Re: [modeller_usage] special restrains for aromatic packing interactions

Hi Thomas,

I would suggest the maximum distance for this “aromatic” pi stacking interaction would be 4 angstrom. As for the constraints...not sure on the how to

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Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
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From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Thomas Evangelidis
Sent: Saturday, 27 February 2010 3:47 p.m.
To: modeller_usage@salilab.org
Subject: Re: [modeller_usage] special restrains for aromatic packing interactions

Dear Modellers,

I'm trying to apply restrains to the interactions of cavity residues with ATP. Apart from electrostatic interactions between atom pairs, a Tyr residue is always packed parallel with the Adenine ring of ATP, as shown in this pic:

http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_packing.png

I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here:

http://salilab.org/modeller/manual/node196.html

Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome.

thanks,
Tom

By the way, what should be the maximum distance of electrostatic interactions. Usually the maximum distance between H-bond donor and acceptor is set to 3.2 A. (although sometimes may be 3.5 A.), but considering the resolution of crystal structures shouldn't it be a bit longer? Also in the tutorial is set to 3.5+-0.1 .