[Molvis-list] Will the real hbonds please stand up?

Dan Bolser dan.bolser at gmail.com
Mon Mar 24 04:06:44 EDT 2008

On 23/03/2008, Eric Martz <emartz at microbio.umass.edu> wrote:
> On 3/23/08, Frieda Reichsman asked
>  (about FirstGlance in Jmol [FGiJ]'s Contacts display):
>  >Hi Eric,
>  >
>  >In a [protein chain] dimer, if I click on either chain and look at
>  >putatively hbonded
>  >non-water, shouldn't I see the same number of contacts from one
>  >protein chain to the other, regardless of which is the target?
>  >
>  >In 1LLI, I see 6 for chain A and 8 for chain B.
>  >In 1YSA, I see 3 for chain C and 5 for chain D.
>  >
>  >Maybe I am missing something about hbonds, but this doesn't make sense
>  >to me right now.
>  [Here's how to show these putative hbonds in FGiJ:
>   - Display 1YSA in FGiJ
>   - click "Contacts"
>   - click on one of the protein chains (it is now the "target")
>   - click "Show Atoms Contacting Target"
>  To limit the display to the putatively hbonded non-water:
>   - click "Uncheck"
>   - check "Show putatively hydrogen bonded non-water"
>   - click the 4th thumbnail display mode (all balls and sticks)]
>  You are right: If FGiJ could really determine where hydrogen bonds
>  are, in most cases there would be an equal number of donors +
>  acceptors on each chain.
>  The problem is the crudeness of FGiJ's reporting of "putative hbonds".
>  As you know, FGiJ (and Protein Explorer) designate any oxygens or
>  nitrogens within 3.5 A of other oxygens or nitrogens as "putatively
>  hbonded". They don't know where the hydrogens are, and don't take
>  angles into account. So no donor or acceptor assignments are made,
>  just proximities of possible donor/acceptor pairs.
>  Take your second case, 1YSA.
>  There are two simple atom pairs:
>    Glu270:C.OE2 - Lys275:D.NZ. 3.1A
>    Asn264:C.OD1 - Asn264:D.ND2 2.6A
>  Each puts one "putatively hbonded" atom in each chain. So far, no problem.
>  The third interaction is ambiguous:
>    Asn264:D.OD1 is close enough to three possible partners:
>      Asn264:C.N  2.8A
>      Lys263:C.NZ 3.1A
>      Leu260:C.O  3.2A
>  That is why you get two more "putatively hbonded" atoms in :C than in :D.
>  Which one of these is really hbonded? (Or might two be sharing one hbond?)
>  A next step could be to add hydrogens to the PDB file model with
>  Molprobity, and let Molprobity flip the Asn264's in both chains or
>  not as it sees fit. Then one could try to pick out donors and
>  acceptors. However, analysis of the relevant angles is something I
>  don't know how to do.

This feature (geometric analysis and putative quantification of
h-bonds) was available here;


For details see, http://www.ncbi.nlm.nih.gov/pubmed/12824323

I wish that site would 'temporarily' come back on line!


>  The resolution of 1YSA is 2.9A, perhaps a bit low to be trying to
>  make precise assignments. The temperature factors of the above-listed
>  atoms are relatively low, so that isn't an additional problem (but
>  its always important to check). (In FGiJ, while showing these
>  contacts, click "More Views.." and then "Color by Uncertainty".)
>  Hope that helps, -Eric
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