To follow up, This is what I use to teach to our undergrads:

Current Opinion in Chemical Biology 2002, 6:736–741

Shows a nice representation (and justification) for edge to face interactions

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Savvas Savvides
Sent: Thursday, 15 September 2016 5:20 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Tryptophan-Adenine interaction: T-shaped stacking?

Dear Wenhe and colleagues,

I would highly recommend the paper by Hunter, Singh, and Thornton in JMB.

(doi:10.1016/0022-2836(91)90271-7)
In particular, Figure 5 is very informative with its 'Ramachandran-like' representation of repulsive vs attractive stacking combinations. 

best wishes

Savvas

----

Savvas Savvides

Professor of Structural Biology

Ghent University & VIB Inflammation Research Center

Technology Park 927, B-9052 Ghent (Zwijnaarde), Belgium
+32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: savvas.savvides_skype

http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx

On 14 Sep 2016, at 16:57, Phoebe A. Rice <[log in to unmask]> wrote:

Some dusty neurons in the back of my head recall a discussion as to if there was really anything particularly favorable about perpendicular aromatic stacking, or if it is just the most statistically likely arrangement.  Might be worth looking up for your case. 
 Phoebe

________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of William G. Scott [[log in to unmask]]
Sent: Tuesday, September 13, 2016 6:05 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Tryptophan-Adenine interaction: T-shaped stacking?

On Sep 6, 2016, at 8:07 PM, WENHE ZHONG <[log in to unmask]> wrote:

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?

Dear Wenhe:

Please take a look at these references:


Aromatic-Aromatic Interaction: A Mechanism of Protein Structure Stabilization
S. K. Burley and G. A. Petsko
Science  Vol. 229, No. 4708 (Jul. 5, 1985), pp. 23-28

Stable URL: http://www.jstor.org/stable/1695415



also, the basis in pi orbital stabilization interactions comes from this, I believe:

Symmetry, Topology and Aromaticity, M. J. Goldstein and Roald Hoffmann.  Journal of the American Chemical Society / 93:23 / November 17,1971

https://www.dropbox.com/s/y7blru2u37dsfiu/67s_0.pdf




William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA

http://scottlab.ucsc.edu