**************************************************************************** This structure has broken O3'[i] to P[i+1] linkages **************************************************************************** 3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab. **************************************************************************** 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: RNA_old.PDB Date and time: Thu Sep 22 22:47:36 2011 Number of base-pairs: 56 Number of atoms: 3194 **************************************************************************** HEADER LIGASE/RNA 28-AUG-06 2DXI COMPND TRNA; EXPDTA X-RAY DIFFRACTION **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.010) C:.501_:[..G]G-----C[..C]:.572_:C (0.006) | 2 (0.014) C:.502_:[..G]G-*---U[..U]:.571_:C (0.008) | 3 (0.008) C:.503_:[..C]C-----G[..G]:.570_:C (0.010) | 4 (0.004) C:.504_:[..C]C-----G[..G]:.569_:C (0.008) | 5 (0.010) C:.505_:[..C]C-----G[..G]:.568_:C (0.010) | 6 (0.006) C:.506_:[..C]C-----G[..G]:.567_:C (0.007) | 7 (0.008) C:.507_:[..A]Ax----U[..U]:.566_:C (0.006) | 8 (0.007) C:.549_:[..G]G-----C[..C]:.565_:C (0.004) | 9 (0.004) C:.550_:[..G]G-----C[..C]:.564_:C (0.007) | 10 (0.006) C:.551_:[..G]G-----C[..C]:.563_:C (0.003) | 11 (0.004) C:.552_:[..G]G-----C[..C]:.562_:C (0.005) | 12 (0.004) C:.553_:[..G]G----xC[..C]:.561_:C (0.004) | 13 (0.005) C:.554_:[..U]U-**-xA[..A]:.558_:C (0.003) | 14 (0.007) C:.555_:[..U]Ux**+xG[..G]:.518_:C (0.008) x 15 (0.006) C:.519_:[..G]Gx---xC[..C]:.556_:C (0.002) + 16 (0.007) C:.538_:[..A]A-*---C[..C]:.532_:C (0.004) | 17 (0.005) C:.539_:[..G]G-----C[..C]:.531_:C (0.004) | 18 (0.010) C:.540_:[..G]G-----C[..C]:.530_:C (0.007) | 19 (0.005) C:.541_:[..C]C-----G[..G]:.529_:C (0.004) | 20 (0.003) C:.542_:[..C]C-----G[..G]:.528_:C (0.007) | 21 (0.009) C:.543_:[..G]G-----C[..C]:.527_:C (0.006) | 22 (0.006) C:.544_:[..A]Ax*---G[..G]:.526_:C (0.008) | 23 (0.009) C:.510_:[..G]G-----C[..C]:.525_:C (0.007) | 24 (0.007) C:.511_:[..U]U-----A[..A]:.524_:C (0.009) | 25 (0.008) C:.512_:[..C]C-----G[..G]:.523_:C (0.013) | 26 (0.004) C:.513_:[..U]U-*--xG[..G]:.522_:C (0.009) | 27 (0.007) C:.514_:[..A]Ax**-xU[..U]:.508_:C (0.007) | 28 (0.008) C:.520_:[..U]Ux**-xC[..C]:.548_:C (0.011) x 29 (0.014) D:.501_:[..G]G-----C[..C]:.572_:D (0.011) | 30 (0.011) D:.502_:[..G]G-*---U[..U]:.571_:D (0.010) | 31 (0.010) D:.503_:[..C]C-----G[..G]:.570_:D (0.007) | 32 (0.010) D:.504_:[..C]C-----G[..G]:.569_:D (0.003) | 33 (0.015) D:.505_:[..C]C-----G[..G]:.568_:D (0.011) | 34 (0.009) D:.506_:[..C]C-----G[..G]:.567_:D (0.007) | 35 (0.003) D:.507_:[..A]Ax----U[..U]:.566_:D (0.010) | 36 (0.008) D:.549_:[..G]G-----C[..C]:.565_:D (0.002) | 37 (0.003) D:.550_:[..G]G-----C[..C]:.564_:D (0.002) | 38 (0.005) D:.551_:[..G]G-----C[..C]:.563_:D (0.002) | 39 (0.003) D:.552_:[..G]G-----C[..C]:.562_:D (0.005) | 40 (0.005) D:.553_:[..G]G----xC[..C]:.561_:D (0.004) | 41 (0.003) D:.554_:[..U]U-**-xA[..A]:.558_:D (0.003) | 42 (0.005) D:.555_:[..U]Ux**+xG[..G]:.518_:D (0.004) x 43 (0.007) D:.519_:[..G]Gx---xC[..C]:.556_:D (0.003) + 44 (0.013) D:.538_:[..A]A-*---C[..C]:.532_:D (0.009) | 45 (0.011) D:.539_:[..G]G-----C[..C]:.531_:D (0.008) | 46 (0.007) D:.540_:[..G]G-----C[..C]:.530_:D (0.005) | 47 (0.004) D:.541_:[..C]C-----G[..G]:.529_:D (0.004) | 48 (0.006) D:.542_:[..C]C-----G[..G]:.528_:D (0.009) | 49 (0.010) D:.543_:[..G]G-----C[..C]:.527_:D (0.003) | 50 (0.010) D:.544_:[..A]Ax*---G[..G]:.526_:D (0.012) | 51 (0.007) D:.510_:[..G]G-----C[..C]:.525_:D (0.005) | 52 (0.004) D:.511_:[..U]U-----A[..A]:.524_:D (0.011) | 53 (0.005) D:.512_:[..C]C-----G[..G]:.523_:D (0.008) | 54 (0.008) D:.513_:[..U]U-*--xG[..G]:.522_:D (0.013) | 55 (0.007) D:.514_:[..A]Ax**-xU[..U]:.508_:D (0.006) | 56 (0.005) D:.520_:[..U]U-**--C[..C]:.548_:D (0.005) | Note: This structure contains 16[8] non-Watson-Crick base-pairs. **************************************************************************** Detailed H-bond information: atom-name pair and length [ON] 1 G-----C [3] O6 - N4 2.68 N1 - N3 2.91 N2 - O2 3.13 2 G-*---U [2] O6 - N3 2.74 N1 - O2 2.79 3 C-----G [3] O2 - N2 2.97 N3 - N1 2.92 N4 - O6 2.87 4 C-----G [3] O2 - N2 2.76 N3 - N1 2.87 N4 - O6 2.88 5 C-----G [3] O2 - N2 3.06 N3 - N1 2.94 N4 - O6 2.76 6 C-----G [3] O2 - N2 2.72 N3 - N1 2.84 N4 - O6 2.86 7 A-----U [2] N6 - O4 2.91 N1 - N3 3.07 8 G-----C [3] O6 - N4 3.57 N1 - N3 3.41 N2 - O2 3.13 9 G-----C [3] O6 - N4 2.99 N1 - N3 3.00 N2 - O2 2.89 10 G-----C [3] O6 - N4 3.01 N1 - N3 2.84 N2 - O2 2.54 11 G-----C [3] O6 - N4 2.93 N1 - N3 2.85 N2 - O2 2.65 12 G-----C [3] O6 - N4 2.70 N1 - N3 2.86 N2 - O2 2.93 13 U-**--A [3] O2 - N6 2.96 N3 - N7 3.01 O4 * O2P 3.42 14 U-**+-G [2] O2'- O6 3.62 O2 - N1 2.60 15 G-----C [3] O6 - N4 3.49 N1 - N3 3.18 N2 - O2 3.10 16 A-*---C [1] N6 - O2 3.04 17 G-----C [3] O6 - N4 3.00 N1 - N3 2.86 N2 - O2 2.67 18 G-----C [3] O6 - N4 3.12 N1 - N3 2.89 N2 - O2 2.61 19 C-----G [3] O2 - N2 2.64 N3 - N1 2.77 N4 - O6 2.82 20 C-----G [3] O2 - N2 2.61 N3 - N1 2.80 N4 - O6 2.93 21 G-----C [3] O6 - N4 3.10 N1 - N3 2.93 N2 - O2 2.85 22 A-*---G [2] N6 - O6 2.95 N1 - N1 2.87 23 G-----C [3] O6 - N4 2.85 N1 - N3 2.89 N2 - O2 2.82 24 U-----A [2] N3 - N1 2.74 O4 - N6 3.08 25 C-----G [3] O2 - N2 2.73 N3 - N1 2.89 N4 - O6 2.96 26 U-*---G [2] O2 - N1 2.72 N3 - O6 3.08 27 A-**--U [3] O2P* O4 3.40 N7 - N3 2.85 N6 - O2 2.74 28 U-**--C [1] O4 - N4 2.77 29 G-----C [3] O6 - N4 2.66 N1 - N3 2.77 N2 - O2 2.91 30 G-*---U [2] O6 - N3 2.77 N1 - O2 2.80 31 C-----G [3] O2 - N2 3.01 N3 - N1 2.92 N4 - O6 2.78 32 C-----G [3] O2 - N2 2.79 N3 - N1 2.87 N4 - O6 2.85 33 C-----G [3] O2 - N2 2.91 N3 - N1 2.86 N4 - O6 2.73 34 C-----G [3] O2 - N2 2.72 N3 - N1 2.79 N4 - O6 2.75 35 A-----U [2] N6 - O4 2.93 N1 - N3 3.07 36 G-----C [3] O6 - N4 2.88 N1 - N3 2.71 N2 - O2 2.45 37 G-----C [3] O6 - N4 3.02 N1 - N3 3.05 N2 - O2 2.95 38 G-----C [3] O6 - N4 3.06 N1 - N3 2.88 N2 - O2 2.59 39 G-----C [3] O6 - N4 2.91 N1 - N3 2.83 N2 - O2 2.63 40 G-----C [3] O6 - N4 2.83 N1 - N3 3.01 N2 - O2 3.10 41 U-**--A [3] O2 - N6 2.95 N3 - N7 2.99 O4 * O2P 3.40 42 U-**+-G [2] O2'- O6 3.76 O2 - N2 2.70 43 G-----C [3] O6 - N4 3.70 N1 - N3 3.30 N2 - O2 3.16 44 A-*---C [1] N6 - O2 2.97 45 G-----C [3] O6 - N4 2.92 N1 - N3 2.85 N2 - O2 2.72 46 G-----C [3] O6 - N4 3.16 N1 - N3 2.92 N2 - O2 2.66 47 C-----G [3] O2 - N2 2.66 N3 - N1 2.77 N4 - O6 2.82 48 C-----G [3] O2 - N2 2.57 N3 - N1 2.74 N4 - O6 2.85 49 G-----C [3] O6 - N4 3.15 N1 - N3 2.92 N2 - O2 2.82 50 A-*---G [2] N6 - O6 2.91 N1 - N1 2.86 51 G-----C [3] O6 - N4 2.92 N1 - N3 2.90 N2 - O2 2.76 52 U-----A [2] N3 - N1 2.78 O4 - N6 3.13 53 C-----G [3] O2 - N2 2.66 N3 - N1 2.92 N4 - O6 3.04 54 U-*---G [2] O2 - N1 2.62 N3 - O6 3.01 55 A-**--U [3] O2P* O4 3.47 N7 - N3 2.81 N6 - O2 2.77 56 U-**--C [1] O4 - N4 2.66 **************************************************************************** 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 1 GG/UC 1.05( 0.06) 0.00( 0.00) 0.00( 0.00) 1.37( 0.00) 2.42( 0.06) 2 GC/GU 7.07( 4.32) 0.00( 0.00) 0.00( 0.00) 6.67( 4.16) 13.74( 8.48) 3 CC/GG 0.16( 0.02) 0.00( 0.00) 0.29( 0.00) 2.96( 1.51) 3.41( 1.53) 4 CC/GG 0.00( 0.00) 0.00( 0.00) 0.26( 0.00) 3.73( 2.34) 3.98( 2.34) 5 CC/GG 0.54( 0.10) 0.00( 0.00) 0.12( 0.00) 2.99( 1.55) 3.65( 1.66) 6 CA/UG 0.01( 0.00) 0.00( 0.00) 2.58( 0.87) 0.11( 0.00) 2.70( 0.87) 7 AG/CU 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 1.94( 0.60) 1.94( 0.60) 8 GG/CC 1.97( 0.56) 0.00( 0.00) 0.14( 0.00) 0.58( 0.10) 2.70( 0.66) 9 GG/CC 3.76( 2.39) 0.00( 0.00) 0.24( 0.00) 0.32( 0.00) 4.32( 2.39) 10 GG/CC 4.39( 3.09) 0.00( 0.00) 0.29( 0.00) 0.00( 0.00) 4.68( 3.09) 11 GG/CC 4.22( 2.37) 0.00( 0.00) 0.56( 0.00) 0.00( 0.00) 4.78( 2.37) 12 GU/AC 6.53( 3.74) 0.00( 0.00) 0.00( 0.00) 2.00( 0.29) 8.53( 4.03) 13 UU/GA 5.74( 2.64) 0.00( 0.00) 0.00( 0.00) 5.06( 2.34) 10.80( 4.98) 14 UG/CG 0.00( 0.00) 0.27( 0.00) 0.58( 0.00) 2.07( 0.30) 2.92( 0.30) 15 GA/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 16 AG/CC 4.41( 2.45) 0.00( 0.00) 0.00( 0.00) 5.62( 2.75) 10.03( 5.20) 17 GG/CC 2.77( 1.26) 0.00( 0.00) 0.67( 0.00) 0.24( 0.00) 3.67( 1.26) 18 GC/GC 6.88( 3.75) 0.00( 0.00) 0.00( 0.00) 6.56( 3.44) 13.44( 7.19) 19 CC/GG 0.24( 0.01) 0.00( 0.00) 0.61( 0.00) 2.73( 1.24) 3.58( 1.25) 20 CG/CG 0.00( 0.00) 0.00( 0.00) 4.71( 2.02) 0.00( 0.00) 4.71( 2.02) 21 GA/GC 1.47( 0.00) 0.00( 0.00) 0.00( 0.00) 5.64( 2.71) 7.11( 2.71) 22 AG/CG 0.00( 0.00) 0.00( 0.00) 0.67( 0.00) 1.53( 0.92) 2.20( 0.92) 23 GU/AC 4.63( 2.05) 0.00( 0.00) 0.00( 0.00) 3.22( 2.14) 7.85( 4.19) 24 UC/GA 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.78( 2.31) 3.78( 2.31) 25 CU/GG 1.38( 0.13) 0.00( 0.00) 0.00( 0.00) 2.81( 1.28) 4.19( 1.41) 26 UA/UG 0.00( 0.00) 2.23( 0.06) 5.72( 4.34) 0.00( 0.00) 7.95( 4.40) 27 AU/CU 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 28 UG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 29 GG/UC 1.10( 0.09) 0.00( 0.00) 0.00( 0.00) 1.18( 0.01) 2.28( 0.10) 30 GC/GU 7.02( 4.36) 0.00( 0.00) 0.00( 0.00) 6.62( 4.11) 13.64( 8.47) 31 CC/GG 0.19( 0.00) 0.00( 0.00) 0.24( 0.00) 3.08( 1.66) 3.50( 1.66) 32 CC/GG 0.00( 0.00) 0.00( 0.00) 0.29( 0.00) 3.81( 2.44) 4.10( 2.44) 33 CC/GG 0.54( 0.08) 0.00( 0.00) 0.16( 0.00) 3.23( 1.82) 3.93( 1.91) 34 CA/UG 0.05( 0.00) 0.00( 0.00) 2.46( 0.87) 0.09( 0.00) 2.59( 0.87) 35 AG/CU 0.00( 0.00) 0.00( 0.00) 0.32( 0.00) 1.96( 0.59) 2.28( 0.59) 36 GG/CC 1.73( 0.38) 0.00( 0.00) 1.14( 0.00) 0.00( 0.00) 2.87( 0.38) 37 GG/CC 3.55( 2.13) 0.00( 0.00) 0.23( 0.00) 0.35( 0.00) 4.13( 2.13) 38 GG/CC 4.39( 3.06) 0.00( 0.00) 0.28( 0.00) 0.00( 0.00) 4.67( 3.06) 39 GG/CC 4.34( 2.68) 0.00( 0.00) 0.39( 0.00) 0.00( 0.00) 4.74( 2.68) 40 GU/AC 6.54( 3.76) 0.00( 0.00) 0.00( 0.00) 2.23( 0.35) 8.77( 4.11) 41 UU/GA 5.74( 2.68) 0.00( 0.00) 0.00( 0.00) 4.63( 1.95) 10.37( 4.63) 42 UG/CG 0.00( 0.00) 0.21( 0.00) 0.51( 0.00) 1.81( 0.19) 2.54( 0.19) 43 GA/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 44 AG/CC 4.88( 2.61) 0.00( 0.00) 0.00( 0.00) 6.02( 2.83) 10.90( 5.44) 45 GG/CC 2.88( 1.38) 0.00( 0.00) 0.64( 0.00) 0.15( 0.00) 3.67( 1.38) 46 GC/GC 6.87( 3.74) 0.00( 0.00) 0.00( 0.00) 6.51( 3.39) 13.38( 7.13) 47 CC/GG 0.21( 0.01) 0.00( 0.00) 0.61( 0.00) 2.72( 1.23) 3.54( 1.24) 48 CG/CG 0.00( 0.00) 0.00( 0.00) 4.75( 2.04) 0.00( 0.00) 4.75( 2.04) 49 GA/GC 1.50( 0.00) 0.00( 0.00) 0.00( 0.00) 5.46( 2.57) 6.96( 2.57) 50 AG/CG 0.00( 0.00) 0.00( 0.00) 0.71( 0.00) 1.21( 0.70) 1.92( 0.70) 51 GU/AC 4.69( 2.08) 0.00( 0.00) 0.00( 0.00) 3.47( 2.26) 8.16( 4.35) 52 UC/GA 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.61( 2.13) 3.61( 2.13) 53 CU/GG 1.54( 0.19) 0.00( 0.00) 0.00( 0.00) 2.79( 1.27) 4.34( 1.46) 54 UA/UG 0.00( 0.00) 2.41( 0.12) 6.00( 4.58) 0.00( 0.00) 8.41( 4.70) 55 AU/CU 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) **************************************************************************** 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 G-C 26.03 89.56 67.92 -0.63 -0.16 -0.76 2 G-U 25.11 88.91 65.14 -0.73 -0.26 -0.64 3 C-G 23.28 87.27 62.83 -0.77 -0.28 -0.57 4 C-G 20.86 84.65 61.69 -0.81 -0.28 -0.52 5 C-G 18.28 82.09 60.99 -0.83 -0.31 -0.47 6 C-G 14.62 80.96 60.98 -0.86 -0.22 -0.45 7 A-U 11.07 80.17 60.94 -0.90 0.02 -0.44 8 G-C 6.99 80.05 61.28 -0.87 -0.01 -0.49 9 G-C 3.85 81.96 60.05 -0.87 -0.01 -0.50 10 G-C 1.92 83.09 57.31 -0.83 -0.04 -0.55 