ID code: 2V6W *********************************** ************** ****** 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 0.027 1 : 2) GA 2 0.024 1 : 3) AA 3 0.028 1 : 4) GA 4 0.026 1 : 5) AA 5 0.030 1 : 6) GA 6 0.029 1 : 7) AA 7 0.021 2 : 1) CB 72 0.023 2 : 2) CB 71 0.019 2 : 3) UB 70 0.028 2 : 4) CB 69 0.022 2 : 5) UB 68 0.024 2 : 6) CB 67 0.023 2 : 7) UB 66 0.034 Strand= 2 Nucleo= 14 Atoms = 292 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'): GGAGAGA Strand 2 has 7 bases (3'-5'): CCUCUCU FIRST SUM= 69.833 CPTS: 1.402 0.359 1.585 66.487 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 69.833 DEL= 0.000E+00 STEP 2 SUM= 52.388 DEL= -0.174E+02 STEP 3 SUM= 33.242 DEL= -0.191E+02 STEP 4 SUM= 39.415 DEL= 0.617E+01 STEP 5 SUM= 25.003 DEL= -0.144E+02 STEP 6 SUM= 16.873 DEL= -0.813E+01 STEP 7 SUM= 46.205 DEL= 0.293E+02 STEP 8 SUM= 15.423 DEL= -0.308E+02 STEP 9 SUM= 13.672 DEL= -0.175E+01 STEP 10 SUM= 10.748 DEL= -0.292E+01 STEP 11 SUM= 52.146 DEL= 0.414E+02 STEP 12 SUM= 10.635 DEL= -0.415E+02 STEP 13 SUM= 10.416 DEL= -0.219E+00 STEP 14 SUM= 8.938 DEL= -0.148E+01 STEP 15 SUM= 7.935 DEL= -0.100E+01 STEP 16 SUM= 13.244 DEL= 0.531E+01 STEP 17 SUM= 7.797 DEL= -0.545E+01 STEP 18 SUM= 7.546 DEL= -0.251E+00 STEP 19 SUM= 7.017 DEL= -0.530E+00 STEP 20 SUM= 8.802 DEL= 0.179E+01 STEP 21 SUM= 6.835 DEL= -0.197E+01 STEP 22 SUM= 6.779 DEL= -0.554E-01 STEP 23 SUM= 6.677 DEL= -0.102E+00 STEP 24 SUM= 6.423 DEL= -0.253E+00 STEP 25 SUM= 6.451 DEL= 0.279E-01 STEP 26 SUM= 6.252 DEL= -0.199E+00 STEP 27 SUM= 6.169 DEL= -0.824E-01 STEP 28 SUM= 6.052 DEL= -0.118E+00 STEP 29 SUM= 5.909 DEL= -0.142E+00 STEP 30 SUM= 5.861 DEL= -0.485E-01 STEP 31 SUM= 5.780 DEL= -0.804E-01 STEP 32 SUM= 5.682 DEL= -0.985E-01 STEP 33 SUM= 5.669 DEL= -0.123E-01 STEP 34 SUM= 5.639 DEL= -0.305E-01 STEP 35 SUM= 5.633 DEL= -0.555E-02 STEP 36 SUM= 5.625 DEL= -0.877E-02 STEP 37 SUM= 5.620 DEL= -0.469E-02 STEP 38 SUM= 5.620 DEL= 0.521E-03 STEP 39 SUM= 5.619 DEL= -0.118E-02 STEP 40 SUM= 5.619 DEL= -0.630E-04 STEP 41 SUM= 5.619 DEL= -0.641E-04 STEP 42 SUM= 5.619 DEL= -0.228E-05 STEP 43 SUM= 5.619 DEL= -0.116E-04 STEP 44 SUM= 5.619 DEL= -0.957E-05 STEP 45 SUM= 5.619 DEL= -0.142E-04 STEP 46 SUM= 5.619 DEL= -0.953E-05 STEP 47 SUM= 5.619 DEL= -0.145E-05 STEP 48 SUM= 5.619 DEL= -0.141E-06 STEP 49 SUM= 5.619 