ID code: 1A1L, PDT061 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 20 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 2 0.019 1 : 2) CA 3 0.025 1 : 3) GA 4 0.021 1 : 4) TA 5 0.028 1 : 5) GA 6 0.019 1 : 6) GA 7 0.016 1 : 7) GA 8 0.019 1 : 8) CA 9 0.016 1 : 9) AA 10 0.014 1 : 10) CA 11 0.011 2 : 1) CB 61 0.028 2 : 2) GB 60 0.022 2 : 3) CB 59 0.008 2 : 4) AB 58 0.021 2 : 5) CB 57 0.012 2 : 6) CB 56 0.016 2 : 7) CB 55 0.034 2 : 8) GB 54 0.030 2 : 9) TB 53 0.017 2 : 10) GB 52 0.019 Strand= 2 Nucleo= 20 Atoms = 404 Units = 20 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 10 levels ... Strand 1 has 10 bases (5'-3'): GCGTGGGCAC Strand 2 has 10 bases (3'-5'): CGCACCCGTG FIRST SUM= 43.584 CPTS: 4.610 2.660 7.363 28.950 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 40 STEP 1 SUM= 43.584 DEL= 0.000E+00 STEP 2 SUM= 28.061 DEL= -0.155E+02 STEP 3 SUM= 59.993 DEL= 0.319E+02 STEP 4 SUM= 24.235 DEL= -0.358E+02 STEP 5 SUM= 20.470 DEL= -0.376E+01 STEP 6 SUM= 19.129 DEL= -0.134E+01 STEP 7 SUM= 17.548 DEL= -0.158E+01 STEP 8 SUM= 16.113 DEL= -0.144E+01 STEP 9 SUM= 15.501 DEL= -0.612E+00 STEP 10 SUM= 15.311 DEL= -0.190E+00 STEP 11 SUM= 15.029 DEL= -0.282E+00 STEP 12 SUM= 14.538 DEL= -0.491E+00 STEP 13 SUM= 13.941 DEL= -0.597E+00 STEP 14 SUM= 28.871 DEL= 0.149E+02 STEP 15 SUM= 13.894 DEL= -0.150E+02 STEP 16 SUM= 13.805 DEL= -0.900E-01 STEP 17 SUM= 13.265 DEL= -0.539E+00 STEP 18 SUM= 23.831 DEL= 0.106E+02 STEP 19 SUM= 13.258 DEL= -0.106E+02 STEP 20 SUM= 13.232 DEL= -0.259E-01 STEP 21 SUM= 13.189 DEL= -0.427E-01 STEP 22 SUM= 13.122 DEL= -0.669E-01 STEP 23 SUM= 13.072 DEL= -0.501E-01 STEP 24 SUM= 13.013 DEL= -0.594E-01 STEP 25 SUM= 12.983 DEL= -0.298E-01 STEP 26 SUM= 12.946 DEL= -0.374E-01 STEP 27 SUM= 12.897 DEL= -0.485E-01 STEP 28 SUM= 12.820 DEL= -0.776E-01 STEP 29 SUM= 12.717 DEL= -0.102E+00 STEP 30 SUM= 12.597 DEL= -0.121E+00 STEP 31 SUM= 12.530 DEL= -0.668E-01 STEP 32 SUM= 12.478 DEL= -0.517E-01 STEP 33 SUM= 12.451 DEL= -0.269E-01 STEP 34 SUM= 12.425 DEL= -0.261E-01 STEP 35 SUM= 12.408 DEL= -0.170E-01 STEP 36 SUM= 12.401 DEL= -0.693E-02 STEP 37 SUM= 12.401 DEL= 0.462E-04 STEP 38 SUM= 12.399 DEL= -0.270E-02 STEP 39 SUM= 12.398 DEL= -0.350E-03 STEP 40 SUM= 12.398 DEL= -0.233E-03 STEP 41 SUM= 12.398 DEL= -0.423E-04 STEP 42 SUM= 12.398 DEL= -0.180E-05 STEP 43 SUM= 12.398 DEL= -0.796E-05 STEP 44 SUM= 12.398 DEL= -0.271E-05 STEP 45 SUM= 12.398 DEL= -0.114E-05 STEP 46 SUM= 12.398 DEL= -0.622E-06 STEP 