Q:

Is there a way to color-code the surface of a protein based on hydrophobicity?

A:

We can color a protein surface in DS based on the amino acid hydrophobicity properties. Here are the steps:

1) Structure > Surface > Add, to create the surface (Display style: Solvent).

2) Right-click in Molecule window and select Display Style, in the dialog box select the Protein tab, select Color by: Hydrophobicity from the list, click Apply.

3) Switch to the Surface tab, select Color by: Parent Color from the list. Click Apply. Click OK.

Now the surface coloring will be based on the amino acid residue hydrophobicity scale, a more blue color indicating more hydrophobic and more red color indicating more hydrophilic.