ID code: 2V7R *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 17 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) GA 1 0.020 1 : 2) CA 2 0.023 1 : 3) GA 3 0.024 1 : 4) UA 4 0.032 1 : 5) UA 5 0.021 1 : 6) GA 6 0.020 1 : 7) GA 7 0.025 2 : 1) CB 72 0.028 2 : 2) GB 71 0.024 2 : 3) CB 70 0.020 2 : 4) AB 69 0.042 2 : 5) AB 68 0.030 2 : 6) CB 67 0.017 2 : 7) CB 66 0.021 Strand= 2 Nucleo= 14 Atoms = 293 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'): GCGUUGG Strand 2 has 7 bases (3'-5'): CGCAACC FIRST SUM= 53.008 CPTS: 1.025 0.188 2.936 48.859 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 53.008 DEL= 0.000E+00 STEP 2 SUM= 40.857 DEL= -0.122E+02 STEP 3 SUM= 27.561 DEL= -0.133E+02 STEP 4 SUM= 27.318 DEL= -0.242E+00 STEP 5 SUM= 20.854 DEL= -0.646E+01 STEP 6 SUM= 15.598 DEL= -0.526E+01 STEP 7 SUM= 18.596 DEL= 0.300E+01 STEP 8 SUM= 13.553 DEL= -0.504E+01 STEP 9 SUM= 12.762 DEL= -0.791E+00 STEP 10 SUM= 11.293 DEL= -0.147E+01 STEP 11 SUM= 7.235 DEL= -0.406E+01 STEP 12 SUM= 206.139 DEL= 0.199E+03 STEP 13 SUM= 8.229 DEL= -0.198E+03 STEP 14 SUM= 7.089 DEL= -0.114E+01 STEP 15 SUM= 6.813 DEL= -0.276E+00 STEP 16 SUM= 5.680 DEL= -0.113E+01 STEP 17 SUM= 13.060 DEL= 0.738E+01 STEP 18 SUM= 5.485 DEL= -0.757E+01 STEP 19 SUM= 5.274 DEL= -0.212E+00 STEP 20 SUM= 4.954 DEL= -0.320E+00 STEP 21 SUM= 5.312 DEL= 0.358E+00 STEP 22 SUM= 4.851 DEL= -0.460E+00 STEP 23 SUM= 4.868 DEL= 0.166E-01 STEP 24 SUM= 4.804 DEL= -0.640E-01 STEP 25 SUM= 4.719 DEL= -0.849E-01 STEP 26 SUM= 4.575 DEL= -0.144E+00 STEP 27 SUM= 4.291 DEL= -0.285E+00 STEP 28 SUM= 3.986 DEL= -0.304E+00 STEP 29 SUM= 3.640 DEL= -0.346E+00 STEP 30 SUM= 3.252 DEL= -0.388E+00 STEP 31 SUM= 3.459 DEL= 0.207E+00 STEP 32 SUM= 3.187 DEL= -0.272E+00 STEP 33 SUM= 3.168 DEL= -0.188E-01 STEP 34 SUM= 3.157 DEL= -0.111E-01 STEP 35 SUM= 3.155 DEL= -0.223E-02 STEP 36 SUM= 3.152 DEL= -0.306E-02 STEP 37 SUM= 3.150 DEL= -0.138E-02 STEP 38 SUM= 3.150 DEL= -0.538E-03 STEP 39 SUM= 3.149 DEL= -0.529E-03 STEP 40 SUM= 3.149 DEL= -0.458E-03 STEP 41 SUM= 3.148 DEL= -0.480E-03 STEP 42 SUM= 3.148 DEL= -0.163E-03 STEP 43 SUM= 3.148 DEL= -0.830E-04 STEP 44 SUM= 3.148 DEL= -0.118E-04 STEP 45 SUM= 3.148 DEL= -0.107E-05 STEP 46 SUM= 3.148 DEL= -0.599E-07 STEP 47 SUM= 3.148 DEL= -0.883E-08 STEP 48 SUM= 3.148 DEL= -0.109E-08 STEP 49 SUM= 