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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 > -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "Success is going from failure to failure without losing your enthusiasm." - Anon. “We are the people we have been waiting for.” - A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)