11 G-C 0.46 83.04 53.91 -0.76 -0.11 -0.64 12 G-C -0.35 81.50 50.66 -0.78 -0.22 -0.58 13 U-A -1.17 78.85 46.89 -0.81 -0.20 -0.55 14 U+G -5.24 78.53 47.81 -0.83 -0.35 -0.43 15 G-C -7.34 73.56 40.30 -0.67 -0.41 -0.61 16 A-C 21.16 36.85 54.73 -0.57 0.77 -0.28 17 G-C 18.28 38.95 53.75 -0.61 0.78 -0.15 18 G-C 15.22 40.96 54.62 -0.55 0.84 -0.03 19 C-G 13.07 43.52 55.83 -0.50 0.87 -0.04 20 C-G 12.31 46.76 57.49 -0.40 0.92 -0.02 21 G-C 12.73 50.68 58.29 -0.14 0.98 -0.17 22 A-G 13.30 54.14 59.19 -0.12 0.96 -0.27 23 G-C 16.58 57.89 59.08 -0.02 0.85 -0.53 24 U-A 16.50 59.80 55.46 -0.15 0.84 -0.53 25 C-G 15.57 61.40 52.39 -0.29 0.82 -0.50 26 U-G 12.18 63.05 51.24 -0.35 0.82 -0.46 27 A-U 9.98 64.89 49.33 -0.37 0.79 -0.48 28 U-C 5.25 66.61 48.68 0.25 -0.88 0.40 29 G-C 85.40 90.14 130.89 -0.67 -0.21 -0.71 30 G-U 84.22 89.47 128.02 -0.78 -0.32 -0.54 31 C-G 82.33 87.69 125.97 -0.79 -0.38 -0.48 32 C-G 80.02 84.85 125.08 -0.86 -0.35 -0.37 33 C-G 77.54 82.14 124.86 -0.89 -0.34 -0.32 34 C-G 74.00 80.70 125.37 -0.91 -0.28 -0.31 35 A-U 70.45 79.71 125.76 -0.95 -0.06 -0.30 36 G-C 66.38 79.62 126.74 -0.93 -0.06 -0.36 37 G-C 63.06 81.92 126.13 -0.93 -0.04 -0.37 38 G-C 60.66 83.04 123.78 -0.92 -0.06 -0.40 39 G-C 58.71 82.99 120.76 -0.87 -0.11 -0.48 40 G-C 57.36 81.48 117.77 -0.86 -0.25 -0.44 41 U-A 55.85 78.81 114.34 -0.90 -0.20 -0.39 42 U+G 52.09 78.54 115.87 -0.90 -0.35 -0.25 43 G-C 48.63 73.42 108.96 -0.77 -0.43 -0.46 44 A-C 79.20 37.26 117.58 -0.61 0.77 -0.20 45 G-C 76.34 39.34 117.09 -0.63 0.78 -0.03 46 G-C 73.53 41.31 118.51 -0.54 0.84 0.07 47 C-G 71.65 43.81 120.19 -0.50 0.86 0.08 48 C-G 71.17 46.99 122.13 -0.39 0.92 0.09 49 G-C 71.71 50.77 122.99 -0.18 0.98 -0.11 50 A-G 72.39 54.26 123.91 -0.18 0.97 -0.19 51 G-C 75.57 57.98 123.17 -0.15 0.84 -0.53 52 U-A 74.90 59.94 119.67 -0.23 0.84 -0.49 53 C-G 73.41 61.47 116.85 -0.38 0.81 -0.45 54 U-G 69.88 63.22 116.29 -0.42 0.82 -0.38 55 A-U 67.33 64.97 114.71 -0.44 0.80 -0.40 56 U-C 62.51 66.77 114.90 0.33 -0.88 0.34 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 G-C -0.09 -0.18 0.06 -2.73 -18.63 -7.75 2 G-U -2.37 -0.61 0.20 8.94 -11.43 -3.36 3 C-G -0.03 -0.08 0.15 10.84 -16.01 -3.57 4 C-G 0.12 -0.14 0.13 7.53 -8.92 -0.59 5 C-G 0.17 -0.14 -0.22 8.26 -14.50 -4.76 6 C-G 0.27 -0.19 0.02 0.04 -9.53 0.61 7 A-U 0.22 0.09 -0.15 -2.02 -9.27 -6.24 8 G-C -0.52 0.40 -0.13 -14.74 -10.92 3.76 9 G-C -0.39 -0.05 -0.21 -13.17 -5.79 -0.56 10 G-C -0.29 -0.14 -0.09 -7.08 1.77 4.44 11 G-C 0.01 -0.12 -0.19 -6.98 -6.09 2.32 12 G-C -0.70 -0.48 0.66 -2.91 -6.29 -6.27 13 U-A 4.05 -1.85 1.11 -2.94 5.19 -96.41 14 U+G 0.18 -5.56 0.67 14.96 -0.79 -99.62 15 G-C -0.18 0.32 -0.32 -25.79 -33.71 6.58 16 A-C -4.84 -0.81 1.30 15.56 6.44 3.91 17 G-C -0.23 -0.13 0.36 10.61 -10.38 2.22 18 G-C -0.88 -0.25 0.01 2.96 -11.58 5.71 19 C-G 0.41 -0.29 0.12 3.17 -9.27 0.73 20 C-G 0.27 -0.21 0.01 1.59 -12.44 2.93 21 G-C -0.14 -0.03 -0.09 -18.45 -24.78 2.03 22 A-G 0.00 1.53 -0.08 -20.97 -22.60 -16.01 23 G-C -0.38 -0.19 0.13 6.12 3.19 -1.11 24 U-A -0.10 -0.11 0.15 -5.80 -8.95 6.28 25 C-G 0.30 -0.12 0.01 -3.77 -5.06 2.24 26 U-G 2.34 -0.35 -0.06 6.48 -4.57 7.26 27 A-U -4.13 -2.10 0.84 7.33 15.38 -94.21 28 U-C -1.95 2.38 0.59 8.89 17.51 -100.97 29 G-C -0.23 -0.37 0.28 0.70 -17.82 -6.86 30 G-U -2.36 -0.61 0.45 10.32 -10.50 -4.71 31 C-G 0.07 -0.11 0.01 14.92 -16.35 -5.09 32 C-G 0.12 -0.14 0.06 8.81 -8.32 -0.99 33 C-G 0.17 -0.18 -0.13 11.71 -10.97 -3.89 34 C-G 0.30 -0.27 -0.08 5.49 -8.10 -0.76 35 A-U 0.30 0.08 -0.32 -0.33 -8.13 -5.32 36 G-C -0.59 -0.34 -0.21 -12.48 -9.04 4.48 37 G-C -0.39 0.00 -0.16 -13.82 -4.88 -0.80 38 G-C -0.31 -0.10 -0.10 -9.44 4.07 4.59 39 G-C 0.09 -0.13 -0.03 -6.13 -5.01 2.13 40 G-C -0.66 -0.26 0.46 -3.99 -7.61 -6.65 41 U-A 4.02 -1.84 1.19 -2.98 6.17 -96.74 42 U+G 0.16 -5.94 0.75 14.28 -0.07 -100.41 43 G-C 0.06 0.48 -0.23 -26.77 -33.83 7.82 44 A-C -4.78 -0.81 1.31 15.26 2.02 2.64 45 G-C -0.34 -0.19 0.40 9.36 -11.75 0.60 46 G-C -0.86 -0.23 0.08 2.10 -13.28 5.26 47 C-G 0.50 -0.32 0.08 2.97 -11.84 0.71 48 C-G 0.15 -0.25 -0.01 -0.45 -12.70 2.65 49 G-C -0.09 -0.02 0.04 -16.48 -25.40 2.61 50 A-G -0.03 1.52 0.08 -19.42 -18.38 -17.05 51 G-C -0.46 -0.17 -0.03 6.89 3.39 0.63 52 U-A -0.13 -0.09 0.14 -4.48 -8.41 6.75 53 C-G 0.39 -0.13 -0.10 -0.92 -5.23 3.28 54 U-G 2.47 -0.43 -0.01 5.04 -4.27 7.74 55 A-U -4.11 -2.09 0.74 8.49 15.06 -95.30 56 U-C -2.04 2.12 0.67 13.37 17.14 -100.85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.31 -0.36 0.18 -0.04 -7.43 -14.00 s.d. 1.62 1.30 0.41 10.84 10.86 35.02 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 GG/UC -0.27 -1.25 2.72 -7.26 8.13 28.89 2 GC/GU -0.06 -1.04 3.21 -1.53 4.55 43.50 3 CC/GG 0.34 -1.80 3.27 0.26 3.43 32.31 4 CC/GG -0.40 -1.79 3.21 3.41 1.42 32.21 5 CC/GG 0.43 -1.71 3.41 -0.47 5.76 31.01 6 CA/UG -0.76 -1.44 3.24 4.31 13.34 33.67 7 AG/CU -1.83 -1.23 3.45 -3.43 1.73 48.96 8 GG/CC -0.60 -1.90 3.32 -0.05 0.30 32.79 9 GG/CC 0.39 -1.74 3.05 0.41 4.03 29.44 10 GG/CC 0.62 -1.76 3.20 4.41 6.44 30.96 11 GG/CC 0.96 -2.10 2.87 -3.31 6.73 25.88 12 GU/AC -1.57 -2.87 3.35 -2.27 1.22 99.68 13 UU/GA 2.27 -1.85 2.98 10.95 -2.71 44.85 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GA/CC ---- ---- ---- ---- ---- ---- 16 AG/CC -0.17 -1.04 3.54 1.11 8.19 48.37 17 GG/CC 0.14 -1.76 3.32 0.29 7.98 30.42 18 GC/GC -0.03 -1.42 3.26 -1.66 2.84 37.98 19 CC/GG 0.31 -1.89 3.18 3.14 5.98 29.90 20 CG/CG 0.24 -1.85 3.57 4.58 17.01 32.08 21 GA/GC -1.35 -1.34 3.08 -0.42 5.89 35.06 22 AG/CG -3.03 -2.30 3.22 13.08 10.98 57.63 23 GU/AC 0.21 -2.05 3.53 -1.31 7.21 36.54 24 UC/GA -0.50 -1.71 3.11 2.65 7.52 36.27 25 CU/GG 1.30 -2.23 2.97 1.88 3.90 26.85 26 UA/UG -0.97 -0.95 3.18 0.73 -2.37 66.66 27 AU/CU 4.29 -0.45 2.68 99.70 -138.17 -73.09 28 UG/CC ---- ---- ---- ---- ---- ---- 29 GG/UC -0.36 -1.36 2.85 -10.14 8.48 29.81 30 GC/GU -0.08 -1.01 3.15 0.80 4.71 43.89 31 CC/GG 0.24 -1.75 3.32 -1.39 7.34 32.47 32 CC/GG -0.41 -1.82 3.18 1.37 3.24 31.96 33 CC/GG 0.28 -1.67 3.46 -0.70 3.42 31.14 34 CA/UG -0.66 -1.38 3.38 3.87 12.31 34.04 35 AG/CU -1.70 -1.51 3.51 -2.52 3.08 49.09 36 GG/CC -0.78 -2.43 3.19 1.28 0.30 33.82 37 GG/CC 0.29 -1.76 3.06 0.41 1.97 29.66 38 GG/CC 0.60 -1.77 3.07 3.33 4.76 31.29 39 GG/CC 0.91 -2.08 2.81 -1.23 8.33 25.67 40 GU/AC -1.48 -2.79 3.34 -4.17 2.08 99.36 41 UU/GA 2.17 -1.71 2.99 11.47 -2.75 45.89 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GA/CC ---- ---- ---- ---- ---- ---- 44 AG/CC -0.14 -0.93 3.44 0.81 9.94 48.15 45 GG/CC 0.22 -1.74 3.28 -0.31 8.02 31.74 46 GC/GC 0.01 -1.47 3.22 -0.30 2.99 38.10 47 CC/GG 0.30 -1.93 3.20 3.28 6.16 28.23 48 CG/CG 0.25 -1.83 3.46 3.33 17.02 33.05 49 GA/GC -1.33 -1.38 3.13 -0.66 4.38 34.88 50 AG/CG -2.92 -2.46 3.15 14.66 14.73 58.46 51 GU/AC 0.15 -1.97 3.55 -2.10 4.74 36.68 52 UC/GA -0.40 -1.74 3.05 3.68 7.97 36.50 53 CU/GG 1.31 -2.16 3.07 1.03 4.72 27.76 54 UA/UG -1.12 -0.96 3.14 0.34 -2.00 65.85 55 AU/CU 4.50 -0.54 2.45 101.54 -137.94 -83.01 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.00 -1.67 3.19 5.14 -0.21 35.07 s.d. 1.38 0.50 0.24 20.18 28.78 28.11 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 GG/UC -3.60 -0.61 2.29 15.61 13.94 30.84 2 GC/GU -1.82 -0.07 3.09 6.12 2.06 43.75 3 CC/GG -3.80 -0.56 3.07 6.14 -0.47 32.49 4 CC/GG -3.45 1.29 3.07 2.55 -6.12 32.42 5 CC/GG -4.21 -0.88 3.04 10.67 0.87 31.53 6 CA/UG -3.98 1.76 2.41 21.89 -7.07 36.40 7 AG/CU -1.62 1.93 3.52 2.09 4.13 49.10 8 GG/CC -3.42 1.06 3.30 0.53 0.09 32.79 9 GG/CC -4.16 -0.69 2.80 7.89 -0.80 29.71 10 GG/CC -4.30 -0.38 2.84 11.84 -8.10 31.90 11 GG/CC -5.85 -2.72 2.13 14.64 7.19 26.93 12 GU/AC -1.90 0.99 3.35 0.80 1.48 99.70 13 UU/GA -2.13 -1.95 3.52 -3.48 -14.08 46.18 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GA/CC ---- ---- ---- ---- ---- ---- 16 AG/CC -1.91 0.30 3.33 9.91 -1.34 49.03 17 GG/CC -4.66 -0.20 2.78 14.88 -0.54 31.42 18 GC/GC -2.53 -0.17 3.15 4.35 2.54 38.12 19 CC/GG -4.67 -0.01 2.78 11.40 -5.99 30.64 20 CG/CG -5.23 0.23 2.34 28.27 -7.62 36.49 21 GA/GC -2.98 2.16 2.84 9.70 0.68 35.54 22 AG/CG -2.76 3.58 2.12 11.13 -13.25 59.90 23 GU/AC -4.19 -0.51 3.08 11.35 2.06 37.25 24 UC/GA -3.59 1.10 2.67 11.90 -4.20 37.11 25 CU/GG -5.61 -2.35 2.71 8.33 -4.01 27.19 26 UA/UG -0.78 0.91 3.19 -2.15 -0.67 66.70 27 AU/CU 0.63 2.44 -0.71 70.66 50.98 -172.28 28 UG/CC ---- ---- ---- ---- ---- ---- 29 GG/UC -3.67 -0.83 2.38 15.56 18.61 32.55 30 GC/GU -1.77 0.17 3.03 6.28 -1.06 44.14 31 CC/GG -4.23 -0.64 2.86 12.92 2.45 33.30 32 CC/GG -3.82 0.97 2.96 5.86 -2.48 32.15 33 CC/GG -3.75 -0.66 3.26 6.34 1.31 31.33 34 CA/UG -3.85 1.58 2.65 20.15 -6.34 36.34 35 AG/CU -2.06 1.84 3.50 3.70 3.02 49.24 36 GG/CC -4.22 1.53 3.14 0.51 -2.19 33.85 37 GG/CC -3.81 -0.50 2.94 3.85 -0.80 29.73 38 GG/CC -4.02 -0.54 2.83 8.73 -6.11 31.81 39 GG/CC -6.06 -2.18 2.01 18.13 2.68 27.00 40 GU/AC -1.86 0.90 3.34 1.36 2.73 99.44 41 UU/GA -1.90 -1.76 3.50 -3.46 -14.44 47.30 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GA/CC ---- ---- ---- ---- ---- ---- 44 AG/CC -1.88 0.23 3.20 12.04 -0.98 49.12 45 GG/CC -4.40 -0.44 2.77 14.38 0.56 32.71 46 GC/GC -2.62 -0.05 3.10 4.57 0.46 38.21 47 CC/GG -5.10 0.07 2.75 12.40 -6.59 29.07 48 CG/CG -4.99 0.02 2.29 27.68 -5.41 37.21 49 GA/GC -2.89 2.11 2.96 7.28 1.10 35.15 50 AG/CG -2.94 3.38 1.83 14.59 -14.52 61.74 51 GU/AC -3.78 -0.53 3.27 7.48 3.32 37.03 52 UC/GA -3.62 1.05 2.57 12.51 -5.78 37.50 53 CU/GG -5.43 -2.48 2.72 9.74 -2.12 28.17 54 UA/UG -0.81 1.05 3.16 -1.84 -0.31 65.88 55 AU/CU 0.59 2.49 -0.70 70.15 51.64 -173.48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -3.31 0.27 2.74 11.56 0.61 32.15 s.d. 1.51 1.45 0.82 14.04 12.12 45.04 **************************************************************************** Structure classification: This structure contains more than one helical regions This is a right-handed nucleic acid structure **************************************************************************** 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 G-C 49.0 49.7 11.0 9.1 9.8 2 G-U 39.9 66.4 10.5 8.8 9.7 3 C-G 51.8 52.6 10.9 9.1 9.9 4 C-G 53.6 53.8 10.7 9.0 9.9 5 C-G 52.0 52.0 10.9 9.0 9.9 6 C-G 56.1 52.9 10.6 8.9 9.9 7 A-U 52.8 50.3 11.1 9.2 10.0 8 G-C 53.6 58.0 11.0 9.4 10.4 9 G-C 52.1 55.2 10.8 9.0 9.9 10 G-C 55.6 57.5 10.4 8.8 9.9 11 G-C 56.1 55.0 10.6 8.9 9.9 12 G-C 46.9 54.2 10.6 8.8 9.6 13 U-A 31.4 18.2 9.9 7.4 6.4 14 U+G 106.5 30.1 8.7 8.1 9.7 15 G-C 58.5 54.0 10.7 9.1 10.1 16 A-C 28.3 82.3 11.0 9.5 10.3 17 G-C 54.0 56.6 10.5 8.9 9.9 18 G-C 51.8 60.9 10.4 8.8 9.8 19 C-G 56.5 53.3 10.5 8.8 9.7 20 C-G 57.2 55.0 10.5 8.8 9.8 21 G-C 55.3 54.4 10.6 8.9 9.9 22 A-G 49.3 46.5 12.7 10.7 11.1 23 G-C 52.2 54.7 10.7 8.9 9.8 24 U-A 57.5 58.9 10.3 8.7 9.8 25 C-G 57.0 54.8 10.6 8.9 9.9 26 U-G 71.9 46.3 10.3 8.8 9.9 27 A-U 17.3 33.5 9.7 7.2 6.3 28 U-C 7.8 14.8 13.2 10.3 9.1 29 G-C 47.9 50.3 10.8 8.9 9.6 30 G-U 38.9 65.8 10.6 8.8 9.7 31 C-G 51.2 52.1 10.8 9.0 9.8 32 C-G 54.7 53.7 10.7 9.0 9.9 33 C-G 52.3 52.5 10.7 9.0 9.8 34 C-G 55.4 52.6 10.6 8.8 9.8 35 A-U 54.9 50.6 11.0 9.2 10.0 36 G-C 53.6 59.0 10.3 8.6 9.6 37 G-C 52.1 55.5 10.8 9.1 10.0 38 G-C 55.5 57.7 10.5 8.9 9.9 39 G-C 56.2 54.5 10.6 8.9 9.9 40 G-C 46.6 53.5 10.9 9.0 9.8 41 U-A 30.8 18.5 9.9 7.3 6.3 42 U+G 108.0 32.1 8.8 8.3 9.9 43 G-C 60.5 53.4 10.8 9.2 10.2 44 A-C 27.5 80.9 11.0 9.5 10.3 45 G-C 52.5 56.1 10.6 8.9 9.8 46 G-C 51.0 60.6 10.4 8.8 9.8 