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