To Pete / Uppsula:
Thanks for the clarification about nomenclature.
I will try to adjust the model to put the hydrophobic face of that helix on
the inside of the protein, and the face which is mostly Ala on the surface.
But, this is the first time that I have done such modelling, and it will be
an adventure to see if I can get Quanta to cooperate with my wishes. Does
anyone know if this is a reasonable expectation of that software, or is
there another program that I should be checking out?
>Or is the situation the same for cheY (confession: I haven't
>looked!)?
So far as I can tell, CheY does not have the same situation. Phe's 14 and
111 are close to solvent, but these are not conserved in DctD; if you check
out the NMR structure of CheY, it is well defined in this helix (and all
regions except the ends); but this helix of NtrC, a homolog of DctD and thus
containing a similar NT domain, is not well defined by NMR (while the rest
is). It seems to me that this could mean the NMR of NtrC is showing lack of
structure in helix 4 rather than underdetermination (if that is the other
alternative).
>Or do you expect a hydrophobic surface there to be involved in
>protein-protein or domain-domain interactions?
I am excited about that prospect - it might explain the phenotype of some of
the mutants locating in the region being discussed, and the NMR structure of
NtrC.
>Maybe we can all be part of the first global effort to produce a correct
model >over the web!! Zounds, this is exciting!!
For me too - as it is my first structural model in any case!
Tracy / PSU