ID code: 8ICP, PDE077 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 26 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 0.113 1 : 2) AA 2 0.064 1 : 3) TA 3 0.060 1 : 4) TA 4 0.253 1 : 5) AA 5 0.046 1 : 6) GA 6 0.032 1 : 7) AA 7 0.088 2 : 1) GB 7 0.183 2 : 2) TB 6 0.183 2 : 3) AB 5 0.085 2 : 4) AB 4 0.025 2 : 5) TB 3 0.137 2 : 6) CB 2 0.089 2 : 7) TB 1 0.217 Strand= 2 Nucleo= 14 Atoms = 281 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'): CATTAGA Strand 2 has 7 bases (3'-5'): GTAATCT FIRST SUM= 15.585 CPTS: 0.907 4.563 2.804 7.310 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 15.585 DEL= 0.000E+00 STEP 2 SUM= 12.869 DEL= -0.272E+01 STEP 3 SUM= 16.318 DEL= 0.345E+01 STEP 4 SUM= 12.038 DEL= -0.428E+01 STEP 5 SUM= 11.690 DEL= -0.349E+00 STEP 6 SUM= 11.123 DEL= -0.567E+00 STEP 7 SUM= 10.477 DEL= -0.647E+00 STEP 8 SUM= 9.757 DEL= -0.720E+00 STEP 9 SUM= 8.696 DEL= -0.106E+01 STEP 10 SUM= 9.524 DEL= 0.828E+00 STEP 11 SUM= 8.314 DEL= -0.121E+01 STEP 12 SUM= 7.770 DEL= -0.544E+00 STEP 13 SUM= 6.948 DEL= -0.822E+00 STEP 14 SUM= 11.133 DEL= 0.419E+01 STEP 15 SUM= 6.832 DEL= -0.430E+01 STEP 16 SUM= 6.871 DEL= 0.385E-01 STEP 17 SUM= 6.782 DEL= -0.882E-01 STEP 18 SUM= 6.688 DEL= -0.942E-01 STEP 19 SUM= 6.319 DEL= -0.370E+00 STEP 20 SUM= 8.356 DEL= 0.204E+01 STEP 21 SUM= 6.246 DEL= -0.211E+01 STEP 22 SUM= 6.120 DEL= -0.126E+00 STEP 23 SUM= 5.965 DEL= -0.155E+00 STEP 24 SUM= 6.417 DEL= 0.452E+00 STEP 25 SUM= 5.887 DEL= -0.530E+00 STEP 26 SUM= 5.806 DEL= -0.811E-01 STEP 27 SUM= 5.670 DEL= -0.136E+00 STEP 28 SUM= 5.506 DEL= -0.164E+00 STEP 29 SUM= 5.534 DEL= 0.283E-01 STEP 30 SUM= 5.456 DEL= -0.783E-01 STEP 31 SUM= 5.458 DEL= 0.220E-02 STEP 32 SUM= 5.446 DEL= -0.124E-01 STEP 33 SUM= 5.453 DEL= 0.692E-02 STEP 34 SUM= 5.442 DEL= -0.102E-01 STEP 35 SUM= 5.440 DEL= -0.233E-02 STEP 36 SUM= 5.440 DEL= -0.512E-03 STEP 37 SUM= 5.440 DEL= 0.488E-03 STEP 38 SUM= 5.439 DEL= -0.579E-03 STEP 39 SUM= 5.439 DEL= -0.831E-04 STEP 40 SUM= 5.439 DEL= -0.111E-03 STEP 41 SUM= 5.439 DEL= -0.273E-04 STEP 42 SUM= 5.439 DEL= -0.339E-04 STEP 43 SUM= 5.439 DEL= -0.116E-05 STEP 44 SUM= 5.439 DEL= -0.374E-05 STEP 45 SUM= 5.439 DEL= 0.217E-05 STEP 46 SUM= 5.439 DEL= -0.366E-05 STEP 47 SUM= 5.439 DEL= -0.755E-07 STEP 48 SUM= 5.439 DEL= -0.299E-08 STEP 49 SUM= 5.439 DEL= -0.367E-09 STEP 50 SUM= 5.439 DEL= -0.128E-10 STEP 51 SUM= 5.439 DEL= -0.290E-12 STEP 52 SUM= 5.439 DEL= 0.000E+00 STEP 53 SUM= 5.439 DEL= -0.888E-15 STEP 54 SUM= 5.439 DEL= 0.000E+00 FINAL SUM= 5.439 CPTS: 0.638 3.665 0.150 0.986 GRA=-0.24E-11-0.35E-10-0.11E-11-0.45E-11 0.39E-11 0.33E-11 0.79E-12 0.55E-11 GRA= 0.17E-10 0.69E-11 0.88E-12-0.12E-12-0.16E-10 0.15E-10 0.37E-11-0.11E-11 GRA= 0.34E-10-0.30E-10 0.11E-11 0.47E-12-0.11E-10-0.66E-11-0.77E-12 0.89E-11 GRA= 0.26E-10 0.58E-10 0.18E-11-0.15E-11 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.493 -0.858 -0.145 P: 60.137 35.553 47.108 D: 0.550 2) U: -0.512 -0.849 -0.133 P: 58.591 32.594 46.379 D: 1.022 3) U: -0.543 -0.829 -0.132 P: 56.634 30.031 46.107 D: 0.730 