Oct 21 2010 Feedback.
Contents
 
Introduction
How To Guide
Getting Started
Molecular Graphics
Slides and Documents
ActiveICM
Movie Making
Sequences & Alignments
Protein Structure Analysis
 Related Chains
 Calculate RMSD
 Contact Areas
 Closed Cavities
 Surface Area
 Distances
 Planar Angle
 Dihedral Angle
 Ramachandran Plot
 Ramachandran Export
Protein Superposition
Crystallographic Analysis
Homology & Modeling
3D Predict
Molecular Mechanics
Cheminformatics
Chemsitry Menu
Docking
Ligand Editor
Tables
Local Databases
FAQs
Tutorials
 
Index
PrevICM User's Guide
9.3 Contact Areas
Next

  • Read in a protein structure (File/Open or PDB Search)
  • Select the region you wish to analyse.
  • Tools/Analyze/Contact Areas
  • The xstick display in the region will be scaled according to the atom/residue contact area. For example, residues making large contacts with a ligand will be displayed in thicker xstick representation than those making small contacts.
  • A table as shown below will be displayed. Residues making key contacts will be displayed in xstick (radius represents contribution size). Carbon atoms are colored light green, nitrogen atoms are colored light blue and oxygen atoms are colored light red. The table lists the contact area, exposed area and the percentage of contact area compared to exposed.

NOTE: You can slso right click on the molecule in the ICM Workspace and select "Analyze Residue Contacts"


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