Molecular Toolkit Index Toolkit Help

Protein Hydrophobicity Plots

Input a protein sequence and obtain plots that characterize its hydrophobic character, which may be useful in predicting membrane-spanning domains, potential antigenic sites and regions that are likely exposed on the protein's surface.
Enter or paste a protein sequence (single letter codes only) into the text box, set the type of plot desired and the window size, then click the Plot button to obtain a plot. If you change a parameter, click Plot again to have the plot redrawn. To test the program, click the Demo Protein button to obtain a protein sequence. Suggestions on parameters:

Setting the type of plot determines the hydrophobic scale utilized:
  • Kyte-Doolittle is a widely applied scale for delineating hydrophobic character of a protein. Regions with values above 0 are hydrophobic in character.
  • Hopp-Woods scale was designed for predicting potentially antigenic regions of polypeptides. Values greater than 0 are hydrophilic and thus likely to be exposed on the surface of a folded protein.
Window size refers to the number of amino acids examined at a time to determine a point of hydrophobic character. Window size can be varied from 5 to 25 (default 7) and one should choose a window that corresponds to the expected size of the structural motif under investigation:
  • Window size of 5-7 is good for finding hydrophilic regions that are likely exposed on the surface and may possibly be antigenic.
  • Window size of 19-21 will make hydrophobic, membrane-spanning domains stand out rather clearly (typically > 1.6 on the Kyte-Doolittle scale). The demonstration protein is the glycoprotein of vesicular stomatitis virus, which has a transmembrane domain near the carboxy-terminus (right side of plot).
Clicking a position (x coordinant) on the graph will generate a message describing the approximate position (amino acid) of that point.

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Last updated on June 20, 1998
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