3.148 DEL= -0.464E-11 STEP 50 SUM= 3.148 DEL= -0.284E-12 STEP 51 SUM= 3.148 DEL= 0.133E-14 STEP 52 SUM= 3.148 DEL= -0.133E-14 FINAL SUM= 3.148 CPTS: 0.672 1.412 0.362 0.701 GRA=-0.20E-08-0.17E-07 0.84E-09-0.11E-10 0.90E-08-0.58E-08-0.10E-08-0.37E-09 GRA= 0.37E-08 0.21E-07 0.71E-09 0.58E-09 0.29E-09-0.28E-07-0.85E-10-0.26E-08 GRA= 0.84E-08 0.32E-07 0.10E-08 0.32E-08 0.24E-08-0.26E-07-0.50E-09-0.18E-08 GRA=-0.40E-09 0.19E-07-0.48E-10 0.11E-08 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: 0.609 -0.015 0.793 P: -14.120 7.499 -11.232 D: 0.611 2) U: 0.623 0.044 0.781 P: -12.537 7.578 -8.760 D: 0.455 3) U: 0.688 -0.003 0.726 P: -10.844 7.792 -6.769 D: 0.338 4) U: 0.711 -0.033 0.703 P: -8.833 7.845 -4.886 D: 0.556 5) U: 0.693 -0.050 0.719 P: -6.795 7.882 -2.775 D: 0.435 6) U: 0.710 -0.046 0.702 P: -4.908 7.580 -0.752 D: 0.753 7) U: 0.725 -0.015 0.688 P: -2.701 7.767 0.974 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 1 -4.42 0.26 9.72 0.27 1 0 2) CA 2 -4.31 0.06 14.42 -4.30 3 -13 3) GA 3 -4.32 0.19 13.72 -6.33 1 14 4) UA 4 -4.21 0.16 14.06 -10.82 4 -23 5) UA 5 -4.31 0.18 12.03 -6.73 4 -26 6) GA 6 -4.62 0.02 10.07 -6.72 1 11 7) GA 7 -4.46 -0.21 9.84 -5.19 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 72 -4.16 -0.26 9.56 -5.04 3 0 2) GB 71 -4.26 0.05 8.74 -7.08 1 13 3) CB 70 -4.28 0.21 14.30 -10.10 3 -14 4) AB 69 -4.16 0.10 16.17 -12.80 2 23 5) AB 68 -4.20 -0.14 15.09 -4.80 2 26 6) CB 67 -4.51 -0.04 13.75 -2.65 3 -11 7) CB 66 -4.20 0.37 11.63 -0.81 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) G 1-C 72 -4.29 0.26 9.64 2.66 1 0 2) C 2-G 71 -4.28 0.01 11.58 1.39 3 -13 3) G 3-C 70 -4.30 -0.01 14.01 1.89 1 14 4) U 4-A 69 -4.18 0.03 15.11 0.99 4 -23 5) U 5-A 68 -4.26 0.16 13.56 -0.96 4 -26 6) G 6-C 67 -4.56 0.03 11.91 -2.03 1 11 7) G 7-C 66 -4.33 -0.29 10.74 -2.19 1 0 Average: -4.32 0.03 12.36 0.25 --------------------------------- |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) G 1-C 72 -0.26 -0.00 0.05 0.16 -4.77 0.31 1 0 2) C 2-G 71 -0.05 0.12 -0.15 5.68 -11.38 0.53 3 -13 3) G 3-C 70 -0.04 0.41 -0.18 -0.58 -16.43 5.37 1 14 4) U 4-A 69 -0.06 0.26 -0.28 -2.11 -23.62 3.52 4 -23 5) U 5-A 68 -0.11 0.03 -0.03 -3.06 -11.53 0.60 4 -26 6) G 6-C 67 -0.10 -0.02 -0.26 -3.68 -9.37 -1.14 1 11 7) G 7-C 66 -0.25 0.16 -0.13 -1.78 -6.01 2.48 1 0 