[Chimera-users] TM tendency hydrophobicity scale

Shyam Saladi saladi at caltech.edu
Thu Feb 8 18:26:00 PST 2018


Hi all --

I have put together a Chimera attribute definitions to color residues
according to the TM tendency hydrophobicity scale:

Zhao and London, Protein Sci 15:8 (2006), doi: 10.1110/ps.062286306
An amino acid "transmembrane tendency" scale that approaches the
theoretical limit to accuracy for prediction of transmembrane helices:
relationship to biological hydrophobicity


In case it's helpful to others, it's attached to this message. Perhaps the
Chimera team would also be interested in including it with the other scales
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
online as well.

Thanks,
Shyam

--
Shyam Saladi <http://shyam.saladi.org>
NSF Graduate Research Fellow
Biochemistry and Molecular Biophysics
California Institute of Technology
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#  Amino acid hydrophobicity scale from
#  "An amino acid "transmembrane tendency" scale that approaches the
#   theoretical limit to accuracy for prediction of transmembrane helices:
#   relationship to biological hydrophobicity,"
#  Zhao and London, Protein Sci 15:8 (2006), doi: 10.1110/ps.062286306.
#
#  Zero should be at the middle of the extents (-3.46+1.98)/2 = -0.74
#
#  More positive means more hydrophobic.
#
#  Use this file to assign the attribute in Chimera with the
#  Define Attribute tool or the command defattr.
#
#
attribute: ttHydrophobicity
recipient: residues
	:asp	-3.27
	:glu	-2.90
	:asn	-1.62
	:gln	-1.84
	:lys	-3.46
	:arg	-2.57
	:his	-1.44
	:gly	-0.19
	:pro	-1.44
	:ser	-0.53
	:thr	-0.32
	:cys	-0.30
	:met	1.40
	:ala	0.38
	:val	1.46
	:ile	1.97
	:leu	1.82
	:phe	1.98
	:trp	1.53
	:tyr	0.49


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