>Date: Sun, 23 Mar 2008 17:19:49 -0500 >To: Frieda Reichsman <[EMAIL PROTECTED]> >From: Eric Martz <[EMAIL PROTECTED]> >Subject: Will the real hbonds please stand up? >Cc: [EMAIL PROTECTED], [EMAIL PROTECTED], >[EMAIL PROTECTED], [EMAIL PROTECTED], >[EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED], >[EMAIL PROTECTED], [EMAIL PROTECTED] > >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. > >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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