While working on PDB entries 1F0N and 1F0P, I aligned the side-chain
dipoles of 4 asparagines with the side-chain dipoles of tryptophans
(ring nitrogen is slightly negative, the rest of the 5-membered ring is
slightly positive). Aligning dipoles simultaneously optimized hydrogen
bonding for
to look at than I have time for!
cheers
michael
From: Tomas Malinauskas
Sent: Sunday, November 11, 2018 3:11 AM
To: Michael Jarva
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Asn/Gln - pi-stacking prevalence
Dear Michael,
On Sat, Nov 10, 2018 at 9:56 AM
Dear Michael,
On Sat, Nov 10, 2018 at 9:56 AM Michael Jarva wrote:
>
> Dear ccp4 community,
>
>
> I have recently been working with a structure that has an Asparagine that
> makes a planar stacking connection with a Tryptophan ring
> (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking
Hi Michael:
It always makes me happy to see that there are people who care about this.
3.3 to 3.4 Å should be an ideal distance for this, and, as you note, the lone
pair
residing on the (sp^3-hybridized) nitrogen would have to be oriented for
favorable overlap, which is a bit harder to deduce