Average: -0.13 0.13 -0.14 -0.77 -11.87 1.67 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/C 2 0.04 -0.47 2.83 3.25 -7.78 32.23 5 3) C 2/G 3 -0.15 0.21 2.60 -2.76 3.19 36.65 8 4) G 3/U 4 0.20 0.10 2.70 1.44 -2.24 31.86 6 5) U 4/U 5 -0.08 0.18 3.06 -1.49 2.51 33.89 -4 6) U 5/G 6 -0.49 -0.20 2.66 -1.05 1.01 31.06 -9 7) G 6/G 7 0.47 -0.48 2.84 0.70 3.48 31.62 1 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 72/G 71 -0.17 0.59 3.02 -2.27 1.18 32.01 5 3) G 71/C 70 -0.17 0.08 2.64 3.50 -8.24 31.81 8 4) C 70/A 69 0.21 -0.25 2.80 2.97 -4.96 33.71 -6 5) A 69/A 68 -0.03 -0.40 2.80 -0.54 9.59 36.81 4 6) A 68/C 67 -0.49 0.15 2.89 -0.42 1.15 32.79 9 7) C 67/C 66 0.62 0.66 2.71 -1.20 -0.12 28.01 -1 --------------------------------------- |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) G 1/C 2 -0.06 -0.53 2.92 0.49 -4.48 32.12 5 3) C 2/G 3 -0.16 0.06 2.62 0.37 5.71 34.23 8 4) G 3/U 4 0.20 0.17 2.75 2.21 1.36 32.79 6 5) U 4/U 5 -0.06 0.29 2.93 -1.02 -3.54 35.35 -4 6) U 5/G 6 -0.49 -0.18 2.78 -0.74 -0.07 31.93 -9 7) G 6/G 7 0.55 -0.57 2.78 -0.25 1.80 29.82 1 Average: -0.00 -0.13 2.80 0.18 0.13 32.71 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/C 2 0.02 -2.27 3.14 4.17 -0.88 32.08 5 3) C 2/G 3 0.08 -1.73 3.51 0.55 11.95 34.42 8 4) G 3/U 4 0.57 -1.49 3.28 5.99 5.37 29.84 6 5) U 4/U 5 0.34 -1.65 3.36 3.63 9.90 33.34 -4 6) U 5/G 6 -0.15 -2.04 3.22 2.54 6.88 30.23 -9 7) G 6/G 7 0.85 -2.42 3.37 3.90 8.79 30.64 1 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 72/G 71 -0.54 -2.45 3.16 -5.57 3.80 31.74 5 3) G 71/C 70 -0.62 -1.81 3.37 -1.34 14.25 30.43 8 4) C 70/A 69 -0.38 -1.41 3.43 -3.55 13.55 32.03 -6 5) A 69/A 68 -0.51 -1.41 3.18 -5.85 0.62 35.39 4 6) A 68/C 67 -0.74 -1.80 3.48 -2.39 6.96 31.45 9 7) C 67/C 66 0.61 -2.08 3.41 -1.96 6.22 26.86 -1 -------------------------------------- |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) G 1/C 2 -0.26 -2.36 3.16 -0.69 1.48 31.88 5 3) C 2/G 3 -0.27 -1.76 3.47 -0.36 13.13 32.61 8 4) G 3/U 4 0.10 -1.43 3.39 1.42 9.63 31.38 6 5) U 4/U 5 -0.10 -1.52 3.29 -1.22 5.35 34.58 -4 6) U 5/G 6 -0.44 -1.92 3.36 0.07 6.92 30.95 -9 7) G 6/G 7 0.73 -2.25 3.40 0.96 7.53 28.76 1 Average: -0.04 -1.87 3.35 0.03 7.34 31.69 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 1/C 2 -0.07 -0.27 -1.45 -3.21 0.28 3.52 