Michael Wise brings up an excellent point: several different amino acid hydrophobicity scales have been developed, and although the Kyte-Doolittle scale is one of the earliest and most-used, be aware that the ordering of residue types may be surprising if considered on purely physicochemical grounds. The "hydrophobicity surface" is for qualitative visual interpretation, so we are not highly concerned about the precise values, but users performing detailed or quantitative analyses may want to consider using alternative scales. Below I describe how other scales can be defined in Chimera, and mention that data for two alternative scales are already included with Chimera and merely need to be read in to be used in your own analyses.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
Elaine Begin forwarded message:
From: Elaine Meng <meng@cgl.ucsf.edu> Date: June 11, 2010 9:45:28 AM PDT
On Jun 10, 2010, at 6:48 PM, Michael Wise wrote:
Dear Elaine Have you ever considered using an alternative hydrophobicity scale rather than K&D? I'm attaching a PPT slide from one of my bioinformatics lectures which compares the two scales. You'll note some real oddities in the KD scale. Most notable is Proline (hydrophilic, despite being a cyclised aromatic), but also see W, Y, G, H (which is usually thought of as only slightly basic at physiological pH). KD is by now very well established so I guess you can simply change to an alternative, but it would be a good idea to give users the option. Just a thought Cheers MichaelW
Hi Michael, It seemed like the "classical" choice, out of dozens (hundreds?) of published hydrophobicity scales, each with their own strengths and weaknesses.
However, it is very easy (really!) to use whatever scale you like in Chimera. You would just create an attribute definition file and read it in with command "defattr" or the tool Define Attribute. It's a simple text format, and we include examples that define additional hydrophobicity scales, Wimley-White (as published in Nat Struct Biol 1996) and Hessa-von Heijne (as published in Nature 2005). The files look something like this:
attribute: wwHydrophobicity recipient: residues :asp -1.23 :glu -2.02 :asn -0.42 [ ... etc. ...]
The three scales are shown in this table: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
Attribute file format: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>
and the complete definition files are linked to both those pages. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco