Intra-basepair parameters

According to the IUPAC-IUB convention, the spatial arrangement of one base with respect to each other in a pair can be quantitatively defined with the help of three rotational and three translational intra-basepair parameters - Buckle, Open-angle, Propeller, Stagger, Shear and Stretch [See figure].



Among these six parameters, shear, stretch and open-angle relate directly to the hydrogen bonding pattern and proximity, while buckle, propeller and stagger describe the overall non-planarity of a basepair compared to the ideal coplanar geometry.


Short description of the parameters:

The axis systems (X1,Y1,Z1) and (X2,Y2,Z2) of the bases are determined based on their corresponding hydrogen-boding edges within a specific basepairing pattern. (Xm,Ym,Zm) defines the mean axis system and M is a vector passing through the pivot points of the two bases of a basepair.