From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 05 2009 - 19:17:49 CST

Hi,
  Yes, they are just a list of residue names.
You'll see that "hydrophobic" isn't actualy a hard-coded
atom selection keyword, but rather an atom selection macro:
vmd > atomselect macro hydrophobic
resname ALA LEU VAL ILE PRO PHE MET TRP

This one is provided by default in one of the VMD startup
scripts, it was written by Andrew Dalke, one of the original
VMD developers, here's his comment on their origination:

# APD's hydrophobic residue list, from Branden and Tooze (pp6-7).
hydrophobic resname ALA LEU VAL ILE PRO PHE MET TRP

Perhaps someone else can comment on the hydrophobicity in terms
of a numerical scale as you've asked for.

Cheers,
  John

On Thu, Mar 05, 2009 at 04:58:41PM -0800, Goutham wrote:
> Hey,
> I am trying to find the hydrophobicity of the residues in the protein. The
> hydrophobic keyword just acts like a boolean switch. Is there a way to find
> the extent of hydrophobicity?
>
> Thanks
> Goutham

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