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. Author manuscript; available in PMC: 2013 May 8.

Published in final edited form as: J Chem Theory Comput. 2012 Mar 15;8(5):1750–1764. doi: 10.1021/ct200680g

Fig. 8 — Definitions of the distances and angles plotted in Figure 9. (A) The kink angle η between the long axes of helices A and B of SBD, computed from the C^α coordinates. Helix A extends from residue E511 to residue N522 and helix B from residue A525 to residue E551. (B) The angle δ between the center of mass of subdomain Ib, the center mass of combined subdomains Ia and IIa, and the center of mass of subdomain IIb. (C) The dihedral angle τ that specifies the displacement of NBD-I and NBD-II out of the largest plane ( ) intersecting the whole NBD. This plane is spanned by the two shortest principal axes of NBD. The angle τ is the dihedral angle between planes 1 and 2, where plane 1 is spanned by vectors c and a and plane 2 is spanned by vectors c and b. Vectors a and b are the longest axes of NBD-I and NBD-II, respectively, while vector c is the projection of the vector linking the centers of NBD-I and NBD-II on the plane . (D) The distances between the selected residues from NBD-I, NBD-II, SBD-α, and SBD-β discussed in the text.

Inline graphic — Definitions of the distances and angles plotted in Figure 9. (A) The kink angle η between the long axes of helices A and B of SBD, computed from the C^α coordinates. Helix A extends from residue E511 to residue N522 and helix B from residue A525 to residue E551. (B) The angle δ between the center of mass of subdomain Ib, the center mass of combined subdomains Ia and IIa, and the center of mass of subdomain IIb. (C) The dihedral angle τ that specifies the displacement of NBD-I and NBD-II out of the largest plane ( ) intersecting the whole NBD. This plane is spanned by the two shortest principal axes of NBD. The angle τ is the dihedral angle between planes 1 and 2, where plane 1 is spanned by vectors c and a and plane 2 is spanned by vectors c and b. Vectors a and b are the longest axes of NBD-I and NBD-II, respectively, while vector c is the projection of the vector linking the centers of NBD-I and NBD-II on the plane . (D) The distances between the selected residues from NBD-I, NBD-II, SBD-α, and SBD-β discussed in the text.