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. 2005 Nov 27;33(20):6621–6634. doi: 10.1093/nar/gki935

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© The Author 2005. Published by Oxford University Press. All rights reserved

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(A) Interaction energies (locally-averaged, and in kcal/mol) of DNA with the linker domain (residues 636–712) as a function of the extent of rotation. (B) Interaction energy of DNA with the right nose-cone helix (α5, Thr303 to Gln318). (C) Interaction energy of DNA with left nose-cone helix (α6, Lys321 to Tyr338). (D) The variation of the distance (in angstroms) of the distal clamp (His367–Ala499) in all four systems, as a function of the extent of rotation of downstream DNA. (E) The corresponding plot for the proximal clamp (Gly365–Ser534). All distances are measured between the two C_α atoms. Legends in inset are the same for all panels.