ID code: 1AAY, PDT039 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 2 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 0.026 1 : 3) GA 4 0.022 1 : 4) TA 5 0.018 1 : 5) GA 6 0.016 1 : 6) GA 7 0.019 1 : 7) GA 8 0.016 1 : 8) CA 9 0.014 1 : 9) GA 10 0.020 1 : 10) TA 11 0.016 2 : 1) CB 61 0.015 2 : 2) GB 60 0.017 2 : 3) CB 59 0.011 2 : 4) AB 58 0.016 2 : 5) CB 57 0.012 2 : 6) CB 56 0.018 2 : 7) CB 55 0.042 2 : 8) GB 54 0.021 2 : 9) CB 53 0.020 2 : 10) AB 52 0.015 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'): GCGTGGGCGT Strand 2 has 10 bases (3'-5'): CGCACCCGCA FIRST SUM= 31.756 CPTS: 2.552 0.645 3.989 24.571 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 40 STEP 1 SUM= 31.756 DEL= 0.000E+00 STEP 2 SUM= 22.248 DEL= -0.951E+01 STEP 3 SUM= 26.169 DEL= 0.392E+01 STEP 4 SUM= 18.308 DEL= -0.786E+01 STEP 5 SUM= 16.110 DEL= -0.220E+01 STEP 6 SUM= 15.789 DEL= -0.321E+00 STEP 7 SUM= 14.924 DEL= -0.865E+00 STEP 8 SUM= 13.738 DEL= -0.119E+01 STEP 9 SUM= 13.067 DEL= -0.671E+00 STEP 10 SUM= 12.399 DEL= -0.668E+00 STEP 11 SUM= 12.388 DEL= -0.114E-01 STEP 12 SUM= 12.063 DEL= -0.325E+00 STEP 13 SUM= 11.960 DEL= -0.103E+00 STEP 14 SUM= 11.771 DEL= -0.189E+00 STEP 15 SUM= 11.315 DEL= -0.455E+00 STEP 16 SUM= 13.617 DEL= 0.230E+01 STEP 17 SUM= 11.200 DEL= -0.242E+01 STEP 18 SUM= 10.993 DEL= -0.206E+00 STEP 19 SUM= 10.667 DEL= -0.326E+00 STEP 20 SUM= 11.884 DEL= 0.122E+01 STEP 21 SUM= 10.543 DEL= -0.134E+01 STEP 22 SUM= 11.547 DEL= 0.100E+01 STEP 23 SUM= 10.531 DEL= -0.102E+01 STEP 24 SUM= 10.508 DEL= -0.230E-01 STEP 25 SUM= 10.440 DEL= -0.679E-01 STEP 26 SUM= 10.388 DEL= -0.521E-01 STEP 27 SUM= 10.337 DEL= -0.504E-01 STEP 28 SUM= 10.329 DEL= -0.825E-02 STEP 29 SUM= 10.310 DEL= -0.192E-01 STEP 30 SUM= 10.273 DEL= -0.371E-01 STEP 31 SUM= 10.219 DEL= -0.539E-01 STEP 32 SUM= 10.123 DEL= -0.961E-01 STEP 33 SUM= 9.972 DEL= -0.151E+00 STEP 34 SUM= 9.819 DEL= -0.153E+00 STEP 35 SUM= 9.748 DEL= -0.711E-01 STEP 36 SUM= 9.674 DEL= -0.733E-01 STEP 37 SUM= 9.675 DEL= 0.148E-03 STEP 38 SUM= 9.639 DEL= -0.351E-01 STEP 39 SUM= 9.634 DEL= -0.537E-02 STEP 40 SUM= 9.620 DEL= -0.136E-01 STEP 41 SUM= 9.612 DEL= -0.898E-02 STEP 42 SUM= 9.599 DEL= -0.124E-01 STEP 43 SUM= 9.597 DEL= -0.258E-02 STEP 44 SUM= 9.595 DEL= -0.111E-02 STEP 45 SUM= 9.595 DEL= -0.716E-03 STEP 46 SUM= 9.595 DEL= 0.277E-03 STEP 47 SUM= 9.594 DEL= -0.517E-03 STEP 48 SUM= 9.594 DEL= -0.647E-04 STEP 49 SUM= 9.594 DEL= 0.198E-04 STEP 50 SUM= 9.594 DEL= -0.386E-04 STEP 51 SUM= 9.594 DEL= -0.277E-04 STEP 52 SUM= 9.594 DEL= -0.381E-04 STEP 53 SUM= 9.594 DEL= -0.180E-04 STEP 54 SUM= 9.594 DEL= 0.304E-05 STEP 55 SUM= 9.594 DEL= -0.838E-05 STEP 56 SUM= 9.594 DEL= -0.808E-06 STEP 57 SUM= 9.594 DEL= -0.166E-06 STEP 58 SUM= 9.594 DEL= -0.255E-06 STEP 59 SUM= 9.594 DEL= -0.118E-06 