Which scale should I use?

Kyte-Doolittle is the classic choice for finding hydrophobic/transmembrane regions (use a ~19-residue window). Eisenberg is another hydrophobicity consensus scale. Hopp-Woods is a hydrophilicity scale whose peaks predict surface-exposed, potentially antigenic regions.

What window size is best?

A window of about 19 residues is standard for detecting membrane-spanning α-helices; smaller windows (7–9) give a more local, noisier profile. The window is always made odd so it centres on a residue.

Can I export the plot?

Yes — export the hydropathy plot as a vector SVG or a high-resolution PNG.

Protein Hydrophobicity Plot — Kyte-Doolittle, Hopp-Woods, Eisenberg

Sliding-window hydropathy plot to spot transmembrane and surface regions.

🔒 Local processing — pasted sequences are not uploaded

Visualise a protein's hydropathy along its sequence. Paste a protein, pick a scale (Kyte-Doolittle, Hopp-Woods or Eisenberg) and a window size, and see the sliding-window profile — sustained hydrophobic peaks suggest transmembrane helices, while Hopp-Woods peaks mark likely surface/antigenic regions. Export the plot as a vector SVG or PNG for figures.

Protein sequence

0 aa

ScaleWindow: 9

Paste a protein sequence longer than the window.

Sliding-window average over the selected amino-acid scale (ProtScale-style). Kyte-Doolittle and Eisenberg are hydrophobicity scales; Hopp-Woods is hydrophilicity. Export the plot as SVG/PNG.

How to use the Hydrophobicity Plot tool

1Paste a protein sequence.
2Choose a hydropathy scale and window size (≈19 for transmembrane spans).
3Read the profile and export the plot as SVG/PNG.

Frequently asked questions

Which scale should I use?: Kyte-Doolittle is the classic choice for finding hydrophobic/transmembrane regions (use a ~19-residue window). Eisenberg is another hydrophobicity consensus scale. Hopp-Woods is a hydrophilicity scale whose peaks predict surface-exposed, potentially antigenic regions.
What window size is best?: A window of about 19 residues is standard for detecting membrane-spanning α-helices; smaller windows (7–9) give a more local, noisier profile. The window is always made odd so it centres on a residue.
Can I export the plot?: Yes — export the hydropathy plot as a vector SVG or a high-resolution PNG.

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