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Pi stack cartoon thin

Possible pi stacking between two tryptophan segments.

Pi stacking is a special type of bonding which may occur between aromatic rings. The wikipedia article Stacking (Chemistry) discusses pi stacking and how it applies to proteins and drug design.

Pi stacking would most likely involve the rings: tryptophan, tyrosine, and phenylalanine.

In Foldit, it's not clear whether there's any special scoring for pi stacking. There is no option to visualize pi stacking. Many player designs seem to contain potential pi stacking, for example having two tryptophans adjacent to each other. So it's possible that general scoring in Foldit recognizes that pi stacking is favorable.

The "Sphere" protein view option (described in view options) gives a clue as to why pi stacking might score well. Two tryptophans seem well-separated in the "Cartoon Thin" view, but "Sphere" shows that they are almost touching. Tryptophan tends to score well on its own, probably because it has lots of atoms. Two tryptophans in this arrangement should have a good packing score, with a low clashing score.

Thanks to veteran player Susume for pointing out pi stacking.

Pi stack sphere

Possible pi-stacked tryptophans seen in Sphere protein view.

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