47 SUM= 12.398 DEL= -0.470E-06 STEP 48 SUM= 12.398 DEL= -0.212E-06 STEP 49 SUM= 12.398 DEL= -0.738E-07 STEP 50 SUM= 12.398 DEL= -0.743E-07 STEP 51 SUM= 12.398 DEL= -0.854E-07 STEP 52 SUM= 12.398 DEL= -0.197E-07 STEP 53 SUM= 12.398 DEL= -0.100E-07 STEP 54 SUM= 12.398 DEL= -0.266E-09 STEP 55 SUM= 12.398 DEL= -0.117E-10 STEP 56 SUM= 12.398 DEL= -0.186E-11 STEP 57 SUM= 12.398 DEL= -0.142E-13 STEP 58 SUM= 12.398 DEL= 0.000E+00 FINAL SUM= 12.398 CPTS: 2.676 5.580 0.581 3.561 GRA=-0.33E-08-0.93E-08-0.16E-08 0.27E-09 0.40E-08-0.13E-08 0.14E-08-0.78E-09 GRA= 0.15E-07 0.87E-08 0.48E-09-0.10E-08-0.11E-07-0.44E-09 0.23E-08-0.61E-09 GRA=-0.11E-07-0.12E-07-0.14E-08 0.24E-08 0.80E-08 0.29E-07 0.38E-09 0.25E-08 GRA=-0.27E-08-0.16E-07 0.83E-09-0.10E-08 0.13E-07-0.74E-08 0.37E-09-0.12E-08 GRA=-0.18E-07 0.27E-08-0.56E-09-0.11E-08 0.85E-08 0.57E-08-0.11E-08 0.24E-08 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.635 -0.772 0.045 P: 10.791 21.256 48.475 D: 1.926 2) U: -0.659 -0.751 0.052 P: 8.754 19.467 48.459 D: 1.956 3) U: -0.637 -0.771 -0.013 P: 6.707 16.634 48.930 D: 1.489 4) U: -0.685 -0.728 -0.025 P: 4.529 14.384 48.420 D: 1.246 5) U: -0.661 -0.751 -0.003 P: 2.116 11.857 48.752 D: 0.425 6) U: -0.648 -0.761 -0.030 P: -0.222 9.510 48.635 D: 0.184 7) U: -0.613 -0.788 -0.059 P: -2.315 6.994 48.595 D: 2.074 8) U: -0.579 -0.807 -0.118 P: -3.593 4.290 48.648 D: 2.222 9) U: -0.623 -0.776 -0.092 P: -5.865 1.629 47.667 D: 0.876 10) U: -0.571 -0.817 -0.076 P: -7.592 -0.650 47.664 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 2 -2.03 -0.13 0.70 -5.56 1 0 2) CA 3 -1.33 -0.03 13.96 -0.74 3 -13 3) GA 4 -2.23 0.04 3.91 1.66 1 14 4) TA 5 -1.44 0.02 10.79 4.23 4 -29 5) GA 6 -1.97 0.25 7.58 0.48 1 11 6) GA 7 -2.21 -0.02 5.32 -0.35 1 1 7) GA 8 -2.27 -0.06 4.57 0.34 1 5 8) CA 9 -1.45 -0.19 10.14 3.49 3 -15 9) AA 10 -2.13 -0.22 3.46 1.12 2 29 10) CA 11 -1.82 -0.11 12.26 -1.85 3 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 61 -2.04 0.31 12.08 0.15 3 0 2) GB 60 -1.91 0.33 0.89 -1.70 1 13 3) CB 59 -1.93 0.22 6.26 -5.33 3 -14 4) AB 58 -1.81 0.40 3.81 -5.06 2 29 5) CB 57 -1.97 0.16 3.17 -10.91 3 -11 6) CB 56 -2.14 0.30 6.30 -9.47 3 -1 7) CB 55 -2.16 0.30 7.49 -4.96 3 -5 8) GB 54 -1.76 0.51 3.82 -4.45 1 15 9) TB 53 -2.30 0.35 6.72 -9.74 4 -29 10) GB 52 -2.18 0.72 2.70 -7.92 1 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 2-C 61 -2.03 -0.22 6.39 -2.85 1 0 2) C 3-G 60 -1.62 -0.18 7.42 0.48 3 -13 3) G 4-C 59 -2.08 -0.09 5.08 3.49 1 14 4) T 5-A 58 -1.63 -0.19 7.30 4.65 4 -29 5) G 6-C 57 -1.97 0.05 5.37 5.70 1 11 6) G 7-C 56 -2.18 -0.16 5.81 4.56 1 1 7) G 8-C 55 -2.21 -0.18 6.03 2.65 1 5 8) C 9-G 54 -1.60 -0.35 6.98 3.97 3 -15 9) A 10-T 53 -2.21 -0.28 5.09 5.43 2 29 10) C 11-G 52 -2.00 -0.42 7.48 3.04 3 0 Average: -1.95 -0.20 6.30 3.11 --------------------------------- |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 2-C 61 0.01 0.18 -0.28 -11.38 -5.41 3.04 1 0 2) C 3-G 60 0.58 0.29 -0.38 13.07 -2.44 5.65 3 -13 3) G 4-C 59 -0.29 0.26 0.01 -2.35 -3.67 1.75 1 14 4) T 5-A 58 0.36 0.42 -0.36 6.98 -0.83 5.56 4 -29 5) G 6-C 57 0.01 0.42 0.12 4.41 -10.42 4.14 1 11 6) G 7-C 56 -0.07 0.28 -0.15 -0.98 -9.82 1.79 1 1 7) G 8-C 55 -0.11 0.24 -0.15 -2.92 -4.62 0.88 1 5 8) C 9-G 54 0.30 0.31 -0.16 6.32 -0.95 3.76 3 -15 9) A 10-T 53 0.16 0.13 0.38 -3.26 -8.62 1.07 2 29 10) C 11-G 52 0.36 0.61 -0.09 9.56 -9.78 6.78 3 0 Average: 0.13 0.31 -0.11 1.95 -5.66 3.44 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 2/C 3 1.11 0.02 2.63 14.54 6.19 25.35 5 3) C 3/G 4 -1.38 0.12 3.69 -13.42 4.77 33.23 8 4) G 4/T 5 1.23 -0.18 2.95 10.60 3.14 30.73 6 5) T 5/G 6 -0.88 0.37 3.73 -5.48 -3.74 34.03 -9 6) G 6/G 7 -0.44 -0.42 3.17 -1.19 0.64 31.87 1 7) G 7/G 8 -0.07 0.07 3.27 1.38 2.80 35.88 1 8) G 8/C 9 1.46 -0.33 2.91 9.52 2.30 30.04 5 9) C 9/A 10 -1.32 0.03 3.85 -10.02 -1.65 32.40 9 10) A 10/C 11 0.54 0.04 2.61 12.69 -3.35 35.02 -6 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 61/G 60 0.55 0.09 2.73 -9.92 -3.22 22.74 5 3) G 60/C 59 -0.51 -0.15 3.30 2.00 -6.00 37.13 8 4) C 59/A 58 0.57 0.34 3.32 1.28 -0.29 26.92 -6 5) A 58/C 57 -0.53 -0.38 3.25 -2.92 -5.85 35.45 9 6) C 57/C 56 -0.36 0.28 3.44 4.20 -0.03 34.21 -1 7) C 56/C 55 -0.03 -0.11 3.27 3.32 2.40 36.80 -1 8) C 55/G 54 1.05 0.41 2.92 0.28 1.37 27.16 5 9) G 54/T 53 -1.18 -0.21 3.31 -0.44 -6.02 35.09 -9 10) T 53/G 52 0.34 0.44 3.09 -0.13 2.19 29.31 6 --------------------------------------- |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 2/C 3 0.83 -0.03 2.68 2.31 4.70 24.05 5 3) C 3/G 4 -0.95 0.13 3.50 -5.71 5.39 35.18 8 4) G 4/T 5 0.90 -0.26 3.14 5.94 1.72 28.82 6 5) T 5/G 6 -0.71 0.37 3.49 -4.20 1.06 34.74 -9 6) G 6/G 7 -0.40 -0.35 3.31 1.51 0.34 33.04 1 7) G 7/G 8 -0.05 0.09 3.27 2.35 0.20 36.34 1 8) G 8/C 9 1.25 -0.37 2.92 4.90 0.46 28.60 5 9) C 9/A 10 -1.25 0.12 3.58 -5.23 2.19 33.74 9 10) A 10/C 11 0.44 -0.20 2.85 6.28 -2.77 32.16 -6 Average: 0.01 -0.06 3.19 0.91 1.48 