Hydrophobicity plot
(v1.0.0)Docs
Explore local protein hydrophobicity with 24 amino acid scales, including Eisenberg and Hopp-Woods, and an adjustable sliding window.
Paste a protein or peptide sequence, FASTA records, or a PDB file, pick one of 24 amino acid hydrophobicity scales, and set the window. The Hydrophobicity plot averages the scale's per-residue hydrophobicity index over every window of that many residues and plots each average at the window's center, so you can see which stretches of the chain are hydrophobic, hydrophilic, or, on the Welling scale, likely antigenic.
The Insulin example uses the Hopp-Woods scale with a 7-residue window:
>sp|P01308|INS_HUMAN Insulin OS=Homo sapiens OX=9606 GN=INS PE=1 SV=1
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCNHopp-Woods rises with hydrophilicity, so the tallest peak marks the most water-exposed stretch. It reaches 2.01 at positions 56 and 57, in the charged TRREAED segment where the B chain joins the C-peptide, and the chart labels values above 0 as hydrophilic. On the default Eisenberg scale the same kind of profile is flipped: peaks are hydrophobic.
The first and last three residues have no full 7-residue window, so the plot runs from position 4 to 107. The values match ExPASy ProtScale for the same scale and window.
A peptide's hydrophobicity index on a scale is the mean of its residues' values. When the peptide length is an odd number from 5 to 21, set the window to that length: the plot then has exactly one point, and that point is the whole-peptide mean. Temporin A, a 13-residue antimicrobial peptide from the European common frog, with a 13-residue window:
>temporin_A
FLPLIGRVLSGIL| Scale | Hydrophobicity index |
|---|---|
| Eisenberg Consensus | 0.588 |
| Fauchere-Pliska | 1.006 |
| Hopp-Woods | -0.885 |
All three say the same thing in their own units: the peptide is strongly hydrophobic, and Hopp-Woods shows it as a negative hydrophilicity. For the Kyte-Doolittle mean of a sequence of any length, use the GRAVY calculator, which returns 1.808 for temporin A. An even-length peptide or one longer than 21 residues gives a local profile here rather than a single value.
| Input | Accepted |
|---|---|
| Pasted text | One or more protein sequences, with or without FASTA headers |
| Files | .txt, .fasta, .fa, .fas, .pdb |
| Databases | Fetch an entry from RCSB PDB in the upload menu |
Headers are kept whole as sequence names, and a plain name line above an unheaded sequence becomes its name. Spaces, numbers, and stop markers (*) are removed, and the page says when stop markers or alignment gaps were dropped. PDB files give one sequence per chain. Sequences shorter than the window are skipped with a note, and DNA pasted by mistake is flagged; translate it with DNA to Protein first.
| Setting | What it does | Default |
|---|---|---|
Sliding window | Residues averaged for each point, an odd number from 5 to 21. | 9 |
Hydrophobicity scale | The amino acid values to average. See the scale table below. | Eisenberg Consensus (1984) |
Windows of 5 to 9 keep detail such as surface loops, and Hopp and Woods used 6 for antigenic sites. Windows near 19 match the length of a membrane-spanning helix.
| Tab | Contents |
|---|---|
Chart | The profile, a reference line, the selected scale's values, and length, window, average, minimum, and maximum. The legend and tooltip say which side of the line is hydrophobic, hydrophilic, or antigenic for that scale. |
Data table | Position, residue, and value for every point of the first sequence, downloadable as CSV. |
Export the chart as an image from the camera button. When the input has several sequences, choose one from the menu beside the chart.
The reference line sits at 0 for scales with positive and negative values. Seven scales never go below zero (Aboderin, Black-Mould, Chothia, Manavalan-Ponnuswamy, Miyazawa-Jernigan, Rao-Argos, and Rose), so zero would label every residue hydrophobic; for them the line sits at the mean of the 20 values, and the chart reads above it as more hydrophobic than average.
Rare residue codes follow ProtScale: B is the mean of D and N, Z the mean of E and Q, and X the mean of all 20 values. U, O, and J have no value on these scales, so windows that contain them average over their other residues, and the page lists them.
