Contact Surfaces

If you want an overview of the noncovalent bonds to a moiety of interest, try the Contact Surfaces capability of Protein Explorer. (In addition to the "DISPLAY, Contacts" menu option in QuickViews, Advanced Explorer has a Contact Surfaces page with much more control over the contact displayed and its rendering.

Noncovalent Bond Finder

Use the Noncovalent Bond Finder when you want a more detailed (bond by bond) visualization. The Noncovalent Bond Finder makes it very easy to find and display the atoms closest to any ligand or group of "target atoms" you select. Starting at 2.5 Angstroms, it moves out in steps of 0.1 Angstrom and displays the atoms found. It can be restricted to show only desired categories of atoms, such as carbons in hydrophobic sidechains. It has an introductory tutorial.

To use the Noncovalent Bind Finder:

1. Write down the PDB ID code(s), URL's or filepath names of the molecules of interest (or print this page):
2. Start the Noncovalent Bond Finder.