DEL= -0.543E-08 STEP 50 SUM= 5.619 DEL= -0.695E-09 STEP 51 SUM= 5.619 DEL= -0.433E-11 STEP 52 SUM= 5.619 DEL= -0.922E-12 STEP 53 SUM= 5.619 DEL= -0.711E-14 STEP 54 SUM= 5.619 DEL= 0.000E+00 FINAL SUM= 5.619 CPTS: 0.804 2.395 0.347 2.073 GRA=-0.29E-09 0.65E-08 0.41E-10 0.13E-08-0.11E-08-0.20E-07-0.71E-09-0.33E-08 GRA= 0.28E-08 0.21E-07 0.63E-09 0.36E-08-0.20E-08-0.17E-07 0.85E-10-0.25E-08 GRA=-0.26E-10 0.18E-07-0.18E-09 0.19E-08-0.94E-09-0.15E-07 0.22E-09-0.91E-09 GRA=-0.63E-09 0.39E-08-0.17E-09 0.30E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.646 -0.054 -0.762 P: 14.118 0.397 11.336 D: 0.408 2) U: -0.657 -0.060 -0.751 P: 12.268 0.273 8.918 D: 0.706 3) U: -0.688 -0.050 -0.724 P: 10.318 0.363 6.906 D: 2.269 4) U: -0.726 -0.109 -0.679 P: 8.185 -0.447 5.274 D: 1.411 5) U: -0.711 -0.045 -0.702 P: 6.541 -0.804 2.862 D: 0.371 6) U: -0.734 -0.005 -0.679 P: 4.575 -0.774 0.901 D: 0.455 7) U: -0.749 -0.024 -0.662 P: 2.400 -0.545 -1.065 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 1 -4.49 0.42 4.68 -3.49 1 0 2) GA 2 -4.51 0.29 3.58 -7.70 1 2 3) AA 3 -4.52 0.46 6.79 -3.43 2 17 4) GA 4 -4.03 0.09 6.61 -5.65 1 4 5) AA 5 -4.50 -0.08 8.67 -3.09 2 17 6) GA 6 -4.43 -0.10 9.12 -8.24 1 4 7) AA 7 -3.98 -0.03 9.60 -8.42 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 72 -4.24 -0.42 12.07 -1.77 3 0 2) CB 71 -4.27 -0.14 14.42 -6.21 3 -2 3) UB 70 -4.52 -0.36 8.93 -0.07 4 -17 4) CB 69 -3.93 0.11 11.96 -6.63 3 -4 5) UB 68 -4.42 -0.04 12.00 -3.66 4 -17 6) CB 67 -4.26 0.07 14.79 -7.02 3 -4 7) UB 66 -4.18 0.17 16.02 -4.64 4 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 -4.37 0.42 8.38 -0.86 1 0 2) G 2-C 71 -4.39 0.22 9.00 -0.74 1 2 3) A 3-U 70 -4.52 0.41 7.86 -1.68 2 17 4) G 4-C 69 -3.98 -0.01 9.28 0.49 1 4 5) A 5-U 68 -4.46 -0.02 10.33 0.28 2 17 6) G 6-C 67 -4.35 -0.09 11.96 -0.61 1 4 7) A 7-U 66 -4.08 -0.10 12.81 -1.89 2 0 Average: -4.31 0.12 9.95 -0.72 --------------------------------- |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 -0.25 -0.00 -0.21 -7.39 -5.26 0.47 1 0 2) G 2-C 71 -0.24 0.15 -0.35 -10.84 -13.91 1.67 1 2 3) A 3-U 70 0.00 0.10 -0.02 -2.14 -3.51 1.40 2 17 4) G 4-C 69 -0.10 0.20 -0.22 -5.35 -12.29 2.32 1 4 5) A 5-U 68 -0.08 -0.12 -0.04 -3.33 -6.74 -1.53 2 17 6) G 6-C 67 -0.17 -0.03 -0.22 -5.67 -15.26 -0.57 1 4 7) A 7-U 66 0.20 0.14 -0.21 -6.42 -13.06 2.33 2 0 Average: -0.09 0.06 -0.18 -5.88 -10.00 0.87 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/G 2 -0.09 -0.30 2.97 -1.93 -3.76 32.83 1 3) G 2/A 3 -0.14 0.39 2.96 1.03 5.37 32.29 2 4) A 3/G 4 1.01 -0.81 2.62 1.85 2.09 27.57 3 5) G 4/A 5 -1.08 -0.19 2.97 -1.83 1.72 32.84 2 6) A 5/G 6 0.09 0.08 2.68 0.11 -2.22 32.91 3 7) G 6/A 7 0.72 0.12 2.93 1.96 -0.98 37.50 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 72/C 71 -0.10 0.45 3.11 1.52 -4.89 31.63 -1 3) C 71/U 70 -0.38 -0.44 2.62 -7.67 5.03 32.56 -2 4) U 70/C 69 1.12 0.91 2.82 5.06 -10.87 26.65 -3 5) C 69/U 68 -1.10 -0.13 2.79 -3.85 3.82 36.68 -2 6) U 68/C 67 0.18 0.00 2.87 2.45 -6.30 31.96 -3 7) C 67/U 66 0.35 0.05 2.92 2.72 3.19 34.60 -2 --------------------------------------- |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/G 2 -0.09 -0.37 3.04 -0.21 0.57 32.23 1 3) G 2/A 3 -0.26 0.42 2.79 -3.32 0.17 32.42 2 4) A 3/G 4 1.06 -0.86 2.72 3.46 6.48 27.11 3 5) G 4/A 5 -1.09 -0.03 2.88 -2.84 -1.05 34.76 2 6) A 5/G 6 0.14 0.04 2.78 1.28 2.04 32.44 3 7) G 6/A 7 0.54 0.04 2.93 2.34 -2.08 36.05 2 Average: 0.05 -0.13 2.86 0.12 1.02 32.50 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/G 2 0.02 -2.59 3.23 1.28 -1.25 32.75 1 3) G 2/A 3 -0.08 -1.89 3.21 4.00 8.11 31.89 2 4) A 3/G 4 1.10 -2.48 3.18 4.03 5.27 26.65 3 5) G 4/A 5 -0.84 -2.22 3.27 0.54 5.94 32.73 2 6) A 5/G 6 0.44 -1.95 3.23 3.19 2.97 31.88 3 7) G 6/A 7 1.18 -2.11 3.12 7.21 5.01 36.53 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 72/C 71 -0.51 -2.03 3.64 -0.69 11.87 30.86 -1 3) C 71/U 70 -0.64 -1.42 3.05 -9.17 1.66 31.26 -2 4) U 70/C 69 0.82 -2.29 3.65 3.49 15.45 25.87 -3 5) C 69/U 68 -1.32 -1.89 3.10 -7.02 3.81 35.60 -2 6) U 68/C 67 -0.15 -1.66 3.55 -0.44 13.42 30.66 -3 7) C 67/U 66 0.07 -1.72 3.46 -0.71 6.02 33.69 -2 -------------------------------------- |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/G 2 -0.24 -2.32 3.45 0.37 5.33 32.30 1 3) G 2/A 3 -0.36 -1.64 3.15 -2.64 5.00 31.36 2 4) A 3/G 4 0.97 -2.39 3.42 3.85 10.36 26.45 3 5) G 4/A 5 -1.09 -2.05 3.20 -3.25 4.90 34.20 2 6) A 5/G 6 0.15 -1.81 3.40 1.34 8.18 31.58 3 7) G 6/A 7 0.63 -1.92 3.34 3.28 5.54 35.33 2 Average: 0.01 -2.02 3.33 0.49 6.55 31.87 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 1/G 2 -0.07 -0.17 -0.83 0.45 0.18 0.94 3.05 