Interesting discussion is coming out of this question. I thank all that have
provided input.
Let me go a bit further concerning Daniel's considerations. What other
dipole interaction might be distinctively ascribed by programs out of hydrogen
bonds (and of course, they use to describe salt bridges in addition, as an
ionic interaction)? Possibly difficult for programs that use only atom
positions, distances and angles (excluding the question of pH dependence, let
us suppose neutral pH)?
I might here be specific with program PISA, which lists Hydrogen Bonds and
Salt Bridges. They seem to use these bonds to estimate a Gibbs energy for the
formation of the interface.
Sheila
________________________________
De: Daniel M. Himmel, Ph. D. <[email protected]>
Enviado: terça-feira, 18 de setembro de 2018 15:10
Para: [email protected]
Cc: [email protected]
Assunto: Re: [ccp4bb] collective term for hydrogen bonds and salt bridges
Sorry. I may have been unclear. H-bonds are actually a subset of dipole
interactions.
On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D.
<[email protected]<mailto:[email protected]>> wrote:
By the way, distinguishing between dipole and ionic (salt bridge) interactions
could
be a slippery slope, because which one you have sometimes depends on the
protonation
state of the protein(s), which is pH dependent.
-Daniel
On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D.
<[email protected]<mailto:[email protected]>> wrote:
Sheila,
Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions are
often collectively called
electrostatic interactions. Note that dipole interactions involve partial
charges. If you want to exclude
dipole interactions, you have say so specifically in your manuscript.
Non-bonded interactions include
both electrostatic and van der Waals contacts (where hydrophobic interactions
result from van der Waals
forces in an aqueous environment). Water can also interact with dipoles
(partial charges), so it would
NOT be correct to use the term "hydrophilic" if you were excluding dipolar
interactions.
-Daniel
On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko
<[email protected]<mailto:[email protected]>> wrote:
Dear all,
I had some literature search, but could not find clearly. Would there be
an appropriate term to call the sum of hydrogen bonds (HB) and salt bridges
(SB)? What about "hydrophilic interactions" or "polar interactions"? I am
analyzing the different number of theses interactions in different monomers of
my protein, as a totality I wanted to cite (compare) the number of HB + SB, yet
I think to specify them separately could take out some focus of the discussion.
Thank you,
Sheila
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