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If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2?
And would you define these numbers as area of overlap of the bases?
The stacking interactions are quantified in 3DNA by the shared overlap area, in Å2, of closely associated base rings, i.e. the nine-membered ring of a purine R (A or G) and the six- membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane. ... To account for the stacking interactions (overlap areas) of exocyclic atoms over base rings, ... an extended polygon, which includes exocyclic atoms, is used. For cytosine, the extended polygon is defined by the C1'-O2-N3-N4-C5-C6-C1' atomic sequence.
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.