How To List & Visualize Covalent Glycoprotein Bonds
in FirstGlance in Jmol

Covalent bond between sidechain nitrogen of Asn459 and C1 of N-acetyl glucosamine NAG802 in 9bvo.

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List:
Example of such a listing from an enzyme pre-processed by ConSurf to reveal evolutionary conservation. Another example: salt bridges.

To get a list of these saccharides and the amino acids to which they are covalently bonded (glycoprotein bonds), in the Find.. dialog:

1. Click Contacts to Found Atoms.
2. In the Select Targets for Contacts panel, click Show Atoms Contacting Target.
3. In the Contacts Shown panel, click List Contacting Atoms & Bonds.
4. At the top of the list of pairs of Target Atoms and Contacting Atoms, those with bond type Cov. are the saccharide atoms that form covalent bonds.

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Visualize:
The middle panel on the left must still say "Halos around: ~GLYCOPROTEINSUGARS". If it does not, click Find/List/See covalent glycoprotein bonds again.

1. In the Tools tab, click Contacts & Non-Covalent Interactions. OK the selection of new targets, if asked.
   
   
2. Check Cartoon at the top so you can see the carbohydrates more easily.
   
   
3. Check Residues/Groups.
   
   
4. Click on just one of the green carbohydrates with yellow halos.
   
   
5. Click Show Atoms Contacting Target.
   
   
6. Now you can Center Contacts, Label Contacts, try the four Contacts Views, and use any of the controls in the Contacts Shown panel.
   
   

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