Hydrophobicity plot

What is hydrophobicity plot?

A hydrophobicity plot visualizes the local hydrophobicity along a protein sequence using a sliding window average. This smooths out residue-by-residue variations and reveals structural patterns that correlate with protein function and topology.

This tool provides 24 different hydrophobicity scales, each optimized for specific applications. Some scales derive from partition coefficients between water and organic solvents, others from accessible surface area measurements, and some from empirical correlations with membrane proteins or antigenic sites.

For the original Kyte-Doolittle hydropathy analysis, use our dedicated Hydropathy Plot tool. For a single-value summary of overall protein hydrophobicity, see GRAVY.

How does hydrophobicity plot work?

The algorithm assigns each amino acid a hydrophobicity index based on the selected scale. A sliding window then moves along the sequence, calculating the average hydrophobicity at each position.

Sliding window calculation

For a window of size $w$ centered at position $i$, the local hydrophobicity $H_i$ is calculated as:

$$H_i = \frac{1}{w} \sum_{j=i-\lfloor w/2 \rfloor}^{i+\lfloor w/2 \rfloor} h_j$$

where $h_j$ is the hydrophobicity value of the amino acid at position $j$.

This averaging smooths out single-residue fluctuations. Smaller windows (5-7 residues) preserve local variations but produce noisier plots. Larger windows (15-21 residues) emphasize extended domains like transmembrane helices.

Scale conventions

Most scales assign positive values to hydrophobic residues and negative values to hydrophilic residues. However, some scales like Hopp-Woods use the opposite convention, assigning positive values to hydrophilic residues to highlight potential epitopes.

Available scales

General hydrophobicity

• Eisenberg Consensus (1984) — Normalized consensus from five experimental measurements. We recommend this as the default.
• Fauchere-Pliska (1983) — Based on octanol-water partition coefficients.
• Tanford (1962) — One of the earliest scales, derived from solubility measurements.
• Rose (1985) — Based on amino acid accessible surface areas.

Transmembrane prediction

• Janin (1979) — Calculated from burial frequencies in protein structures.
• Chothia (1976) — Derived from accessible surface area in globular proteins.
• Guy (1985) — Optimized for membrane protein analysis.
• Miyazawa-Jernigen (1985) — Based on inter-residue contact potentials.
• Rao-Argos (1986) — Designed for transmembrane helix detection.

Epitope and antigenicity prediction

• Hopp-Woods (1981) — Predicts antigenic determinants. Uses inverted convention (positive = hydrophilic).
• Welling Antigenicity (1985) — Based on amino acid frequencies in antigenic regions.
• Parker HPLC (1986) — Derived from HPLC retention times.

HPLC retention scales

Useful for predicting peptide behavior in reversed-phase chromatography:

• Wilson HPLC (1981) — Reversed-phase retention.
• Meek HPLC pH 2.1 (1980) — Retention at acidic pH.
• Cowan-Whittaker pH 3.4 (1990) — Retention at moderately acidic pH.
• Cowan-Whittaker pH 7.5 (1990) — Retention at physiological pH.

Specialized scales

• Wolfenden (1981) — Water-to-vapor phase transfer energies.
• Abraham-Leo (1987) — Solute partition coefficients.
• Roseman (1988) — Chromatographic measurements on hydrophobic matrices.
• Bull-Breese (1974) — Surface tension increment values.
• Black-Mould (1991) — Empirically optimized scale.
• OMH Sweet-Eisenberg — Optimal matching hydrophobicity.
• Aboderin (1971) — Early scale based on partition behavior.
• Manavalan-Ponnuswamy (1978) — Derived from surrounding residue compositions.

Settings

Sliding window: The number of residues averaged at each position. Use 9 for surface region analysis and epitope prediction. Use 19 for transmembrane helix prediction, as this matches typical helix length spanning a lipid bilayer.

Hydrophobicity scale: Select based on your analysis goal. We recommend Eisenberg for general analysis, Hopp-Woods for epitope prediction, and Janin or Rao-Argos for transmembrane prediction.

Understanding the results

The interactive chart displays hydrophobicity values along the sequence length. Hover over any point to see the exact position, residue, and calculated value.

For standard scales

Positive values indicate hydrophobic regions likely to be buried in the protein core or embedded in membranes. Extended peaks above +1.6 with window size 19 suggest potential transmembrane helices.

Negative values indicate hydrophilic regions typically found on protein surfaces or in aqueous environments.

For inverted scales (Hopp-Woods, Welling)

Hopp-Woods and Welling use inverted conventions where positive values indicate hydrophilic residues. For these scales, peaks indicate surface-exposed, potentially antigenic regions suitable for antibody binding.

Exporting data

Download results as CSV for quantitative analysis or PNG for publication figures. The CSV includes position, residue identity, and hydrophobicity value for each data point.

Scale selection guide

Limitations

Hydrophobicity plots assume that local sequence determines local properties. They cannot account for three-dimensional structure effects, long-range interactions, or post-translational modifications.

For dedicated transmembrane topology prediction, specialized tools like TMHMM or Phobius typically achieve higher accuracy by incorporating evolutionary profiles and topology grammar rules.