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From: Eric Martz <emartz@mi...> - 2008-03-23 22:22:41
>Date: Sun, 23 Mar 2008 17:19:49 -0500
>To: Frieda Reichsman <friedar@...>
>From: Eric Martz <emartz@...>
>Subject: Will the real hbonds please stand up?
>Cc: molvis-list@..., Joel.Sussman@...,
>reichsman@..., Oberhols@..., jsr@...,
>On 3/23/08, Frieda Reichsman asked
>(about FirstGlance in Jmol [FGiJ]'s Contacts display):
>>In a [protein chain] dimer, if I click on either chain and look at
>>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.
>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