**************************************************************************** 3DNA v2.2-2015jun09, created and maintained by Xiang-Jun Lu (PhD) **************************************************************************** 1. The list of the parameters given below correspond to the 5' to 3' direction of strand I and 3' to 5' direction of strand II. 2. All angular parameters, except for the phase angle of sugar pseudo- rotation, are measured in degrees in the range of [-180, +180], and all displacements are measured in Angstrom units. **************************************************************************** File name: 1ehz-U8-A14-3DNA.pdb Date and time: Wed Sep 2 00:46:27 2015 Number of base-pair: 1 Number of atoms: 20 **************************************************************************** **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.000) ....>A:...1_:[..U]U-**--A[..A]:...2_:B<.... (0.000) + Note: This structure contains 1[1] non-Watson-Crick base-pair. **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 U-**--A [2] O2 - N6 3.07 N3 - N7 2.73 **************************************************************************** Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step. Values in parentheses measure the overlap of base ring atoms only. Those outside parentheses include exocyclic atoms on the ring. Intra- and inter-strand overlap is designated according to the following diagram: i2 3' 5' j2 /|\ | | | Strand I | | II | | | | | \|/ i1 5' 3' j1 step i1-i2 i1-j2 j1-i2 j1-j2 sum **************************************************************************** Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure bp Ox Oy Oz Nx Ny Nz 1 U-A 0.000 -0.000 -0.000 -0.000 -0.000 1.000 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 U-A 4.14 -1.91 0.77 -4.60 12.12 -103.09 **************************************************************************** Local base-pair step parameters **************************************************************************** Local base-pair helical parameters **************************************************************************** Structure classification: This structure contains only one base-pair **************************************************************************** lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the base-pair C1'-C1' line C1'-C1': distance between C1' atoms for each base-pair RN9-YN1: distance between RN9-YN1 atoms for each base-pair RC8-YC6: distance between RC8-YC6 atoms for each base-pair bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6 1 U-A 28.8 22.8 9.6 7.0 6.0 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz