ID code: 1O3Z, AR0046 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 12 May 24 * *********************************** ************** FILE : duplex.pdb lis : dna : axin : axout: daf : pdb : acc : 0.000 wid : 0.750 maxn : 500 ior : 0 ibond: 0 splin: 3 break: -1 NLEVE: 0 NBAC : 7 ends : F supp : T COMB : T dinu : F mini : T rest : F LINE : F zaxe : F FIT : T test : F GRV : F old : T axonl: F Least squares fitting of standard bases ... Str Pos Base Rms (ang) 1 : 1) CA 1 0.018 1 : 2) UA 2 0.016 1 : 3) UA 3 0.016 1 : 4) GA 4 0.016 1 : 5) CA 5 0.010 1 : 6) UA 6 0.012 1 : 7) GA 7 0.017 2 : 1) GB 23 0.025 2 : 2) AB 22 0.019 2 : 3) AB 21 0.018 2 : 4) CB 20 0.011 2 : 5) GB 19 0.018 2 : 6) AB 18 0.023 2 : 7) CB 17 0.011 Strand= 2 Nucleo= 14 Atoms = 295 Units = 14 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 7 levels ... Strand 1 has 7 bases (5'-3'): CUUGCUG Strand 2 has 7 bases (3'-5'): GAACGAC FIRST SUM= 52.157 CPTS: 1.281 1.382 7.994 41.499 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 52.157 DEL= 0.000E+00 STEP 2 SUM= 40.227 DEL= -0.119E+02 STEP 3 SUM= 26.874 DEL= -0.134E+02 STEP 4 SUM= 43.424 DEL= 0.165E+02 STEP 5 SUM= 22.754 DEL= -0.207E+02 STEP 6 SUM= 17.630 DEL= -0.512E+01 STEP 7 SUM= 31.456 DEL= 0.138E+02 STEP 8 SUM= 16.538 DEL= -0.149E+02 STEP 9 SUM= 15.124 DEL= -0.141E+01 STEP 10 SUM= 12.768 DEL= -0.236E+01 STEP 11 SUM= 50.089 DEL= 0.373E+02 STEP 12 SUM= 12.717 DEL= -0.374E+02 STEP 13 SUM= 12.617 DEL= -0.101E+00 STEP 14 SUM= 11.850 DEL= -0.767E+00 STEP 15 SUM= 10.388 DEL= -0.146E+01 STEP 16 SUM= 9.919 DEL= -0.469E+00 STEP 17 SUM= 9.414 DEL= -0.505E+00 STEP 18 SUM= 8.810 DEL= -0.604E+00 STEP 19 SUM= 7.831 DEL= -0.979E+00 STEP 20 SUM= 6.778 DEL= -0.105E+01 STEP 21 SUM= 5.491 DEL= -0.129E+01 STEP 22 SUM= 5.702 DEL= 0.211E+00 STEP 23 SUM= 4.885 DEL= -0.817E+00 STEP 24 SUM= 4.654 DEL= -0.232E+00 STEP 25 SUM= 4.277 DEL= -0.376E+00 STEP 26 SUM= 3.757 DEL= -0.520E+00 STEP 27 SUM= 4.105 DEL= 0.348E+00 STEP 28 SUM= 3.557 DEL= -0.548E+00 STEP 29 SUM= 3.313 DEL= -0.244E+00 STEP 30 SUM= 3.498 DEL= 0.186E+00 STEP 31 SUM= 3.234 DEL= -0.265E+00 STEP 32 SUM= 3.200 DEL= -0.333E-01 STEP 33 SUM= 3.199 DEL= -0.117E-02 STEP 34 SUM= 3.183 DEL= -0.157E-01 STEP 35 SUM= 3.192 DEL= 0.829E-02 STEP 36 SUM= 3.177 DEL= -0.146E-01 STEP 37 SUM= 3.182 DEL= 0.510E-02 STEP 38 SUM= 3.176 DEL= -0.628E-02 STEP 39 SUM= 3.176 DEL= 0.127E-03 STEP 40 SUM= 3.176 DEL= -0.249E-03 STEP 41 SUM= 3.176 DEL= 0.205E-04 STEP 42 SUM= 3.176 DEL= -0.771E-04 STEP 43 SUM= 3.176 DEL= -0.145E-04 STEP 44 SUM= 3.176 DEL= -0.782E-05 STEP 45 SUM= 3.176 DEL= -0.694E-05 STEP 46 SUM= 3.176 DEL= -0.295E-05 STEP 47 SUM= 3.176 DEL= -0.617E-06 STEP 48 SUM= 3.176 DEL= -0.186E-07 STEP 49 SUM= 3.176 DEL= -0.328E-09 STEP 50 SUM= 3.176 DEL= -0.579E-10 STEP 51 SUM= 3.176 DEL= -0.266E-11 STEP 52 SUM= 3.176 DEL= -0.190E-12 STEP 53 SUM= 3.176 DEL= -0.577E-14 STEP 54 SUM= 3.176 DEL= 0.000E+00 FINAL SUM= 3.176 CPTS: 0.840 1.637 0.204 0.495 GRA=-0.28E-08 0.82E-08-0.14E-09 0.41E-09-0.24E-08-0.15E-07-0.29E-09-0.12E-08 GRA= 0.21E-08-0.41E-08 0.32E-09 0.82E-10 0.20E-08 0.37E-08 0.38E-09-0.23E-09 GRA= 0.19E-09 0.85E-09 0.14E-09 0.29E-10 0.86E-09 0.29E-08-0.19E-09 0.72E-09 GRA=-0.20E-08 0.51E-09-0.38E-10-0.19E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -1.000 -0.010 -0.019 P: 92.883 15.755 19.402 D: 0.678 2) U: -1.000 -0.018 -0.021 P: 90.043 15.765 19.415 D: 0.126 3) U: -1.000 -0.024 -0.008 P: 87.280 15.688 19.467 D: 0.504 4) U: -0.999 -0.031 -0.018 P: 84.515 15.406 19.281 D: 0.865 5) U: -0.999 0.034 -0.022 P: 81.660 15.595 18.948 D: 0.803 6) U: -1.000 -0.011 -0.008 P: 79.376 15.665 19.116 D: 0.200 7) U: -0.999 0.025 0.036 P: 77.164 15.732 19.257 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -4.53 0.03 31.97 -7.98 3 0 2) UA 2 -4.48 0.31 23.98 -9.28 4 -19 3) UA 3 -4.49 0.22 20.13 -7.21 4 -26 4) GA 4 -4.39 0.09 15.26 -5.75 1 15 5) CA 5 -4.46 -0.25 13.22 -7.65 3 -7 6) UA 6 -4.49 -0.10 20.03 -8.10 4 -25 7) GA 7 -4.31 -0.31 22.09 -7.03 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 23 -4.16 -0.19 8.48 -10.20 1 0 2) AB 22 -4.37 0.18 16.21 -11.57 2 19 3) AB 21 -4.50 0.08 16.75 -8.81 2 26 4) CB 20 -4.37 0.46 22.04 -8.18 3 -15 5) GB 19 -4.87 0.22 23.92 -7.24 1 7 6) AB 18 -4.42 0.47 25.68 -6.00 2 25 7) CB 17 -4.38 0.42 24.58 -6.66 3 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) C 1-G 23 -4.35 0.11 20.23 1.11 3 0 2) U 2-A 22 -4.43 0.06 20.10 1.14 4 -19 3) U 3-A 21 -4.50 0.07 18.44 0.80 4 -26 4) G 4-C 20 -4.38 -0.19 18.65 1.22 1 15 5) C 5-G 19 -4.66 -0.24 18.57 -0.20 3 -7 6) U 6-A 18 -4.45 -0.29 22.86 -1.05 4 -25 7) G 7-C 17 -4.35 -0.37 23.33 -0.18 1 0 Average: -4.44 -0.12 20.31 0.41 --------------------------------- |D| Global Base-Base Parameters | --------------------------------- Strand 1 with strand 2 ... Duplex Shear Stretch Stagger Buckle Propel Opening Bc Tc (Sx) (Sy) (Sz) (kappa) (omega) (sigma) 1) C 1-G 23 -0.36 -0.15 -0.12 23.49 -18.19 -2.57 3 0 2) U 2-A 22 -0.11 0.49 -0.68 7.77 -20.85 7.37 4 -19 3) U 3-A 21 0.01 0.30 -0.46 3.37 -16.02 6.50 4 -26 4) G 4-C 20 -0.02 0.54 -0.05 -6.77 -13.92 4.44 1 15 5) C 5-G 19 0.40 -0.03 0.26 -10.70 -14.89 0.33 3 -7 6) U 6-A 18 -0.07 0.37 -0.32 -5.65 -14.10 5.27 4 -25 7) G 7-C 17 0.07 0.11 -0.20 -2.49 -13.69 0.96 1 0 Average: -0.01 0.23 -0.22 1.29 -15.95 3.19 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/U 2 -0.04 0.29 2.56 -8.23 -0.93 44.04 -3 3) U 2/U 3 -0.01 0.00 2.87 -4.68 2.28 34.37 -4 4) U 3/G 4 0.23 -0.35 2.98 -4.16 1.57 32.81 -9 5) G 4/C 5 -0.40 -0.34 3.02 -5.00 -4.16 32.86 5 6) C 5/U 6 0.17 0.19 1.99 9.42 0.39 35.81 -3 7) U 6/G 7 0.30 -0.23 2.27 1.74 4.32 32.66 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 23/A 22 -0.29 0.36 3.12 7.49 -1.74 34.10 3 3) A 22/A 21 -0.13 -0.19 2.65 -0.28 2.55 35.25 4 4) A 21/C 20 0.27 0.59 2.57 5.98 0.53 34.87 9 5) C 20/G 19 -0.83 -0.23 2.71 -1.08 3.20 36.97 5 6) G 19/A 18 0.65 0.21 2.57 4.38 0.40 30.87 3 7) A 18/C 17 0.16 -0.03 2.16 -1.42 -3.91 36.97 9 --------------------------------------- |F| Global Inter-Base pair Parameters | --------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/U 2 -0.17 -0.04 2.84 -0.37 0.41 39.07 -3 3) U 2/U 3 -0.07 0.10 2.76 -2.48 -0.14 34.81 -4 4) U 3/G 4 0.25 -0.47 2.77 0.91 0.52 33.84 -9 5) G 4/C 5 -0.61 -0.05 2.86 -3.04 -3.68 34.92 5 6) C 5/U 6 0.41 -0.01 2.28 6.90 -0.00 33.34 -3 7) U 6/G 7 0.23 -0.10 2.22 0.16 4.12 34.82 -9 Average: 0.01 -0.09 2.62 0.35 0.20 35.13 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/U 2 0.44 -1.63 3.73 -1.93 19.37 39.84 -3 3) U 2/U 3 0.38 -1.45 3.66 0.05 14.97 32.31 -4 4) U 3/G 4 0.57 -1.87 3.66 -0.46 11.33 31.61 -9 5) G 4/C 5 0.05 -2.05 3.48 -1.21 4.02 32.77 5 6) C 5/U 6 0.59 -1.91 2.65 13.75 10.34 32.78 -3 7) U 6/G 7 0.80 -1.66 3.25 5.64 15.67 29.02 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 23/A 22 -1.01 -2.16 3.54 0.84 8.85 34.10 3 3) A 22/A 21 -0.61 -1.65 3.21 -6.22 7.36 33.22 4 4) A 21/C 20 -0.11 -2.23 3.52 0.90 10.95 33.46 9 5) C 20/G 19 -1.02 -1.57 3.29 -5.78 11.15 34.61 5 6) G 19/A 18 0.41 -1.36 3.58 1.13 12.44 28.06 3 7) A 18/C 17 0.10 -1.54 3.39 -5.05 19.06 32.03 9 -------------------------------------- |H| Local Inter-Base pair Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/U 2 -0.26 -1.87 3.71 -0.66 14.19 37.85 -3 3) U 2/U 3 -0.14 -1.53 3.48 -3.36 11.31 33.22 -4 4) U 3/G 4 0.21 -2.03 3.61 0.21 11.10 32.75 -9 5) G 4/C 5 -0.50 -1.79 3.44 -3.43 7.68 34.11 5 6) C 5/U 6 0.54 -1.66 3.12 7.52 11.51 30.57 -3 7) U 6/G 7 0.45 -1.59 3.34 0.36 17.52 30.73 -9 Average: 0.05 -1.75 3.45 0.11 12.22 33.20 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/U 2 -0.09 0.01 -0.23 0.37 0.09 0.44 2.84 -3 3) U 2/U 3 -0.00 0.09 -0.82 0.20 0.09 0.85 2.76 -4 4) U 3/G 4 0.14 -0.21 0.70 0.11 0.25 0.71 2.79 -9 5) G 4/C 5 -0.33 -0.00 -2.96 -2.26 0.33 3.73 2.88 5 6) C 5/U 6 0.20 0.04 2.61 0.84 0.21 2.75 2.29 -3 7) U 6/G 7 0.12 -0.02 -0.31 3.25 0.12 3.27 2.22 -9 Overall axis bend ... UU= 3.75 PP= 3.71 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) U 2 0.04 -44.13 3) U 3 0.13 -124.85 4) G 4 0.34 131.82 5) C 5 0.38 38.57 6) U 6 0.18 4.00 7) G 7 0.00 0.00 Path length= 15.78 End-to-end= 15.72 Shortening= 0.38 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 -24.20 36.22 15.95 38.49 C3'-endo 107.7 101.5 102.2 2)UA 2 -26.37 38.51 14.13 40.48 C3'-endo 107.1 101.1 101.9 3)UA 3 -26.65 39.22 14.77 41.39 C3'-endo 107.1 100.9 101.7 4)GA 4 -25.53 38.06 15.64 40.34 C3'-endo 107.3 101.3 101.8 5)CA 5 -28.75 40.56 11.92 42.23 C3'-endo 106.8 100.8 101.5 6)UA 6 -25.54 39.23 17.22 41.83 C3'-endo 107.1 101.0 101.6 7)GA 7 -22.93 39.40 22.98 43.51 C3'-endo 107.2 101.0 101.4 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CA 1 -161.57 62.15 83.87 -150.92 -65.88 -77.08 -172.17 2)UA 2 -152.50 45.61 81.08 -153.23 -68.36 -66.94 178.68 3)UA 3 -155.89 47.57 80.03 -152.06 -73.03 -57.40 170.85 4)GA 4 -161.63 53.28 81.49 -163.92 -64.88 -69.66 -174.35 5)CA 5 -162.03 49.11 80.12 -155.41 -63.66 -69.47 -174.16 6)UA 6 -147.16 48.52 79.15 -157.59 -63.21 -59.40 175.82 7)GA 7 -150.96 45.08 77.63 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 23 -25.27 38.53 16.69 40.97 C3'-endo 107.2 101.1 101.9 2)AB 22 -26.73 40.23 15.81 42.52 C3'-endo 106.9 100.9 101.6 3)AB 21 -26.82 38.61 13.37 40.49 C3'-endo 107.0 101.1 101.8 4)CB 20 -26.77 40.53 16.22 42.93 C3'-endo 106.8 100.9 101.3 5)GB 19 -27.11 39.61 14.03 41.56 C3'-endo 107.0 100.9 101.8 6)AB 18 -27.28 38.67 12.42 40.42 C3'-endo 107.1 101.1 101.8 7)CB 17 -26.20 39.34 15.95 41.71 C3'-endo 107.1 101.0 101.6 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 23 -165.00 52.91 73.21 ...... ...... ...... ...... 2)AB 22 -157.66 49.41 79.24 -155.18 -69.08 -57.18 173.49 3)AB 21 -159.88 48.61 81.79 -150.26 -70.86 -65.32 173.84 4)CB 20 -162.58 59.55 80.63 -158.80 -67.47 -66.20 -173.71 5)GB 19 -161.21 54.53 81.34 -140.20 -77.42 -65.82 162.62 6)AB 18 -150.72 52.79 82.30 -162.25 -68.78 -75.10 177.54 7)CB 17 -154.71 51.90 80.83 -159.18 -69.15 -75.55 -173.13