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Hello.

First, I think you might find the Suns Search tool helpful (the link to the tool and associated information is this: http://degradolab.org/suns/). The tool is authored by the DeGrado group, and is available as a PyMOL plugin. It might be helpful in identifying any other similar interactions that occur in other biological assemblies in the PDB. 

Second, the CaPTURE tool (available for use online: http://capture.caltech.edu/) is built to identify cation-pi interactions. I don't know enough about the tool to know whether it will recognize the adenine ring, but anyway, the associated publication (http://www.pnas.org/content/96/17/9459.abstract) and the literature related to it might give you more insight.

Wish you well,

Emily.


On Tue, Sep 6, 2016 at 11:07 PM, WENHE ZHONG <[log in to unmask]> wrote:
Dear CCP4BB,

One tryptophan residue (side chain) in my case regulates the binding of AMP. The attached figure representing the relative position of the tryptophan and AMP. I am not very familiar with the chemistry in terms of π-stacking. So I am wondering whether it is a T-shaped stacking interaction between the aromatic rings? Any thought? 

Thanks!


Kind regards,
Wenhe



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