47 C-G 56.9 52.1 10.5 8.8 9.7 48 C-G 56.1 55.0 10.4 8.8 9.8 49 G-C 56.4 54.1 10.6 8.9 9.9 50 A-G 49.4 46.7 12.7 10.7 11.1 51 G-C 52.1 56.1 10.6 8.9 9.8 52 U-A 58.0 59.4 10.2 8.7 9.8 53 C-G 57.2 54.8 10.5 8.9 9.9 54 U-G 72.6 45.6 10.2 8.8 9.9 55 A-U 17.8 33.0 9.7 7.1 6.2 56 U-C 9.0 15.0 12.9 10.0 8.8 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like; intermediate of A and B, or other cases step Xp Yp Zp XpH YpH ZpH Form 1 GG/UC -1.26 8.21 2.20 -4.53 7.34 4.34 A 2 GC/GU -1.27 8.41 2.44 -2.93 8.12 3.28 A 3 CC/GG -1.29 8.23 2.73 -4.94 7.91 3.56 A 4 CC/GG -1.14 8.15 2.69 -4.48 8.03 3.04 A 5 CC/GG -1.30 8.28 2.60 -5.35 7.68 4.04 A 6 CA/UG -1.52 8.27 2.45 -5.23 6.86 5.19 A 7 AG/CU -2.40 7.64 2.79 -3.88 7.55 3.11 A 8 GG/CC -1.56 8.17 2.70 -4.85 8.15 2.77 A 9 GG/CC -1.30 8.24 2.68 -5.31 7.82 3.75 A 10 GG/CC -1.59 8.18 2.66 -5.65 7.50 4.17 A 11 GG/CC -1.86 8.07 3.02 -7.57 7.06 4.97 A 12 GU/AC -1.00 6.77 4.14 -2.24 6.74 4.15 13 UU/GA 4.03 4.30 0.47 1.50 4.34 0.94 14 UG/CG --- --- --- --- --- --- --- 15 GA/CC --- --- --- --- --- --- --- 16 AG/CC -1.61 8.36 3.06 -3.37 7.78 4.30 A 17 GG/CC -1.81 8.12 2.72 -6.30 7.19 4.64 A 18 GC/GC -1.70 8.26 2.55 -4.08 8.06 3.14 A 19 CC/GG -1.66 8.15 2.71 -6.15 7.48 4.22 A 20 CG/CG -1.99 8.28 2.54 -6.88 6.22 5.99 A 21 GA/GC -1.20 8.75 2.15 -4.06 8.29 3.53 A 22 AG/CG -2.35 7.11 4.47 -4.86 6.28 5.20 23 GU/AC -1.60 7.68 3.17 -5.56 6.95 4.56 A 24 UC/GA -1.61 7.92 2.85 -4.98 7.21 4.34 A 25 CU/GG -1.72 8.37 2.60 -7.15 7.92 3.77 A 26 UA/UG -1.46 6.53 2.50 -2.12 6.60 2.32 27 AU/CU 4.07 0.78 9.85 2.80 -5.29 5.03 28 UG/CC --- --- --- --- --- --- --- 29 GG/UC -1.28 8.13 2.33 -4.43 7.24 4.38 A 30 GC/GU -1.13 8.42 2.46 -2.79 8.13 3.29 A 31 CC/GG -1.27 8.27 2.64 -5.29 7.51 4.34 A 32 CC/GG -1.14 8.18 2.65 -4.83 7.88 3.45 A 33 CC/GG -1.20 8.24 2.60 -4.81 7.92 3.46 A 34 CA/UG -1.44 8.20 2.47 -5.06 6.93 5.00 A 35 AG/CU -2.39 7.22 3.01 -4.26 7.03 3.47 36 GG/CC -1.67 7.75 2.87 -5.69 7.73 2.92 A 37 GG/CC -1.31 8.22 2.75 -4.98 8.02 3.27 A 38 GG/CC -1.60 8.15 2.76 -5.40 7.66 3.88 A 39 GG/CC -1.86 8.14 3.04 -7.76 6.83 5.39 A 40 GU/AC -0.98 6.88 4.06 -2.22 6.82 4.06 41 UU/GA 4.05 4.28 0.47 1.73 4.32 0.96 42 UG/CG --- --- --- --- --- --- --- 43 GA/CC --- --- --- --- --- --- --- 44 AG/CC -1.56 8.46 3.01 -3.29 7.73 4.55 A 45 GG/CC -1.70 8.14 2.76 -5.92 7.25 4.63 A 46 GC/GC -1.68 8.22 2.60 -4.15 8.00 3.21 A 47 CC/GG -1.64 8.22 2.67 -6.57 7.48 4.32 A 48 CG/CG -1.97 8.24 2.54 -6.65 6.25 5.92 A 49 GA/GC -1.20 8.75 2.23 -3.99 8.42 3.27 A 50 AG/CG -2.37 6.97 4.59 -5.01 5.84 5.54 51 GU/AC -1.65 7.63 3.14 -5.21 7.18 4.07 A 52 UC/GA -1.64 7.88 2.80 -5.03 7.14 4.35 A 53 CU/GG -1.79 8.39 2.61 -7.05 7.84 3.96 A 54 UA/UG -1.49 6.51 2.60 -2.17 6.58 2.43 55 AU/CU 3.83 0.12 9.73 2.59 -5.22 5.02 **************************************************************************** Minor and major groove widths: direct P-P distances and refined P-P distances which take into account the directions of the sugar-phosphate backbones (Subtract 5.8 Angstrom from the values to take account of the vdw radii of the phosphate groups, and for comparison with FreeHelix and Curves.) Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343. Minor Groove Major Groove P-P Refined P-P Refined 1 GG/UC --- --- --- --- 2 GC/GU --- --- --- --- 3 CC/GG 16.1 --- 14.7 --- 4 CC/GG 15.8 15.1 16.2 13.4 5 CC/GG 16.4 14.9 15.5 13.1 6 CA/UG 16.5 14.5 13.8 11.8 7 AG/CU 16.0 14.4 13.1 11.7 8 GG/CC 16.2 14.9 13.4 12.2 9 GG/CC 16.9 15.8 15.3 11.7 10 GG/CC 17.1 15.8 16.2 13.4 11 GG/CC 16.7 --- 13.4 --- 12 GU/AC --- --- --- --- 13 UU/GA --- --- --- --- 14 UG/CG --- --- --- --- 15 GA/CC --- --- --- --- 16 AG/CC --- --- --- --- 17 GG/CC --- --- --- --- 18 GC/GC 16.5 --- 16.0 --- 19 CC/GG 16.3 15.2 16.0 9.7 20 CG/CG 18.4 15.1 15.4 10.0 21 GA/GC 19.5 15.3 13.6 10.1 22 AG/CG 17.9 15.2 12.1 9.8 23 GU/AC 17.2 15.1 11.4 11.1 24 UC/GA 17.0 15.6 15.0 10.5 25 CU/GG 19.7 --- 8.5 --- 26 UA/UG --- --- --- --- 27 AU/CU --- --- --- --- 28 UG/CC --- --- --- --- 29 GG/UC --- --- --- --- 30 GC/GU --- --- --- --- 31 CC/GG 16.4 --- 14.3 --- 32 CC/GG 16.1 15.4 15.8 12.7 33 CC/GG 16.6 15.0 15.4 12.5 34 CA/UG 16.7 14.4 13.7 11.4 35 AG/CU 15.8 13.9 13.0 11.3 36 GG/CC 15.7 14.2 13.6 12.4 37 GG/CC 16.3 15.2 15.3 11.8 38 GG/CC 16.8 15.6 16.1 13.3 39 GG/CC 16.6 --- 13.0 --- 40 GU/AC --- --- --- --- 41 UU/GA --- --- --- --- 42 UG/CG --- --- --- --- 43 GA/CC --- --- --- --- 44 AG/CC --- --- --- --- 45 GG/CC --- --- --- --- 46 GC/GC 16.4 --- 16.0 --- 47 CC/GG 16.2 15.1 16.0 9.7 48 CG/CG 18.4 15.2 15.4 9.8 49 GA/GC 19.7 15.4 13.6 9.8 50 AG/CG 18.0 15.1 12.0 9.4 51 GU/AC 17.1 15.0 11.3 11.0 52 UC/GA 17.0 15.5 15.0 10.4 53 CU/GG 19.7 --- 8.1 --- 54 UA/UG --- --- --- --- 55 AU/CU --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 0.44(3.50) **************************************************************************** Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 G --- 175.2 50.8 88.3 -145.6 -79.9 -174.3 2 G -76.5 -177.6 54.8 86.2 -146.3 -69.6 -162.6 3 C -68.6 171.9 52.5 81.6 -151.4 -69.3 -159.7 4 C -67.4 170.8 58.1 80.7 -153.8 -80.6 -165.9 5 C -55.5 168.0 50.0 81.5 -152.5 -72.3 -158.4 6 C -60.6 168.9 58.3 85.5 -164.3 -70.9 -165.4 7 A -56.5 -167.0 51.7 113.8 --- --- -119.4 8 G --- 148.1 43.5 85.1 -147.7 -71.8 177.8 9 G -66.7 -174.8 51.8 82.1 -161.9 -61.4 -167.2 10 G -70.7 -171.7 49.7 80.3 -174.3 -78.6 -160.4 11 G 165.2 -153.0 163.8 85.4 -105.4 -44.0 179.7 12 G -107.4 85.5 158.3 88.0 -127.7 -62.1 167.5 13 U -61.4 -175.0 33.8 81.0 -121.3 -76.1 -160.4 14 U -49.9 150.4 56.2 80.7 --- --- -152.4 15 G --- -137.5 53.2 112.6 --- --- -63.6 16 A --- 167.5 49.6 86.5 -141.9 -61.6 -168.2 17 G -66.1 