1 3) G 2/A 3 -0.13 0.22 -2.18 1.11 0.26 2.45 2.80 2 4) A 3/G 4 0.53 -0.44 2.03 4.31 0.69 4.76 2.81 3 5) G 4/A 5 -0.61 -0.02 -3.89 -0.84 0.61 3.98 2.94 2 6) A 5/G 6 0.03 0.11 -0.35 2.93 0.11 2.95 2.78 3 7) G 6/A 7 0.27 0.05 1.49 -0.80 0.27 1.69 2.94 2 Overall axis bend ... UU= 8.38 PP= 12.47 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 1 0.00 0.00 2) G 2 0.32 57.50 3) A 3 0.40 -12.73 4) G 4 0.40 117.13 5) A 5 0.65 33.84 6) G 6 0.45 -1.09 7) A 7 0.00 0.00 Path length= 17.31 End-to-end= 17.09 Shortening= 1.31 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 1 -31.40 44.14 10.50 45.25 C3'-endo 104.4 100.2 100.8 2)GA 2 -33.32 45.18 9.51 47.15 C3'-endo 108.4 96.9 101.7 3)AA 3 -33.88 45.38 9.02 47.16 C3'-endo 106.4 98.8 99.8 4)GA 4 -33.73 39.96 358.98 40.76 C2'-exo 105.1 101.3 101.4 5)AA 5 -34.57 45.76 6.57 46.56 C3'-endo 104.3 100.4 100.3 6)GA 6 -31.08 43.57 11.05 45.33 C3'-endo 108.1 97.9 102.1 7)AA 7 -26.51 42.59 19.42 45.79 C3'-endo 105.4 100.5 100.5 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 -179.69 50.63 84.72 -151.92 -73.12 -67.06 179.80 2)GA 2 -164.44 55.95 81.85 -151.67 -72.08 -71.31 -177.51 3)AA 3 -155.95 47.79 77.43 -160.43 -69.01 144.23 -167.78 4)GA 4 -177.63 -174.31 89.48 -150.93 -78.86 -66.99 -174.21 5)AA 5 -166.73 39.99 87.99 -155.44 -71.82 -63.39 170.11 6)GA 6 -164.53 51.85 81.38 -147.81 -70.34 -60.75 170.88 7)AA 7 -162.40 51.79 81.11 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 72 -26.53 40.80 17.51 43.70 C3'-endo 107.1 100.4 101.3 2)CB 71 -27.24 41.58 16.00 43.56 C3'-endo 105.4 101.2 101.3 3)UB 70 -30.09 43.33 13.83 45.81 C3'-endo 107.4 99.4 100.5 4)CB 69 -29.88 43.45 14.31 46.07 C3'-endo 108.2 98.7 100.9 5)UB 68 -32.25 46.39 12.87 48.18 C3'-endo 105.6 100.1 99.2 6)CB 67 -32.24 42.95 8.86 44.87 C3'-endo 109.1 98.0 101.8 7)UB 66 -30.94 42.01 8.81 43.01 C3'-endo 106.2 101.0 101.1 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 -159.46 50.18 81.57 ...... ...... ...... ...... 2)CB 71 -159.44 54.75 83.59 -151.86 -71.40 -65.49 174.51 3)UB 70 -159.78 48.97 78.75 -151.16 -79.76 -59.67 159.77 4)CB 69 -160.26 57.28 82.59 -159.11 -73.16 -74.20 -175.90 5)UB 68 -163.07 52.03 80.88 -153.36 -71.20 -61.26 166.11 6)CB 67 -156.88 53.06 77.70 -148.31 -73.83 -70.17 172.49 7)UB 66 -161.59 45.15 82.54 -161.83 -69.91 -69.83 177.18