Re: [modeller_usage] special restrains for aromatic packing interactions

[Thomas Evangelidis <>]

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 .