4) U: -0.594 -0.794 -0.130 P: 54.802 27.533 45.876 D: 0.914 5) U: -0.599 -0.790 -0.131 P: 52.778 24.573 45.502 D: 1.597 6) U: -0.600 -0.785 -0.151 P: 50.641 22.362 44.900 D: 0.627 7) U: -0.596 -0.794 -0.117 P: 48.729 19.494 44.559 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.70 0.60 10.25 -6.39 3 0 2) AA 2 -1.19 0.71 11.10 -6.44 2 30 3) TA 3 -1.21 0.52 6.78 -10.22 4 -24 4) TA 4 -1.46 0.18 10.12 -7.12 4 -28 5) AA 5 -0.93 0.23 8.75 -5.26 2 27 6) GA 6 -1.42 -0.36 9.33 -4.16 1 4 7) AA 7 -1.20 0.04 16.08 -4.48 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -1.66 -0.31 11.84 -7.87 1 0 2) TB 6 -1.76 -0.49 9.21 -5.14 4 -30 3) AB 5 -1.27 -0.37 6.82 -9.14 2 24 4) AB 4 -1.05 -0.54 6.20 -11.45 2 28 5) TB 3 -1.74 -0.71 6.90 -8.04 4 -27 6) CB 2 -1.00 -0.35 8.62 -8.05 3 -4 7) TB 1 -0.98 -0.41 2.15 -5.73 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) C 1-G 7 -1.18 0.45 11.05 0.74 3 0 2) A 2-T 6 -1.48 0.60 10.15 -0.65 2 30 3) T 3-A 5 -1.24 0.44 6.80 -0.54 4 -24 4) T 4-A 4 -1.25 0.36 8.16 2.17 4 -28 5) A 5-T 3 -1.34 0.47 7.83 1.39 2 27 6) G 6-C 2 -1.21 -0.00 8.97 1.94 1 4 7) A 7-T 1 -1.09 0.22 9.12 0.63 2 0 Average: -1.25 0.36 8.87 0.81 --------------------------------- |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 7 0.96 0.29 -0.31 -1.59 -14.26 13.96 3 0 2) A 2-T 6 0.57 0.22 -0.33 1.88 -11.57 4.81 2 30 3) T 3-A 5 0.07 0.16 0.26 -0.04 -19.36 8.27 4 -24 4) T 4-A 4 -0.41 -0.35 -0.39 3.92 -18.57 7.16 4 -28 5) A 5-T 3 0.81 -0.48 -0.28 1.85 -13.30 -3.15 2 27 6) G 6-C 2 -0.42 -0.71 -0.30 0.71 -12.21 -7.08 1 4 7) A 7-T 1 -0.22 -0.37 -0.18 13.94 -10.21 -0.93 2 0 Average: 0.19 -0.18 -0.22 2.95 -14.21 3.29 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/A 2 -0.76 0.27 3.39 0.99 1.33 18.38 9 3) A 2/T 3 0.27 -0.36 3.51 -4.11 -1.68 37.10 7 4) T 3/T 4 -0.31 -0.52 2.78 5.61 5.81 31.77 -4 5) T 4/A 5 0.39 0.18 3.66 -1.00 2.02 37.80 10 6) A 5/G 6 -0.44 -0.98 3.10 1.12 2.18 19.78 3 7) G 6/A 7 0.28 0.63 3.51 5.00 -1.37 36.43 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.37 -0.34 3.42 -2.49 1.35 27.53 -9 3) T 6/A 5 0.77 0.30 2.93 -2.18 -6.11 33.64 7 4) A 5/A 4 0.17 0.01 3.43 1.64 -5.02 32.87 4 5) A 4/T 3 -0.83 -0.31 3.55 1.07 3.25 48.10 10 6) T 3/C 2 0.79 0.75 3.12 2.26 -1.08 23.71 -3 7) C 2/T 1 0.08 -0.29 3.40 -8.22 3.37 30.29 -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) C 1/A 2 -0.56 0.31 3.40 -0.75 -0.01 22.96 9 3) A 2/T 3 0.52 -0.33 3.22 -3.15 2.21 35.37 7 4) T 3/T 4 -0.07 -0.27 3.10 3.63 5.41 32.32 -4 5) T 4/A 5 -0.22 0.25 3.60 0.04 -0.62 42.95 10 6) A 5/G 6 0.18 -0.87 3.11 1.69 1.63 21.75 3 7) G 6/A 7 0.18 0.46 3.46 -1.61 -2.37 33.36 2 Average: 0.00 -0.07 3.31 -0.03 1.04 31.45 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/A 2 -0.57 0.62 3.45 3.07 4.68 17.59 9 3) A 2/T 3 0.42 -0.55 3.67 1.45 4.14 36.49 7 4) T 3/T 4 -0.09 -0.83 3.05 10.30 10.07 30.00 -4 5) T 4/A 5 0.62 -0.03 3.67 3.04 8.00 37.23 10 6) A 5/G 6 -0.13 -0.88 3.32 2.65 5.26 19.23 3 7) G 6/A 7 0.55 0.53 3.44 7.37 6.48 35.42 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.92 