CCL: calculating and displaying surface residues

 Sent to CCL by: "Elaine  Meng" [meng]=[cgl.ucsf.edu]
 On Mar 6, 2008, at 7:51 PM, Kalpana Krishnaswami kalpuk*_*gmail.com wrote:
 Hi
 We would like to calculate and display exposed hydrophobic surfaces on a
 protein.  We would also like to list the residues on the surface.  Are there
 freeware/ scripts/plugins to pymol/rasmol that would do this?
 Thanks
 --
 Kalpana Krishnaswami
 Hi Kalpana,
 If you want calculations based on the hydrophobicity of each atom, take a look
 at the GetArea server:
 http://pauli.utmb.edu/cgi-bin/get_a_form.tcl
 If you want calculations based on the hydrophobicity of amino acid residues in
 proteins, you may want to try UCSF Chimera - not a web server, but freely
 downloadable for noncommercial use (Windows, Mac, Linux, etc.):
 http://www.cgl.ucsf.edu/chimera/index.html
 I recommend the recent snapshot:
 http://www.cgl.ucsf.edu/chimera/download.html#snapshots
 In Chimera, there are many related possibilities.  After opening the structure
 ("File... Open" for local file or "File... Fetch by ID" to
 get from PDB) you could
 (A) color the surface by amino acid hydrophobicity - simply choosing
 "Presets... interactive 3 (hydrophobicity surface)" from the menu will
 apply a built-in scheme.  Or to specify the color mapping yourself, use the
 "Render by Attribute" tool (under Tools... Depiction) on the residue
 attribute named kdHydrophobicity.
 http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets
 http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html
 (B) calculate surface area values - first calculate the surface areas for all
 atoms, then later you can sum over subsets such as the hydrophobic residues.  To
 calculate atomic surface areas, use the "Area/Volume from Web" tool
 (under Tools... Surface/Binding Analysis) and pick which surface area method and
 parameters you want.
 http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html
 After that, to sum over only residues with a certain hydrophobicity, first
 select them with "Select... by Attribute Value" and then with
 "Attribute Calculator" (under Tools... Structure Analysis), sum the
 surface area values of all selected atoms in the whole model. Similarly, to get
 a list of all surface residues, you could select all atoms with surface area
 >0 and then use "Actions... Write List" to make a text file listing
 those residues or "Actions... Write PDB" to save the coordinates of
 those residues.
 http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html
 The Kyte-Doolittle amino acid hydrophobicity is used by default, but you can use
 different scales.
 http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html
 I realize there is a learning curve with Chimera, but you can do many powerful
 things.  I can provide more details if you try any of these things but get
 stuck.
 Best,
 Elaine
 -----
 Elaine C. Meng, Ph.D.                          meng###cgl.ucsf.edu
 UCSF Computer Graphics Lab and Babbitt Lab
 Department of Pharmaceutical Chemistry
 University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html