Protein hydrophobicity

CLC Protein Workbench can calculate hydrophobicity for several sequences at the same time, and for alignments.

Hydrophobicity plot

The following parameters are to be set:

• One or more of the these hydrophobicity scales:
  - Kyte-Doolittle scale
  - Engelman scale
  - Eisenberg scale
  - Hopp-Woods scale
  - Cornette scale
  - Rose scale
  - Janin scale
• Window size: This is the width of the window within which the hydrophobicity is calculated. The wider the window, the less volatile the graph gets.

CLC Protein Workbench offers these view preferences for the view of the hydrophobicity plot.

Besides this, you can chose preferences for each of the scales your have chosen:

• Dot type. Lets you choose the marking of dots in the graph.
• Dot color. Lets you choose the color of the dots.
• Line width. Applies to the line connecting the dots.
• Line type. Applies to the line connecting the dots.
• Line color. Applies to the line connecting the dots.

Hydrophobicity graphs along sequence

Hydrophobicity graphs along protein sequence can be displayed easily by activating the calculations from the View Preferences for a sequence.

This means that you will be able to turn hydrophobicity graphs on and off as you like.

The level of hydrophocity is calculated on the basis of the different scales. The different scales add different values to each type of amino acid. The hydrophobicity score is then calculated as the sum of the values in a ’window’, which is a particular range of the sequence. The window length can be set from 5 to 25 residues. The wider the window, the less fluctuation will appear in the hydrophobicity scores.

Initially there are three options for displaying the hydrophobicity scores (one, two or all may be chosen):

• Foreground color
• Background color
• Graph

Coloring the letters and/or the background of the letters. When choosing coloring of letters or coloring of the background of the letters; background, the color red is used to indicate high scores of hydrophobicity. A ’color-slider’ allows you to amplify the scores, thereby emphasizing areas with high (or low, blue) levels of hydrophobicity. The color settings mentioned are default settings. By clicking the color bar just below the color slider you get the option of changing color settings.

Graphs along sequences. When selecting graphs, you choose to display the hydrophobicity scores underneath the sequence. This can either by as a line-plot, a bar-plot, or by coloring. The latter option offers you the same possibilities of amplifying the scores as applies for coloring of letters and letter background.

Notice that you can choose the height of the graphs under the sequence.

Click here to read more about Protein Hydrophobicity in our “Bioinformatics explained” section