine unusually flexible.

Class
Nonpolar (hydrophobic)
Free amino acid
C₂H₅NO₂ · 75.07
Residue in a chain
C₂H₃NO · 57.05
Side-chain pKa · hydropathy
— · -0.4

Four ideas behind the numbers

  • 01

    A peptide bond releases water

    When two amino acids join, the carboxyl group of one and the amino group of the next combine and give off one H₂O. That's why a chain's mass is the sum of its residues plus just one water for the two ends.

  • 02

    Average vs monoisotopic mass

    Elements come in isotopes. Average mass weights them by natural abundance — the number you'd use to weigh out material. Monoisotopic mass uses only the most common isotope of each element — the peak a mass spectrometer resolves.

  • 03

    Charge depends on pH

    Acidic side chains (Asp, Glu) lose a proton and turn negative as pH rises; basic ones (Lys, Arg, His) carry a positive charge until pH climbs past their pKa. The isoelectric point is where these balance out.

  • 04

    Modifications change the numbers

    Many real peptides are amidated at the C-terminus, acetylated at the N-terminus or held in shape by disulfide bonds. Each changes the formula and the charge, which is why a label's molecular weight can differ from the bare sequence.

Understanding the numbers →mg vs mcg, concentration and syringe units, from scratch.Molarity calculator →Mass + molecular weight + volume → mM, µM, nM.Test yourself →Short knowledge checks in the Academy.

Sources and limits

Charge and isoelectric point use fixed pKa values; real values shift with neighbouring residues, temperature and solvent. Only the 20 standard L-amino acids are supported. Example sequences illustrate chemistry and say nothing about what any compound does. This tool is for learning, not for preparing anything to use.