2.94 5 3) C 2/G 3 -0.14 0.08 -2.06 5.21 0.16 5.61 2.62 8 4) G 3/U 4 0.08 0.13 1.10 2.26 0.16 2.51 2.76 6 5) U 4/U 5 0.02 0.16 0.54 -1.59 0.16 1.67 2.93 -4 6) U 5/G 6 -0.18 -0.04 0.92 1.00 0.19 1.36 2.78 -9 7) G 6/G 7 0.31 -0.26 0.92 1.96 0.40 2.16 2.81 1 Overall axis bend ... UU= 9.01 PP= 19.46 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 1 0.00 0.00 2) C 2 0.53 63.42 3) G 3 0.69 12.99 4) U 4 0.52 -25.83 5) U 5 0.47 -60.90 6) G 6 0.46 -48.29 7) G 7 0.00 0.00 Path length= 16.84 End-to-end= 16.72 Shortening= 0.73 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 1 -32.64 41.49 4.56 42.44 C3'-endo 106.2 100.3 101.4 2)CA 2 -30.36 42.95 11.95 44.83 C3'-endo 108.2 98.6 101.9 3)GA 3 -33.40 45.87 10.44 47.83 C3'-endo 107.5 98.1 100.5 4)UA 4 -31.52 42.69 9.22 44.15 C3'-endo 106.9 99.8 101.3 5)UA 5 -33.81 47.22 11.12 49.06 C3'-endo 106.6 98.3 99.8 6)GA 6 -30.23 43.34 14.09 46.11 C3'-endo 108.4 98.5 99.9 7)GA 7 -22.70 38.42 22.87 42.63 C3'-endo 106.8 101.4 100.9 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 1 -171.21 64.46 83.69 -152.17 -72.52 -64.53 173.42 2)CA 2 -160.37 54.62 79.72 -151.36 -72.76 -67.49 176.44 3)GA 3 -156.71 49.06 80.38 -145.79 -78.59 -64.57 158.34 4)UA 4 -160.31 63.36 83.08 -148.65 -73.29 -75.81 169.27 5)UA 5 -161.72 56.94 77.37 -158.56 -69.91 -66.88 176.26 6)GA 6 -164.08 52.44 78.44 -148.92 -64.71 -65.46 175.97 7)GA 7 -161.24 54.57 80.67 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 72 -25.25 41.67 21.30 45.53 C3'-endo 106.7 100.7 100.3 2)GB 71 -31.63 44.68 12.50 46.83 C3'-endo 106.6 99.4 99.7 3)CB 70 -30.32 43.86 14.19 46.43 C3'-endo 107.5 99.0 100.2 4)AB 69 -31.72 41.76 7.49 43.33 C3'-endo 108.8 98.0 102.3 5)AB 68 -32.39 42.47 8.31 44.09 C3'-endo 107.5 101.0 99.7 6)CB 67 -32.27 46.52 13.15 48.49 C3'-endo 105.9 99.8 99.3 7)CB 66 -31.92 43.22 9.62 44.92 C3'-endo 107.5 99.3 100.7 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 72 -163.05 54.50 75.08 ...... ...... ...... ...... 2)GB 71 -166.68 56.89 76.68 -154.33 -66.21 -68.65 178.49 3)CB 70 -157.53 50.21 78.30 -150.14 -72.70 -65.66 165.41 4)AB 69 -153.34 56.05 83.36 -143.63 -73.58 -70.35 170.18 5)AB 68 -159.99 64.43 79.57 -157.93 -69.45 -66.94 173.50 6)CB 67 -160.50 49.09 75.67 -145.50 -78.86 -58.05 161.53 7)CB 66 -163.58 57.51 81.32 -153.08 -72.97 -69.45 178.86