Disufide bridges are very important in macromolecular structural studies. These bonds are neither part of the normal intra-residue connectivity, nor part of the normal linear backbone connectivity. When they occur they act as structural scaffolding for a protein, adding support to hold pieces of protein in relative positions they might not hold without the extra support. Therefore it is helpful to be able to mark these bonds differently (just as it is helpful to be able to mark hydrogen bonds).
Yes, a disulfide bridge is a covalent bond. To quote from http://www.ndif.org/Terms/disulfide_bond.html it is a "strong covalent bond, -S-S-, important in linking polypeptide chains in proteins, the linkage arising as a result of the oxidation of the sulfhydryl (SH) groups of two molecules of cysteine".
If you use the ssbonds command with a small value, the disulfide bridges will be drawn as narrow cylinders instead of with dotted lines, and will look like ordinary covalent bonds. For example, if you are looking at a wireframe display and do "ssbonds 1", the disulfide bridges will be inserted just like the rest of the bonds. If you are looking at a stick display, then "ssbonds 80" will put the disulfide bridges in inconspicuously. For ball and stick displays "ssbonds 40" does the trick. Many people, however, like to have their disulfide bridges stand out and will pick a large value, and combine that with a cartoon display.
-- Herbert
At 2:58 PM +0100 11/27/03, Miguel Howard wrote:
I have the following questions about the RasMol script command 'ssbonds'
My general problem is that I do not understand why these bonds are treated specially in RasMol. I understand that they are connections in the sidechain, and that makes them interesting.
I believe I was told that these S-S bonds are regular covalent bonds (unlike hbonds). The questions below are predicated on this assumption. (Simple answers are better ... I'm not a chemist :-)
Q: Why aren't these S-S bonds created as regular covalent bonds automatically during the autobond process?
Q: RasMol shows these bonds as dotted lines. What is the motivation for doing this if they are regular covalent bonds?
Thanks in advance, Miguel
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