Four widely used scales give these values for the 20 standard amino acids. Kyte-Doolittle is included for comparison; it is plotted by the Hydropathy plot, which adds the transmembrane cutoff for that scale.
| Amino acid | Kyte-Doolittle | Eisenberg | Fauchere-Pliska | Hopp-Woods |
|---|---|---|---|---|
Isoleucine (I) | 4.5 | 1.38 | 1.80 | -1.8 |
Valine (V) | 4.2 | 1.08 | 1.22 | -1.5 |
Leucine (L) | 3.8 | 1.06 | 1.70 | -1.8 |
Phenylalanine (F) | 2.8 | 1.19 | 1.79 | -2.5 |
Cysteine (C) | 2.5 | 0.29 | 1.54 | -1.0 |
Methionine (M) | 1.9 | 0.64 | 1.23 | -1.3 |
Alanine (A) | 1.8 | 0.62 | 0.31 | -0.5 |
Glycine (G) | -0.4 | 0.48 | 0.00 | 0.0 |
Threonine (T) | -0.7 | -0.05 | 0.26 | -0.4 |
Serine (S) | -0.8 | -0.18 | -0.04 | 0.3 |
Tryptophan (W) | -0.9 | 0.81 | 2.25 | -3.4 |
Tyrosine (Y) | -1.3 | 0.26 | 0.96 | -2.3 |
Proline (P) | -1.6 | 0.12 | 0.72 | 0.0 |
Histidine (H) | -3.2 | -0.40 | 0.13 | -0.5 |
Glutamate (E) | -3.5 | -0.74 | -0.64 | 3.0 |
Glutamine (Q) | -3.5 | -0.85 | -0.22 | 0.2 |
Aspartate (D) | -3.5 | -0.90 | -0.77 | 3.0 |
Asparagine (N) | -3.5 | -0.78 | -0.60 | 0.2 |
Lysine (K) | -3.9 | -1.50 | -0.99 | 3.0 |
Arginine (R) | -4.5 | -2.53 | -1.01 | 3.0 |
Sources: Kyte and Doolittle (1982), Eisenberg et al. (1984), Fauchere and Pliska (1983), and Hopp and Woods (1981), as tabulated in ExPASy ProtScale. Rows are ordered by the Kyte-Doolittle value.
The scales agree at the extremes. Isoleucine, leucine, valine, and phenylalanine are hydrophobic on every one, and arginine, lysine, aspartate, and glutamate are hydrophilic. The middle of the table is where they part, because each scale measures something different.
Tryptophan is 11th of 20 on Kyte-Doolittle, 5th on Eisenberg, and the most hydrophobic residue of all on Fauchere-Pliska, which measures how a side chain partitions into octanol. Wolfenden's hydration scale puts glycine first, since a side chain of one hydrogen holds almost no water.
The ranges differ too: Kyte-Doolittle runs from -4.5 to 4.5, Eisenberg from -2.53 to 1.38, and Wolfenden from -19.92 to 2.39. Compare profiles drawn on the same scale, and read a cutoff only on the scale it was calibrated for.