31.85 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 2/C 3 1.20 -0.42 2.73 15.71 9.10 24.44 5 3) C 3/G 4 -1.28 -0.35 3.92 -13.27 9.76 32.63 8 4) G 4/T 5 0.97 -0.81 3.18 8.84 6.78 31.05 6 5) T 5/G 6 -1.06 -0.01 3.76 -6.70 1.87 33.36 -9 6) G 6/G 7 -0.48 -1.19 3.38 -1.10 4.17 31.51 1 7) G 7/G 8 -0.03 -1.03 3.44 1.45 5.78 35.59 1 8) G 8/C 9 1.35 -0.96 3.09 8.33 5.89 30.32 5 9) C 9/A 10 -1.27 -0.48 3.96 -11.01 2.29 31.77 9 10) A 10/C 11 0.58 -0.80 2.75 12.49 1.38 34.86 -6 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 61/G 60 0.69 -0.55 2.85 -10.08 5.75 22.41 5 3) G 60/C 59 -0.59 -0.92 3.41 -0.58 7.98 37.01 8 4) C 59/A 58 0.43 -0.91 3.46 -1.08 2.76 26.75 -6 5) A 58/C 57 -0.79 -0.66 3.23 -7.73 7.59 34.77 9 6) C 57/C 56 -0.85 -1.20 3.51 -1.96 2.90 34.17 -1 7) C 56/C 55 -0.27 -0.82 3.46 -1.27 2.18 36.38 -1 8) C 55/G 54 1.01 -1.03 3.06 -1.80 1.38 27.03 5 9) G 54/T 53 -1.32 -0.79 3.30 -4.85 8.87 34.64 -9 10) T 53/G 52 0.16 -1.28 3.22 -4.43 0.38 28.88 6 -------------------------------------- |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 2/C 3 0.94 -0.48 2.78 2.73 7.99 23.31 5 3) C 3/G 4 -0.95 -0.66 3.65 -6.95 8.68 34.77 8 4) G 4/T 5 0.70 -0.85 3.32 3.80 4.94 28.91 6 5) T 5/G 6 -0.95 -0.36 3.49 -7.07 4.74 33.90 -9 6) G 6/G 7 -0.66 -1.19 3.45 -1.55 3.54 32.97 1 7) G 7/G 8 -0.15 -0.92 3.46 0.07 3.99 36.01 1 8) G 8/C 9 1.18 -0.99 3.08 3.21 3.75 28.68 5 9) C 9/A 10 -1.31 -0.64 3.63 -7.86 5.51 33.16 9 10) A 10/C 11 0.38 -1.03 2.99 4.01 1.18 31.89 -6 Average: -0.09 -0.79 3.32 -1.07 4.93 31.51 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 2/C 3 0.41 -0.07 1.28 1.37 0.42 1.87 2.71 5 3) C 3/G 4 -0.49 0.04 -3.37 2.37 0.49 4.12 3.53 8 4) G 4/T 5 0.44 -0.16 3.72 0.56 0.47 3.77 3.17 6 5) T 5/G 6 -0.36 0.14 -2.27 0.01 0.39 2.27 3.51 -9 6) G 6/G 7 -0.19 -0.15 1.07 1.47 0.24 1.82 3.31 1 7) G 7/G 8 -0.01 0.11 2.13 2.11 0.11 3.00 3.27 1 8) G 8/C 9 0.64 -0.20 3.95 -0.85 0.67 4.05 2.99 5 9) C 9/A 10 -0.64 0.05 -3.34 0.73 0.64 3.42 3.63 9 10) A 10/C 11 0.23 -0.06 3.89 -0.38 0.24 3.90 2.86 -6 Overall axis bend ... UU= 8.26 PP= 11.54 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 2 0.00 0.00 2) C 3 0.41 126.43 3) G 4 0.65 25.62 4) T 5 0.43 42.06 5) G 6 0.88 -9.78 6) G 7 1.08 -29.82 7) G 8 1.10 -68.41 8) C 9 0.81 -142.81 9) A 10 0.16 -64.53 10) C 11 0.00 0.00 Path length= 28.99 End-to-end= 28.61 Shortening= 1.32 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 2 36.62 -33.59 156.69 37.48 C2'-endo 