172.9 50.2 82.3 -153.0 -75.0 -163.8 18 G -58.0 175.0 47.5 80.2 -149.9 -69.2 -163.4 19 C -63.3 170.7 53.0 80.9 -152.7 -71.6 -163.6 20 C -67.3 170.7 57.2 80.3 -155.0 -70.6 -163.4 21 G -55.6 172.7 51.8 80.1 -157.9 -78.2 -162.7 22 A -67.6 174.8 52.3 81.2 --- --- -155.9 23 G --- 174.5 56.0 88.2 -143.1 -72.0 179.8 24 U -63.7 179.8 45.3 81.4 -153.0 -72.5 -172.6 25 C -61.0 -175.7 42.6 81.2 -154.4 -61.5 -156.0 26 U 153.8 -165.2 -175.2 84.1 -151.2 -76.1 -174.3 27 A -57.6 -173.7 44.5 80.1 --- --- -164.5 28 U --- 138.3 29.0 85.4 --- --- -112.2 29 G --- 175.4 47.3 85.6 -145.6 -76.8 -171.7 30 G -69.3 179.1 49.4 84.5 -139.5 -73.6 -165.4 31 C -62.0 165.5 51.0 81.9 -148.2 -72.6 -158.4 32 C -63.3 171.5 50.9 80.0 -154.2 -76.7 -163.1 33 C -56.1 172.1 49.5 80.1 -154.9 -70.0 -157.4 34 C -60.1 169.9 56.1 84.2 -167.3 -67.1 -163.4 35 A -57.5 -161.4 47.6 108.9 --- --- -121.5 36 G --- 150.5 43.5 85.4 -145.2 -75.0 174.3 37 G -63.4 -176.7 51.8 82.9 -162.0 -60.8 -168.8 38 G -70.4 -171.9 49.7 81.0 -172.6 -80.5 -162.8 39 G 161.7 -151.0 166.2 85.4 -101.0 -45.0 178.3 40 G -101.9 81.5 159.3 88.1 -126.7 -61.8 167.5 41 U -61.6 -174.8 33.1 80.7 -121.6 -75.5 -161.5 42 U -51.1 151.2 57.2 80.7 --- --- -153.2 43 G --- -136.7 53.2 113.5 --- --- -64.9 44 A --- 168.1 52.8 85.2 -139.2 -61.8 -167.9 45 G -66.6 170.5 49.9 79.6 -150.9 -75.2 -165.5 46 G -54.6 172.0 45.6 78.8 -149.6 -67.6 -165.2 47 C -63.8 172.2 52.3 81.5 -151.1 -72.2 -162.8 48 C -66.9 167.2 59.9 80.1 -153.5 -73.2 -166.3 49 G -54.8 172.6 51.0 80.2 -156.3 -79.4 -161.3 50 A -65.7 173.1 52.6 81.0 --- --- -157.2 51 G --- 174.8 56.8 88.4 -145.6 -72.4 -179.8 52 U -62.3 179.4 43.7 80.9 -155.1 -68.8 -171.9 53 C -67.0 -170.7 47.2 81.5 -157.8 -57.9 -153.2 54 U 152.6 -168.3 -175.2 85.3 -153.7 -75.8 -174.4 55 A -58.1 -172.8 44.5 81.8 --- --- -164.6 56 U --- 136.7 29.3 86.0 --- --- -111.4 Strand II base alpha beta gamma delta epsilon zeta chi 1 C 162.1 -151.9 159.8 92.4 --- --- -158.4 2 U -60.1 171.1 52.5 84.1 -163.4 -91.5 -154.9 3 G -58.7 171.4 53.1 82.4 -152.1 -67.9 -167.7 4 G -55.5 173.0 49.4 82.0 -159.6 -71.6 -169.5 5 G -56.9 168.9 48.9 78.5 -156.2 -68.8 -168.2 6 G -61.0 174.3 48.9 80.0 -147.4 -75.3 -166.3 7 U -65.8 177.0 49.5 82.8 -151.9 -68.3 -159.4 8 C -60.9 163.5 55.1 83.0 -152.5 -66.1 -162.1 9 C -58.3 164.0 55.2 82.6 -147.3 -75.1 -163.8 10 C -71.6 -168.4 47.4 84.9 -152.9 -78.4 -160.4 11 C -68.3 -178.4 49.9 84.4 -165.3 -65.8 -160.8 12 C --- -166.1 44.2 82.1 -150.6 -80.7 -175.9 13 A --- -106.2 -160.6 100.4 --- --- -129.0 14 G --- -153.5 -63.5 103.1 --- --- -110.7 15 C --- 153.7 52.6 84.8 --- --- -165.6 16 C -55.6 164.1 50.9 85.5 --- --- -161.9 17 C -66.0 174.4 56.0 82.6 -138.1 -73.3 -165.0 18 C -71.2 178.7 57.1 84.0 -157.2 -70.4 -162.2 19 G -57.8 171.3 52.4 81.9 -157.0 -68.5 -169.0 20 G -66.4 178.0 47.7 79.4 -151.4 -77.6 -167.3 21 C -64.6 176.5 49.8 80.0 -144.9 -75.1 -156.8 22 G -65.1 168.6 48.6 83.3 -147.6 -67.7 -162.6 23 C -58.7 175.5 52.3 84.3 -144.7 -61.4 -167.0 24 A -65.4 175.5 49.5 80.9 -151.2 -76.6 -167.3 25 G -49.2 167.6 51.5 80.0 -151.8 -71.8 -167.3 26 G --- 143.8 45.5 79.5 -148.3 -80.6 -172.0 27 U --- 168.2 35.4 82.4 --- --- -150.9 28 C --- 105.5 173.0 130.9 --- --- -125.4 29 C 168.5 -148.9 158.6 89.0 --- --- -156.0 30 U -63.7 172.5 54.2 86.5 -169.5 -88.5 -157.5 31 G -59.2 174.1 52.8 83.7 -155.1 -66.6 -165.6 32 G -54.1 173.3 48.2 82.3 -160.7 -70.8 -167.3 33 G -58.3 172.0 48.7 80.1 -157.0 -69.9 -168.4 34 G -62.4 176.3 48.5 80.0 -150.8 -72.6 -167.9 35 U -68.0 178.7 49.6 83.2 -153.9 -66.3 -160.0 36 C -65.0 -177.2 54.5 81.5 -153.3 -64.8 -162.9 37 C -57.7 161.9 52.2 82.3 -158.3 -62.4 -166.7 38 C -70.3 -170.2 47.8 85.5 -153.9 -78.5 -160.3 39 C -69.0 -177.7 49.3 84.0 -164.2 -68.0 -163.3 40 C --- -166.7 44.5 82.7 -151.3 -78.7 -173.7 41 A --- -104.8 -160.7 100.0 --- --- -129.5 42 G --- -155.0 -61.0 103.2 --- --- -108.9 43 C --- 154.7 52.9 85.3 --- --- -165.5 44 C -55.1 159.9 50.6 85.5 --- --- -161.3 45 C -63.9 173.6 55.2 83.9 -137.5 -74.0 -163.1 46 C -71.5 178.4 57.1 84.0 -155.5 -71.5 -163.3 47 G -57.3 169.7 52.0 79.8 -156.0 -66.8 -170.0 48 G -66.9 178.2 47.8 80.3 -152.3 -76.3 -164.9 49 C -61.9 176.1 47.2 79.4 -146.7 -73.7 -157.3 50 G -66.1 172.4 48.6 83.9 -147.0 -67.5 -165.5 51 C -58.0 176.6 50.0 86.0 -144.8 -62.5 -166.1 52 A -66.7 177.1 50.1 82.1 -152.2 -76.9 -167.8 53 G -54.3 171.0 52.7 79.5 -150.9 -71.5 -170.0 54 G --- 141.0 44.7 78.5 -149.2 -77.5 -171.2 55 U --- 173.3 33.2 83.3 --- --- -151.8 56 C --- 107.2 173.2 133.5 --- --- -125.8 **************************************************************************** Sugar conformational parameters: Note: v0: C4'-O4'-C1'-C2' v1: O4'-C1'-C2'-C3' v2: C1'-C2'-C3'-C4' v3: C2'-C3'-C4'-O4' v4: C3'-C4'-O4'-C1' tm: amplitude of pseudorotation of the sugar ring P: phase angle of pseudorotation of the sugar ring Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 G 7.8 -27.9 36.4 -32.7 15.8 36.7 6.5 C3'-endo 2 G 6.7 -28.4 38.3 -35.5 18.2 38.8 9.0 C3'-endo 3 C 5.3 -29.5 41.2 -39.2 21.4 42.1 11.5 C3'-endo 4 C 0.9 -27.1 41.4 -41.9 25.8 43.4 17.3 C3'-endo 5 C 5.6 -28.8 40.0 -37.5 20.0 40.7 10.6 C3'-endo 6 C 0.5 -24.1 37.0 -37.6 23.5 38.8 17.8 C3'-endo 7 A -6.6 17.3 -21.3 18.2 -7.3 21.3 181.3 C3'-exo 8 G 10.3 -31.3 39.2 -34.4 15.2 39.3 3.8 C3'-endo 9 G 3.6 -27.9 40.3 -39.2 22.3 41.4 13.6 C3'-endo 10 G 0.9 -25.1 38.7 -39.1 24.0 40.5 17.3 C3'-endo 11 G 8.4 -29.2 37.8 -34.1 16.3 38.0 6.3 C3'-endo 12 G 10.2 -27.6 33.6 -28.8 11.9 33.6 1.7 C3'-endo 13 U 8.1 -29.7 38.9 -35.4 17.3 39.2 7.1 C3'-endo 14 U 0.5 -26.0 40.5 -41.0 25.6 42.5 17.8 C3'-endo 15 G 0.2 13.4 -21.5 22.3 -13.9 22.8 199.2 C3'-exo 16 A 8.5 -29.1 37.8 -34.0 16.1 38.0 6.1 C3'-endo 17 G 2.6 -27.4 