0.14 3.42 -5.52 3.69 26.37 -9 3) T 6/A 5 0.16 -0.78 3.16 -6.28 10.54 32.63 7 4) A 5/A 4 -0.69 -0.31 3.50 -4.27 8.73 32.16 4 5) A 4/T 3 -1.83 -0.43 3.39 -6.87 2.37 47.30 10 6) T 3/C 2 0.08 -0.89 3.34 -1.00 4.22 23.45 -3 7) C 2/T 1 -0.45 0.10 3.36 -11.57 -0.41 29.17 -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) C 1/A 2 -0.76 0.39 3.43 -1.27 4.52 22.07 9 3) A 2/T 3 0.25 -0.66 3.41 -2.23 7.55 34.79 7 4) T 3/T 4 -0.33 -0.55 3.28 2.99 9.90 31.44 -4 5) T 4/A 5 -0.62 -0.21 3.66 -1.99 5.27 42.69 10 6) A 5/G 6 -0.02 -0.88 3.29 0.85 4.66 21.49 3 7) G 6/A 7 0.05 0.29 3.43 -2.00 2.71 32.51 2 Average: -0.24 -0.27 3.41 -0.61 5.77 30.83 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.26 0.16 0.15 1.38 0.31 1.39 3.42 9 3) A 2/T 3 0.28 -0.18 0.21 2.10 0.33 2.11 3.24 7 4) T 3/T 4 -0.05 -0.18 2.27 2.71 0.19 3.53 3.11 -4 5) T 4/A 5 -0.13 0.13 0.37 0.16 0.19 0.40 3.61 10 6) A 5/G 6 0.05 -0.39 0.54 1.07 0.40 1.21 3.13 3 7) G 6/A 7 0.06 0.23 -1.75 -1.06 0.24 2.05 3.46 2 Overall axis bend ... UU= 7.12 PP= 8.99 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.54 -21.62 3) T 3 0.38 -49.83 4) T 4 0.30 -54.53 5) A 5 0.37 -79.11 6) G 6 0.15 110.62 7) A 7 0.00 0.00 Path length= 19.96 End-to-end= 19.86 Shortening= 0.50 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 21.04 -35.15 203.74 39.89 C3'-exo 109.6 101.3 100.9 2)AA 2 29.44 -33.37 176.29 34.42 C2'-endo 107.8 101.7 103.1 3)TA 3 41.29 -32.31 143.61 41.45 C1'-exo 105.1 100.1 104.1 4)TA 4 48.46 -25.36 120.01 53.21 C1'-exo 101.4 99.7 102.3 5)AA 5 20.44 -28.26 191.73 29.79 C3'-exo 108.1 102.3 103.2 6)GA 6 50.99 -32.86 129.81 52.94 C1'-exo 100.8 98.7 104.3 7)AA 7 33.16 -25.64 145.71 32.70 C2'-endo 108.9 101.5 103.7 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 -45.59 142.22 161.37 146.16 -106.32 -36.92 180.00 2)AA 2 -83.78 42.01 145.74 169.60 -124.37 -27.60 160.93 3)TA 3 -103.79 41.61 128.46 -170.06 -122.96 -18.87 142.66 4)TA 4 -115.51 45.09 110.94 176.39 -96.13 -55.14 -163.91 5)AA 5 -100.96 44.81 142.59 173.81 -79.80 -120.83 -179.24 6)GA 6 -116.70 85.28 128.74 -91.51 164.85 -18.61 116.65 7)AA 7 -83.91 0.92 127.31 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 -18.72 6.54 286.94 23.71 O1'-exo 108.2 105.6 104.5 2)TB 6 37.38 -43.31 177.33 44.23 C2'-endo 104.5 100.5 100.4 3)AB 5 22.27 -6.69 103.32 29.95 O1'-endo 104.8 106.0 104.3 4)AB 4 21.92 -9.51 112.22 26.17 C1'-exo 106.7 105.1 104.2 5)TB 3 47.20 -33.51 137.27 47.78 C1'-exo 104.9 96.8 104.3 6)CB 2 41.30 -51.15 181.87 52.12 C3'-exo 104.6 97.3 99.2 7)TB 1 11.89 16.19 70.04 47.40 C4'-exo 104.7 103.0 103.9 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 7 -120.39 -81.19 126.31 ...... ...... ...... ...... 2)TB 6 -106.37 -64.13 158.99 -153.23 -118.30 39.86 -167.99 3)AB 5 -117.56 46.89 105.73 172.85 -109.17 57.17 171.29 4)AB 4 -122.19 57.98 109.06 -162.28 -82.08 -69.03 165.53 5)TB 3 -94.32 29.82 132.32 -158.34 -128.29 -58.00 157.65 6)CB 2 -86.86 30.11 164.55 -148.73 -142.03 -45.84 148.38 7)TB 1 -153.18 72.20 84.99 -164.44 -83.34 -29.17 173.26