105.5 101.5 103.4 2)CA 3 47.37 -38.06 146.95 47.17 C2'-endo 104.6 98.2 102.8 3)GA 4 34.56 -32.52 158.62 35.66 C2'-endo 105.4 102.4 103.4 4)TA 5 43.69 -34.88 145.75 43.61 C2'-endo 104.8 99.8 103.2 5)GA 6 34.35 -31.82 157.32 35.24 C2'-endo 105.6 102.4 103.6 6)GA 7 36.58 -32.84 154.94 37.17 C2'-endo 105.6 101.7 103.4 7)GA 8 33.12 -31.45 159.79 34.30 C2'-endo 106.0 102.5 103.6 8)CA 9 43.89 -36.44 148.86 43.95 C2'-endo 104.8 99.4 103.1 9)AA 10 33.34 -31.51 159.09 34.46 C2'-endo 105.7 102.5 103.7 10)CA 11 39.99 -34.47 151.66 40.24 C2'-endo 104.9 101.0 103.1 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 2 -96.02 43.29 139.13 -176.22 -93.05 -57.67 177.02 2)CA 3 -79.79 39.20 139.73 -136.49 168.98 -55.60 140.67 3)GA 4 -128.76 43.86 139.40 -161.87 -83.50 -66.47 176.77 4)TA 5 -93.00 36.23 136.20 -143.64 -177.74 -49.45 137.38 5)GA 6 -123.52 48.54 138.65 -165.18 -108.17 -57.93 177.79 6)GA 7 -112.43 41.22 137.78 179.97 -102.76 -65.89 -164.25 7)GA 8 -103.02 43.00 139.30 174.39 -85.91 -52.61 -175.60 8)CA 9 -96.77 38.84 139.20 -148.23 -174.27 -44.13 142.85 9)AA 10 -125.72 44.66 138.65 -169.28 -91.62 -67.08 -177.81 10)CA 11 -96.76 43.66 141.62 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 61 40.24 -34.38 151.12 40.42 C2'-endo 105.1 100.8 103.1 2)GB 60 33.80 -29.05 150.75 34.04 C2'-endo 105.3 103.0 103.8 3)CB 59 35.40 -31.00 152.47 35.79 C2'-endo 105.5 102.2 103.8 4)AB 58 34.05 -29.22 150.80 34.27 C2'-endo 105.5 102.8 103.7 5)CB 57 36.89 -29.86 145.96 36.95 C2'-endo 105.0 102.2 103.7 6)CB 56 32.32 -31.69 162.34 33.94 C2'-endo 105.8 102.7 103.6 7)CB 55 18.85 -17.44 156.51 19.30 C2'-endo 106.8 106.0 105.3 8)GB 54 42.15 -34.86 148.49 42.16 C2'-endo 104.8 100.3 103.1 9)TB 53 36.44 -31.80 152.37 36.80 C2'-endo 105.4 101.9 103.6 10)GB 52 33.20 -31.59 159.64 34.42 C2'-endo 105.7 102.5 103.7 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 61 -97.94 42.03 140.16 ...... ...... ...... ...... 2)GB 60 -108.09 33.51 133.31 -164.81 -116.21 -52.30 165.76 3)CB 59 -110.06 40.74 135.95 -173.97 -104.75 -47.96 179.89 4)AB 58 -97.61 34.34 133.92 174.36 -120.60 -32.47 168.63 5)CB 57 -104.76 34.04 131.67 -177.47 -103.69 -48.38 -176.57 6)CB 56 -119.93 45.52 139.51 -176.21 -84.47 -60.16 -170.12 7)CB 55 -144.85 -133.72 129.50 -161.86 -93.97 -46.71 172.70 8)GB 54 -99.23 37.68 139.06 -122.61 -159.63 46.54 -134.77 9)TB 53 -103.85 40.52 135.96 -177.53 -96.49 -52.44 179.01 10)GB 52 -109.13 44.37 138.41 175.97 -98.72 -56.19 -169.73