40.3 -39.7 23.3 41.7 14.9 C3'-endo 18 G 1.4 -26.4 39.9 -40.2 24.5 41.6 16.7 C3'-endo 19 C -0.9 -24.0 38.2 -39.8 25.6 40.6 19.8 C3'-endo 20 C -1.2 -24.7 39.8 -41.5 27.0 42.4 20.2 C3'-endo 21 G -3.7 -21.4 37.0 -40.1 27.7 40.4 23.7 C3'-endo 22 A 3.5 -27.6 40.0 -38.9 22.4 41.2 13.8 C3'-endo 23 G 7.9 -29.1 37.8 -34.4 16.8 38.1 7.0 C3'-endo 24 U 7.2 -31.2 41.8 -38.7 20.0 42.3 9.0 C3'-endo 25 C 6.7 -28.7 38.7 -35.8 18.3 39.2 9.0 C3'-endo 26 U 6.0 -28.1 38.4 -36.0 19.0 39.0 10.0 C3'-endo 27 A -3.0 -21.2 35.9 -38.7 26.6 39.0 23.0 C3'-endo 28 U -2.7 -18.8 31.8 -34.6 23.5 34.6 23.2 C3'-endo 29 G 6.8 -28.7 38.3 -35.6 18.3 38.8 8.9 C3'-endo 30 G 6.2 -28.5 38.5 -35.9 18.8 39.1 9.6 C3'-endo 31 C 5.7 -29.2 40.4 -38.1 20.5 41.1 10.8 C3'-endo 32 C 4.0 -28.0 40.2 -38.8 22.0 41.3 13.1 C3'-endo 33 C 6.0 -30.5 42.1 -39.5 21.2 42.8 10.6 C3'-endo 34 C 0.1 -24.3 37.7 -38.9 24.5 39.8 18.6 C3'-endo 35 A -4.0 15.4 -20.9 19.4 -9.5 21.1 188.4 C3'-exo 36 G 10.5 -31.7 39.7 -34.7 15.3 39.8 3.6 C3'-endo 37 G 4.8 -28.7 40.4 -38.6 21.2 41.3 11.9 C3'-endo 38 G 1.9 -25.0 37.4 -37.3 22.3 38.9 15.9 C3'-endo 39 G 8.1 -29.2 38.2 -34.7 16.7 38.4 6.8 C3'-endo 40 G 10.0 -27.0 33.0 -28.4 11.6 33.0 1.7 C3'-endo 41 U 6.3 -28.7 39.0 -36.5 19.0 39.6 9.7 C3'-endo 42 U -0.4 -25.0 39.6 -40.8 26.0 41.9 19.1 C3'-endo 43 G 0.1 13.4 -21.4 22.1 -13.7 22.6 198.8 C3'-exo 44 A 5.2 -27.7 38.6 -36.5 19.8 39.3 11.2 C3'-endo 45 G 2.0 -28.2 42.3 -42.1 25.2 44.0 15.9 C3'-endo 46 G 3.4 -28.4 41.2 -40.0 23.2 42.5 13.9 C3'-endo 47 C 0.1 -25.3 39.3 -40.3 25.3 41.4 18.4 C3'-endo 48 C -5.0 -21.9 38.9 -42.7 30.1 42.9 25.0 C3'-endo 49 G -3.2 -21.0 36.0 -38.8 26.5 39.1 23.2 C3'-endo 50 A 2.4 -26.2 38.9 -38.4 22.7 40.3 15.2 C3'-endo 51 G 8.9 -30.6 39.2 -35.2 16.7 39.4 5.8 C3'-endo 52 U 6.9 -31.2 42.4 -39.5 20.6 43.0 9.6 C3'-endo 53 C 6.2 -28.8 39.5 -36.8 19.4 40.1 9.9 C3'-endo 54 U 6.7 -28.7 38.5 -35.7 18.4 39.0 9.0 C3'-endo 55 A -3.8 -21.3 36.7 -39.9 27.6 40.2 23.8 C3'-endo 56 U -4.1 -17.6 31.0 -34.7 24.5 34.4 25.6 C3'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 C 6.6 -24.8 32.3 -29.6 14.6 32.6 7.4 C3'-endo 2 U 4.4 -25.1 35.1 -33.6 18.4 35.8 11.8 C3'-endo 3 G -0.1 -24.6 38.5 -39.5 25.0 40.7 18.6 C3'-endo 4 G 3.3 -26.6 38.2 -37.5 21.6 39.4 14.0 C3'-endo 5 G 1.2 -26.6 40.3 -40.8 25.0 42.1 17.0 C3'-endo 6 G 3.1 -28.1 41.1 -40.4 23.6 42.5 14.5 C3'-endo 7 U 3.7 -27.1 39.1 -38.0 21.6 40.2 13.4 C3'-endo 8 C 0.1 -23.5 36.7 -37.6 23.6 38.7 18.4 C3'-endo 9 C 1.7 -24.5 36.3 -36.4 22.1 37.8 16.1 C3'-endo 10 C 3.9 -25.5 36.2 -35.1 19.6 37.1 12.7 C3'-endo 11 C 4.3 -26.5 37.3 -35.9 20.0 38.2 12.4 C3'-endo 12 C 4.8 -28.0 39.2 -37.4 20.6 40.0 11.8 C3'-endo 13 A 3.4 9.5 -18.5 20.9 -14.9 20.9 207.5 C3'-exo 14 G 5.3 8.2 -18.0 21.7 -16.6 21.3 212.6 C3'-exo 15 C 0.2 -23.5 36.5 -37.5 23.5 38.5 18.4 C3'-endo 16 C 3.0 -26.0 37.8 -37.1 21.6 39.0 14.4 C3'-endo 17 C 1.0 -25.1 38.3 -38.8 23.8 40.1 17.2 C3'-endo 18 C 4.8 -28.1 39.3 -37.6 20.8 40.2 11.9 C3'-endo 19 G -0.8 -23.7 37.9 -39.3 25.2 40.3 19.7 C3'-endo 20 G 1.5 -26.4 39.9 -40.0 24.3 41.6 16.5 C3'-endo 21 C 2.1 -27.7 41.5 -41.1 24.5 43.1 15.7 C3'-endo 22 G 2.9 -27.7 40.7 -40.0 23.2 42.1 14.5 C3'-endo 23 C 4.0 -26.3 37.4 -36.2 20.3 38.3 12.8 C3'-endo 24 A 4.8 -29.3 41.4 -39.5 22.0 42.3 12.1 C3'-endo 25 G 3.8 -29.3 42.1 -40.7 23.4 43.3 13.5 C3'-endo 26 G 8.5 -32.0 42.2 -38.1 18.7 42.5 7.2 C3'-endo 27 U 8.5 -30.4 39.3 -35.5 17.2 39.5 6.6 C3'-endo 28 C -7.4 19.8 -24.2 21.0 -8.6 24.2 181.8 C3'-exo 29 C 0.7 -21.1 32.3 -33.0 20.4 33.9 17.6 C3'-endo 30 U 2.8 -24.7 36.0 -35.3 20.6 37.1 14.4 C3'-endo 31 G -0.3 -23.6 37.1 -38.1 24.2 39.2 18.9 C3'-endo 32 G 1.0 -24.7 37.9 -38.3 23.5 39.7 17.2 C3'-endo 33 G 0.4 -24.7 38.2 -39.1 24.4 40.2 18.1 C3'-endo 34 G 3.0 -27.1 39.5 -38.8 22.6 40.8 14.5 C3'-endo 35 U 3.8 -26.6 37.9 -36.8 20.9 38.9 13.2 C3'-endo 36 C -0.5 -23.2 36.8 -38.2 24.5 39.1 19.4 C3'-endo 37 C 1.4 -25.9 39.3 -39.5 23.9 41.1 16.6 C3'-endo 38 C 3.9 -25.8 36.7 -35.6 19.9 37.6 12.9 C3'-endo 39 C 3.6 -25.7 37.0 -36.0 20.5 38.0 13.4 C3'-endo 40 C 5.2 -28.0 38.8 -36.9 20.0 39.6 11.2 C3'-endo 41 A 2.8 9.9 -18.6 20.6 -14.4 20.7 206.0 C3'-exo 42 G 5.4 8.1 -18.0 21.7 -16.6 21.4 212.7 C3'-exo 43 C 0.4 -23.5 36.3 -37.1 23.1 38.1 18.0 C3'-endo 44 C 1.8 -24.3 36.0 -35.9 21.7 37.4 15.9 C3'-endo 45 C -0.4 -23.9 37.8 -39.0 24.8 40.0 19.2 C3'-endo 46 C 3.9 -27.2 38.7 -37.6 21.4 39.8 13.2 C3'-endo 47 G -1.4 -23.8 38.6 -40.3 26.4 41.2 20.4 C3'-endo 48 G 3.3 -28.3 41.2 -40.2 23.3 42.5 14.1 C3'-endo 49 C 3.0 -28.0 40.9 -40.3 23.4 42.3 14.6 C3'-endo 50 G 3.5 -28.0 40.5 -39.6 22.6 41.7 13.9 C3'-endo 51 C 2.9 -25.5 37.3 -36.7 21.2 38.5 14.4 C3'-endo 52 A 4.4 -28.3 40.1 -38.5 21.5 41.1 12.5 C3'-endo 53 G 4.1 -29.2 41.6 -40.3 23.0 42.7 13.2 C3'-endo 54 G 8.0 -31.8 42.4 -38.7 19.4 42.8 7.9 C3'-endo 55 U 7.6 -29.8 39.3 -36.0 17.9 39.6 7.8 C3'-endo 56 C -7.5 19.7 -23.9 20.8 -8.4 23.9 181.6 C3'-exo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II base P--P C1'--C1' base P--P C1'--C1' 1 G/G 5.7 6.1 1 C/U 6.0 5.4 2 G/C 5.6 5.3 2 U/G 5.9 5.3 3 C/C 5.8 5.4 3 G/G 6.0 5.3 4 C/C 6.0 5.5 4 G/G 5.8 5.3 5 C/C 5.9 5.3 5 G/G 5.5 5.3 6 C/A 6.2 6.0 6 G/U 5.7 5.3 7 A/G 10.3 8.3 7 U/C 6.0 5.3 8 G/G 5.8 6.1 8 C/C 6.0 5.2 9 G/G 5.8 5.6 9 C/C 5.4 5.1 10 G/G 5.9 5.2 10 C/C 5.8 5.7 11 G/G 6.2 4.9 11 C/C 5.2 6.0 12 G/U 6.3 6.0 12 C/A 13.9 8.7 13 U/U 4.6 5.1 13 A/G 13.9 6.1 14 U/G --- --- 14 G/C --- --- 15 G/A --- --- 15 C/C --- --- 16 A/G 5.8 5.4 16 C/C 5.6 5.3 17 G/G 5.8 5.5 17 C/C 6.0 5.5 18 G/C 5.6 5.3 18 C/G 5.9 5.4 19 C/C 5.9 5.3 19 G/G 5.7 5.5 20 C/G 6.0 5.4 20 G/C 5.5 5.8 21 G/A 5.8 5.6 21 C/G 5.7 5.5 22 A/G 14.9 12.6 22 G/C 5.7 5.1 23 G/U 5.8 5.9 23 C/A 5.6 5.8 24 U/C 5.6 6.0 24 