FIGURE 4.

The parameterization of A-minor interactions in the Group I intron (PDB ID: 1GID). On the left is an interaction between an interior loop and a stem, while on the right is an interaction between a hairpin and a stem. Both are parameterized in the same manner, wherein the distance (d) along the interaction vector (the vector between the two closest points on the two interacting elements) is shown in the side view, the angle between the interaction vector and the minor groove of the stem (ψ) is shown in the front view, and the angle between the two interacting elements (φ) is shown in the top-down view. The direction of the view is relative to the receptor stem.