Jul 23 2008
Contents
 
Introduction
Overview - RECOMMENDED READING FOR NEW ICM USERS
File Menu
Graphics Move Tools
Display Tab
Light Tab
Labels Tab
PDB Search Tab
Meshes Tab
View Menu
Selections
Tables
Local DB
Sequences
Bioinfo Menu
Tools Menu - Xray
Tools Menu - 3D Predict
Tools Menu - Analysis
 RMSD
 Contact Areas
 Closed Cavities
 Surface Area
 Distance
 Planar Angle
 Dihedral Angle
 Ramachandran Plot
Tools Menu - Superimpose
Homology and Modelling
Working with Chemistry Tools
Chemsitry Menu
Docking
Ligand Editor
Animations, Slides, & Documents
ActiveICM
Movie Making
Frequently Asked Questions
Tutorial - Graphical Display
Molecular Document
Tutorial - Working with PDB Protein Structures
Tutorial - Working with Sequence Alignments
Tutorial - Ligand Binding Pocket Analysis
Tutorial - Homology and Modeling Tools
Tutorial - Crystallographic Analysis Tools
Tutorial - Working with Chemical Tables
Tutorial - Working with the Molecular Editor
Tutorial - Chemical Searching
Tutorial - Docking and Virtual Ligand Screening
 
Index
PrevICM User's Guide
18.2 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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