A/G 5.8 5.5 25 C/U 5.5 5.1 25 G/G 5.8 5.6 26 U/A 6.9 6.2 26 G/U 16.5 11.5 27 A/U 19.7 12.0 27 U/C 11.2 4.5 28 U/G --- --- 28 C/C --- --- 29 G/G 5.6 6.0 29 C/U 6.3 5.6 30 G/C 5.5 5.3 30 U/G 6.0 5.3 31 C/C 5.8 5.4 31 G/G 5.9 5.4 32 C/C 5.8 5.5 32 G/G 5.8 5.3 33 C/C 5.8 5.2 33 G/G 5.6 5.3 34 C/A 6.2 5.9 34 G/U 5.7 5.3 35 A/G 10.4 8.5 35 U/C 5.8 5.3 36 G/G 5.7 6.1 36 C/C 6.0 5.5 37 G/G 5.9 5.6 37 C/C 5.4 5.0 38 G/G 5.9 5.1 38 C/C 5.8 5.6 39 G/G 6.0 4.7 39 C/C 5.3 6.0 40 G/U 6.3 6.0 40 C/A 13.9 8.8 41 U/U 4.5 5.1 41 A/G 14.2 6.3 42 U/G --- --- 42 G/C --- --- 43 G/A --- --- 43 C/C --- --- 44 A/G 5.7 5.3 44 C/C 5.6 5.2 45 G/G 5.7 5.5 45 C/C 6.0 5.5 46 G/C 5.7 5.4 46 C/G 5.9 5.5 47 C/C 5.8 5.3 47 G/G 5.7 5.4 48 C/G 6.1 5.5 48 G/C 5.5 5.8 49 G/A 5.8 5.5 49 C/G 5.7 5.5 50 A/G 14.9 12.7 50 G/C 5.6 5.2 51 G/U 5.9 5.8 51 C/A 5.7 5.8 52 U/C 5.5 6.0 52 A/G 5.8 5.6 53 C/U 5.5 5.1 53 G/G 5.8 5.5 54 U/A 6.9 6.2 54 G/U 16.4 11.4 55 A/U 19.7 12.0 55 U/C 11.2 4.5 **************************************************************************** Helix radius (radial displacement of P, O4', and C1' atoms in local helix frame of each dimer) Strand I Strand II step P O4' C1' P O4' C1' 1 GG/UC 7.5 8.2 7.6 9.8 8.5 7.8 2 GC/GU 8.5 7.8 7.0 8.8 7.3 6.4 3 CC/GG 8.7 8.4 7.8 10.0 9.3 8.6 4 CC/GG 10.3 9.6 8.8 8.1 7.7 7.2 5 CC/GG 8.4 8.4 7.8 10.3 9.8 9.1 6 CA/UG 10.6 10.1 9.4 6.7 7.5 7.1 7 AG/CU 10.0 9.4 8.5 7.0 6.1 5.4 8 GG/CC 10.4 9.7 9.0 8.5 7.9 7.2 9 GG/CC 9.3 8.9 8.3 9.7 9.5 8.8 10 GG/CC 9.8 9.1 8.5 9.0 9.3 8.7 11 GG/CC 9.1 8.7 8.7 11.8 12.0 11.3 12 GU/AC 9.2 7.8 6.8 7.1 5.3 4.8 13 UU/GA 5.3 3.2 2.0 6.2 7.7 7.3 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GA/CC ---- ---- ---- ---- ---- ---- 16 AG/CC 8.9 8.5 7.8 8.3 6.8 5.8 17 GG/CC 9.4 9.5 9.0 9.7 9.4 8.8 18 GC/GC 9.0 8.0 7.3 9.1 8.2 7.4 19 CC/GG 9.9 9.3 8.8 9.5 9.6 9.0 20 CG/CG 10.2 9.9 9.4 8.4 9.2 8.8 21 GA/GC 11.8 10.4 9.5 6.8 6.8 6.3 22 AG/CG 10.9 11.5 10.6 5.0 5.3 5.0 23 GU/AC 8.4 8.8 8.3 9.4 9.4 8.8 24 UC/GA 9.9 9.6 8.9 7.6 8.0 7.4 25 CU/GG 9.4 8.4 8.1 12.1 12.4 11.7 26 UA/UG 7.7 6.8 5.9 7.4 6.5 5.6 27 AU/CU 11.1 7.2 6.0 7.4 2.4 2.1 28 UG/CC ---- ---- ---- ---- ---- ---- 29 GG/UC 6.9 7.8 7.3 10.1 8.6 8.0 30 GC/GU 8.7 7.9 7.1 8.6 7.0 6.2 31 CC/GG 8.3 8.5 7.9 10.1 9.6 8.9 32 CC/GG 10.0 9.5 8.8 8.5 8.2 7.6 33 CC/GG 8.5 8.2 7.6 10.1 9.3 8.6 34 CA/UG 10.2 9.9 9.1 7.0 7.6 7.2 35 AG/CU 9.4 9.4 8.5 7.0 6.3 5.6 36 GG/CC 11.0 10.4 9.7 8.2 8.0 7.5 37 GG/CC 9.4 8.7 8.1 9.5 9.2 8.5 38 GG/CC 9.6 8.8 8.2 9.2 9.4 8.6 39 GG/CC 9.7 9.1 9.0 11.2 11.6 11.0 40 GU/AC 9.2 7.8 6.8 7.3 5.4 4.9 41 UU/GA 5.5 3.4 2.1 6.1 7.5 7.1 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GA/CC ---- ---- ---- ---- ---- ---- 44 AG/CC 8.7 8.4 7.7 8.3 6.8 5.8 45 GG/CC 9.0 9.1 8.6 9.8 9.3 8.7 46 GC/GC 9.0 8.1 7.4 9.0 8.1 7.3 47 CC/GG 10.2 9.7 9.2 9.7 9.8 9.3 48 CG/CG 9.8 9.5 9.1 8.5 9.2 8.8 49 GA/GC 11.8 10.2 9.4 7.0 6.8 6.3 50 AG/CG 10.7 11.4 10.5 4.8 5.5 5.1 51 GU/AC 8.4 8.6 8.0 9.4 9.2 8.5 52 UC/GA 9.9 9.6 8.8 7.6 8.0 7.5 53 CU/GG 9.1 8.1 7.9 12.1 12.4 11.6 54 UA/UG 7.8 6.9 6.0 7.4 6.4 5.5 55 AU/CU 11.0 7.1 6.0 7.4 2.4 2.1 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step bp Px Py Pz Hx Hy Hz 1 GG/UC 24.44 86.09 67.64 -0.81 0.09 -0.57 2 GC/GU 23.48 87.17 65.20 -0.79 -0.17 -0.59 3 CC/GG 19.92 86.68 65.16 -0.81 -0.18 -0.56 4 CC/GG 17.81 84.36 64.24 -0.87 -0.21 -0.46 5 CC/GG 15.24 85.48 61.12 -0.76 -0.21 -0.61 6 CA/UG 11.94 84.57 61.48 -0.66 -0.05 -0.75 7 AG/CU 8.95 82.40 60.96 -0.90 -0.06 -0.44 8 GG/CC 7.05 81.82 57.75 -0.87 -0.02 -0.49 9 GG/CC 4.61 79.70 56.29 -0.87 -0.14 -0.46 10 GG/CC 2.82 79.30 54.97 -0.83 -0.28 -0.47 11 GG/CC -1.06 76.80 55.14 -0.91 -0.03 -0.41 12 GU/AC -1.09 79.12 49.59 -0.79 -0.20 -0.58 13 UU/GA -3.48 81.31 47.04 -0.93 -0.14 -0.34 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GA/CC ---- ---- ---- ---- ---- ---- 16 AG/CC 19.22 38.00 55.92 -0.46 0.87 -0.19 17 GG/CC 18.93 41.78 57.66 -0.39 0.89 -0.23 18 GC/GC 16.05 43.55 55.85 -0.53 0.84 -0.12 19 CC/GG 16.79 46.66 55.57 -0.39 0.89 -0.24 20 CG/CG 16.32 48.95 54.70 -0.46 0.75 -0.49 21 GA/GC 15.60 52.60 56.38 -0.29 0.93 -0.24 22 AG/CG 16.35 54.68 55.73 -0.32 0.83 -0.46 23 GU/AC 12.57 58.39 57.12 -0.09 0.93 -0.36 24 UC/GA 12.60 60.15 54.72 -0.20 0.92 -0.33 25 CU/GG 13.00 64.24 57.30 -0.24 0.90 -0.37 26 UA/UG 10.54 64.16 51.10 -0.39 0.81 -0.45 27 AU/CU 7.55 65.60 49.06 0.12 -0.43 -0.90 28 UG/CC ---- ---- ---- ---- ---- ---- 29 GG/UC 83.79 86.55 130.64 -0.87 0.09 -0.49 30 GC/GU 82.99 87.49 128.20 -0.85 -0.28 -0.45 31 CC/GG 79.08 86.89 128.99 -0.86 -0.16 -0.49 32 CC/GG 77.10 84.78 128.12 -0.89 -0.25 -0.38 33 CC/GG 74.45 84.82 125.50 -0.86 -0.29 -0.42 34 CA/UG 71.23 84.00 126.08 -0.78 -0.12 -0.61 35 AG/CU 68.23 82.12 125.73 -0.94 -0.14 -0.33 36 GG/CC 66.29 82.02 122.63 -0.91 -0.06 -0.40 37 GG/CC 63.10 79.99 122.49 -0.93 -0.11 -0.36 38 GG/CC 60.89 79.38 121.55 -0.91 -0.23 -0.34 39 GG/CC 58.15 76.63 122.05 -0.98 -0.11 -0.17 40 GU/AC 56.40 79.15 116.92 -0.88 -0.20 -0.43 41 UU/GA 53.69 81.02 114.83 -0.98 -0.13 -0.15 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GA/CC ---- ---- ---- ---- ---- ---- 44 AG/CC 77.55 38.39 119.04 -0.46 0.88 -0.11 45 GG/CC 77.59 42.10 120.59 -0.44 0.89 -0.15 46 GC/GC 74.67 43.82 119.80 -0.52 0.86 -0.00 47 CC/GG 75.70 47.11 119.41 -0.42 0.89 -0.15 48 CG/CG 74.37 49.29 118.87 -0.54 0.76 -0.35 49 GA/GC 74.19 52.80 120.80 -0.30 0.94 -0.14 50 AG/CG 74.58 54.89 119.94 -0.46 0.81 -0.35 51 GU/AC 71.67 58.61 121.90 -0.14 0.91 -0.40 52 UC/GA 70.93 60.19 119.69 -0.27 0.92 -0.27 53 CU/GG 71.85 64.47 121.95 -0.27 0.90 -0.35 54 UA/UG 68.13 64.28 116.48 -0.45 0.81 -0.38 55 AU/CU 64.88 65.74 114.86 -0.05 -0.42 -0.91