This peptide drawing tool turns a sequence into a full chemical structure. Build a peptide from the amino acid buttons or type its sequence, and the generator draws the structure with the charges it carries at the pH you choose. You can download the picture as a PNG image or the structure as a MOL file, and copy its formula, SMILES and InChI. The table beside it gives the mass, isoelectric point, charge and extinction coefficient.
Standard amino acids
Modified and rare amino acids
In the sequence field these are written in brackets, for example GA[pS]K.
| Sequence | |
|---|---|
| Three-letter code | |
| Length | |
| Average mass | |
| Monoisotopic mass | |
| Isoelectric point (pI) | |
| Net charge | |
| Extinction coefficient at 280 nm1 | |
| Extinction coefficient at 280 nm2 |
1 Cysteines paired in disulfide bonds (cystines). 2 All cysteines free.
Peptide structure
The structure appears here after you click Draw peptide. Drawing can take a few seconds.
How to use the peptide structure generator
- Build the sequence with the buttons, or type it into the sequence field in one-letter code. Up to 60 residues are accepted; anything that is not an amino acid code is removed. The properties table updates as you type.
- Choose the end groups and the pH. The pH decides which groups are drawn charged.
- Click Draw peptide. The structure appears below the table, with buttons to download it and the formula, SMILES and InChI underneath.
The options
N-terminus. A free amine is the natural end of a peptide chain. An acetyl group (Ac–) caps it, as in many synthetic peptides; a capped end carries no charge.
C-terminus. A free acid (–COOH) is the natural end. An amide (–CONH2) is common in peptide hormones and synthetic peptides and, like the acetyl cap, carries no charge.
pH. Type a value or drag the slider. In the drawing each acidic or basic group is shown either charged or uncharged, depending on whether the pH is above or below its pKa. The net charge in the table is calculated more precisely, as a fraction, so near a pKa the two can differ slightly.
Neutral form. Draws every group uncharged, as the structure is usually shown in catalogues and databases. The formula and identifiers then refer to that form only.
Colour. Colours the labels of atoms other than carbon: nitrogen blue, oxygen red, sulfur dark yellow, phosphorus orange. Untick it for a black-and-white drawing for print.
Modified and rare amino acids
| Code | Amino acid | What it is |
|---|---|---|
[pS], [pT], [pY] | Phosphoserine, phosphothreonine, phosphotyrosine | The side-chain hydroxyl carries a phosphate group, added in cells by protein kinases. |
[aK] | N6-acetyllysine | Lysine with an acetyl group on its side-chain amine, which removes the positive charge. |
[nL] | Norleucine | An unbranched isomer of leucine that is not used by the genetic code. |
U | Selenocysteine | Cysteine with selenium in place of sulfur; built into a small number of proteins. |
O | Pyrrolysine | A lysine derivative carrying a pyrroline ring, used by some archaea and bacteria. |
Reading the structure
The peptide is drawn as a skeletal formula: carbon atoms sit at the corners and ends of lines, and hydrogens on carbon are not shown. All amino acids are drawn in the L-configuration. A solid wedge points towards the viewer and a hashed wedge away from the viewer, which fixes the configuration at every stereocentre: the α-carbon of each residue except glycine, and the second stereocentre in the side chains of threonine, phosphothreonine and isoleucine. Charged groups are labelled with their charge, for example H3N+ or O−.
Under the picture are the identifiers of the structure. Where the drawn form at your pH differs from the neutral molecule, both are given.
- Molecular formula of the neutral peptide, and the formula at your pH, which differs by the protons gained or lost and shows the net charge.
- SMILES, a one-line text notation of the structure. The
@signs encode the stereochemistry, so the string can be pasted into most chemistry programs to rebuild the molecule. - InChI, the IUPAC International Chemical Identifier, a standard text description of the structure, and the InChIKey, a fixed-length short form of it, convenient for searching chemical databases.
Download PNG saves the picture at double resolution on a white background. Download MOL saves the structure as an MDL molfile with 2D coordinates, the common exchange format that chemical drawing and modelling programs can open and edit.
How the properties are calculated
The table uses the same method as the peptide calculator, so the two tools give the same numbers for the same sequence.
The formula is counted atom by atom from the residues and end groups. The average mass uses the conventional atomic weights recommended by IUPAC[1]; use it to weigh a peptide. The monoisotopic mass counts only the most abundant isotope of each element[2]; compare it with a mass spectrum.
The net charge and isoelectric point are calculated from the pKa values used by the EMBOSS software[3]. Real pKa values shift with their neighbours, so the results are estimates; other calculators use other sets and give somewhat different numbers. EMBOSS does not cover the modified residues. For the second ionisation of the phosphate group the tool uses values measured in short peptides: 6.01 for phosphoserine, 6.30 for phosphothreonine and 5.83 for phosphotyrosine[5]; the first ionisation, near pH 2, is an approximate value. For selenocysteine it uses 4.3, measured for a selenocysteine inside a peptide chain; the free amino acid is less acidic, and the value depends strongly on the neighbouring residues[6]. If a peptide has no acidic or no basic group, its charge never reaches zero and no pI is given.
The extinction coefficient at 280 nm, used to measure peptide concentration by UV absorbance, is the sum of 5500 for each tryptophan, 1490 for each tyrosine and 125 for each disulfide-bonded pair of cysteines[4]. A peptide without tryptophan or tyrosine absorbs very little at 280 nm, and the value shown is then 0.
Limitations
- Only linear chains of L-amino acids are drawn. Disulfide bridges, cyclic peptides and D-amino acids are not supported.
- The structure is a 2D drawing, not a model of the peptide’s shape in solution; a short peptide in water does not have one fixed shape.
- Charges are drawn all-or-nothing at each group’s pKa, while real groups near their pKa are only partly ionised.
References
- Meija J, Coplen TB, Berglund M, et al. (2016). Atomic weights of the elements 2013 (IUPAC Technical Report). Pure and Applied Chemistry 88:265–291. DOI: 10.1515/pac-2015-0305
- Wang M, Audi G, Kondev FG, Huang WJ, Naimi S, Xu X (2017). The AME2016 atomic mass evaluation (II). Tables, graphs and references. Chinese Physics C 41:030003. DOI: 10.1088/1674-1137/41/3/030003
- Rice P, Longden I, Bleasby A (2000). EMBOSS: the European Molecular Biology Open Software Suite. Trends in Genetics 16:276–277. DOI: 10.1016/S0168-9525(00)02024-2. The pKa values are from the data file of the EMBOSS program iep (documentation).
- Pace CN, Vajdos F, Fee L, Grimsley G, Gray T (1995). How to measure and predict the molar absorption coefficient of a protein. Protein Science 4:2411–2423. DOI: 10.1002/pro.5560041120
- Hendus-Altenburger R, Fernandes CB, Bugge K, Kunze MBA, Boomsma W, Kragelund BB (2019). Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range. Journal of Biomolecular NMR 73(12):713–725. DOI: 10.1007/s10858-019-00283-z
- Mobli M, Morgenstern D, King GF, Alewood PF, Muttenthaler M (2011). Site-specific pKa determination of selenocysteine residues in selenovasopressin by using 77Se NMR spectroscopy. Angewandte Chemie International Edition 50(50):11952–11955. DOI: 10.1002/anie.201104169