| Scale | What it measures | Higher values mean |
|---|---|---|
| Eisenberg Consensus (1984) | Normalized consensus of several published scales | Hydrophobic |
| OMH Sweet-Eisenberg (1983) | Optimal matching hydrophobicity from residue substitutions in related proteins | Hydrophobic |
| Fauchere-Pliska (1983) | Side-chain octanol-water partition | Hydrophobic |
| Abraham-Leo (1987) | Side-chain octanol-water partition | Hydrophobic |
| Roseman (1988) | Side-chain partition corrected for neighboring peptide bonds | Hydrophobic |
| Tanford (1962) | Free energy of transfer from water to organic solvent | Hydrophobic |
| Wolfenden (1981) | Hydration potential, water-to-vapor transfer | Hydrophobic (less hydrated) |
| Janin (1979) | Free energy of transfer from the protein interior to the surface | Hydrophobic |
| Chothia (1976) | Fraction of residues that are 95% buried in globular proteins | More often buried |
| Rose (1985) | Mean fraction of surface area lost on folding | More often buried |
| Manavalan-Ponnuswamy (1978) | Surrounding hydrophobicity in globular proteins | Hydrophobic |
| Miyazawa-Jernigan (1985) | Hydrophobicity from residue contact energies | Hydrophobic |
| Rao-Argos (1986) | Membrane-buried helix parameter | Found in membrane helices |
| Black-Mould (1991) | Hydrophobicity parameters that extend to modified residues | Hydrophobic |
| Aboderin (1971) | Paper chromatography mobility | Hydrophobic |
| Wilson HPLC (1981) | Reversed-phase HPLC retention | Hydrophobic (retained longer) |
| Meek HPLC pH 2.1 (1980) | Reversed-phase HPLC retention at pH 2.1 | Hydrophobic |
| Cowan-Whittaker pH 3.4 (1990) | Reversed-phase HPLC retention at pH 3.4 | Hydrophobic |
| Cowan-Whittaker pH 7.5 (1990) | Reversed-phase HPLC retention at pH 7.5 | Hydrophobic |
| Hopp-Woods (1981) | Hydrophilicity for locating antigenic determinants | Hydrophilic |
| Parker HPLC (1986) | Hydrophilicity from peptide HPLC retention | Hydrophilic |
| Bull-Breese (1974) | Surface tension of amino acid solutions | Hydrophilic |
| Guy (1985) | Side-chain partition energies in soluble proteins | Hydrophilic |
| Welling Antigenicity (1985) | Residue frequencies in known antigenic regions | Antigenic |
All values match the scale pages of ExPASy ProtScale.
| Goal | Scales |
|---|---|
| General hydrophobic and hydrophilic regions | Eisenberg, Fauchere-Pliska, Roseman |
| Buried versus exposed residues | Janin, Rose, Chothia |
| Candidate membrane helices | Eisenberg or Rao-Argos with a window near 19, then confirm with the Hydropathy plot |
| Surface-exposed, possibly antigenic stretches | Hopp-Woods, Parker, Welling |
| Peptide retention in reversed-phase HPLC | Wilson, Meek, Cowan-Whittaker |
The 1.6 cutoff for transmembrane helices belongs to the Kyte-Doolittle scale with a 19-residue window; other scales have different ranges, so compare peaks within a plot rather than against that number. For a single number describing the whole protein, use GRAVY.
| Question | Tool |
|---|---|
| Hydrophobic segments on the classic Kyte-Doolittle scale, with the transmembrane cutoff | Hydropathy plot |
| Hydrophobicity, hydrophilicity, or antigenicity on another published scale | Hydrophobicity plot |
| Flexibility, secondary structure propensity, or polarity along the chain | Protein Scale |
| Overall hydrophobicity as one value | GRAVY calculator |
There is no single best scale. Eisenberg's consensus is a balanced default, Kyte-Doolittle is the usual choice for membrane helices, and Hopp-Woods or Parker suit surface and antigenic regions.
No. On Hopp-Woods, Parker, Bull-Breese, and Guy, positive values are hydrophilic, and on Welling they mark antigenic residues. The chart legend states the direction for the selected scale.
Each point averages a full window centered on that residue, so the first and last (window - 1) / 2 residues have no value. This matches ExPASy ProtScale.
It can point to hydrophilic, surface-exposed stretches that antibodies often bind, which is what Hopp-Woods and Parker were designed for. It does not account for structure or sequence conservation, so treat peaks as candidates.
It is the value a hydrophobicity scale assigns to each amino acid, such as 4.5 for isoleucine on Kyte-Doolittle or 1.38 on Eisenberg. The hydrophobicity index of a whole peptide or protein is the mean of its residues' values on one scale; on Kyte-Doolittle that mean is called GRAVY.
Average its residues' values on one scale. Here, set the window to the peptide length when it is odd and 21 or less, and the single plotted point is that average. For any length on the Kyte-Doolittle scale, the GRAVY calculator returns it directly.
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