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Stacking

In our assessments of the A-site anticodon and CAR, base stacking (and stacking of the guanidinium group of R146) likely pay an important role in maintaining the integrity of these structures and in their alignment for hydrogen bonding. Stacking interactions are favorable because they increase van der Waals interactions by aligning the planar sides of these residues. One energetic consideration for stacking is that stacking of identical residues is less favorable because of same-charge dipole interactions. Additionally, there is an entropic penalty to stacking due to the reduction in rotational freedom of the residues involved.