STEP 60 SUM= 9.594 DEL= 0.618E-09 STEP 61 SUM= 9.594 DEL= -0.794E-08 STEP 62 SUM= 9.594 DEL= -0.381E-08 STEP 63 SUM= 9.594 DEL= -0.280E-08 STEP 64 SUM= 9.594 DEL= -0.141E-09 STEP 65 SUM= 9.594 DEL= -0.111E-11 STEP 66 SUM= 9.594 DEL= -0.107E-13 STEP 67 SUM= 9.594 DEL= -0.355E-14 STEP 68 SUM= 9.594 DEL= 0.000E+00 FINAL SUM= 9.594 CPTS: 1.618 3.976 0.718 3.283 GRA=-0.45E-09-0.14E-10-0.24E-09 0.66E-10 0.37E-10-0.28E-09-0.25E-09-0.13E-09 GRA= 0.22E-09-0.54E-09-0.66E-10-0.20E-09 0.51E-09 0.69E-09 0.43E-09 0.31E-09 GRA=-0.15E-09-0.14E-09 0.22E-09 0.21E-09 0.16E-09 0.53E-09 0.13E-09-0.25E-09 GRA= 0.40E-09 0.27E-09 0.90E-10-0.92E-10-0.79E-09-0.56E-09 0.22E-09-0.27E-09 GRA=-0.15E-09 0.36E-09-0.18E-09 0.49E-10 0.45E-09-0.44E-09 0.48E-11 0.40E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.665 -0.746 -0.020 P: 10.543 22.523 48.890 D: 0.944 2) U: -0.675 -0.737 -0.017 P: 8.459 20.607 48.808 D: 1.150 3) U: -0.645 -0.760 -0.076 P: 6.382 17.814 48.855 D: 1.156 4) U: -0.673 -0.733 -0.099 P: 4.059 15.514 48.080 D: 0.552 5) U: -0.658 -0.751 -0.059 P: 1.733 12.992 48.115 D: 0.716 6) U: -0.644 -0.763 -0.059 P: -0.740 10.610 47.756 D: 0.403 7) U: -0.557 -0.830 -0.025 P: -2.593 8.058 47.714 D: 1.472 8) U: -0.580 -0.808 -0.098 P: -4.034 5.269 47.665 D: 1.863 9) U: -0.627 -0.778 -0.044 P: -6.365 2.941 46.926 D: 1.338 10) U: -0.607 -0.794 -0.029 P: -8.388 0.363 47.342 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 2 -2.09 0.46 4.43 -1.92 1 0 2) CA 3 -1.69 0.45 14.54 -2.17 3 -13 3) GA 4 -2.23 0.50 5.25 -1.05 1 14 4) TA 5 -1.73 0.30 6.79 0.66 4 -29 5) GA 6 -2.03 0.58 6.57 -1.13 1 11 6) GA 7 -2.21 0.20 4.94 -1.52 1 1 7) GA 8 -2.02 0.14 6.37 -3.52 1 5 8) CA 9 -1.45 0.05 11.77 -1.82 3 -13 9) GA 10 -2.03 0.17 10.65 -5.61 1 14 10) TA 11 -1.56 -0.08 10.57 -8.62 4 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 61 -2.11 -0.34 12.78 -0.52 3 0 2) GB 60 -1.99 -0.31 3.62 -4.17 1 13 3) CB 59 -2.09 -0.55 6.76 -4.99 3 -14 4) AB 58 -1.67 -0.37 5.65 -6.68 2 29 5) CB 57 -1.87 -0.48 3.49 -9.91 3 -11 6) CB 56 -2.06 -0.18 9.36 -8.03 3 -1 7) CB 55 -1.93 -0.13 9.10 -11.45 3 -5 8) GB 54 -1.58 0.07 8.51 -2.83 1 13 9) CB 53 -2.09 -0.23 6.76 -3.10 3 -14 10) AB 52 -1.66 0.10 4.51 0.43 2 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 -2.10 0.40 8.60 -0.70 1 0 2) C 3-G 60 -1.84 0.38 9.08 1.00 3 -13 3) G 4-C 59 -2.16 0.52 6.01 1.97 1 14 4) T 5-A 58 -1.70 0.34 6.22 3.67 4 -29 5) G 6-C 57 -1.95 0.53 5.03 4.39 1 11 6) G 7-C 56 -2.13 0.19 7.15 3.25 1 1 7) G 8-C 55 -1.97 0.14 7.73 3.96 1 5 8) C 9-G 54 -1.51 -0.01 10.14 0.51 3 -13 9) G 10-C 53 -2.06 0.20 8.70 -1.26 1 14 10) T 11-A 52 -1.61 -0.09 7.54 -4.53 4 0 Average: -1.90 0.26 7.62 1.23 --------------------------------- |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 0.02 0.13 -0.30 -8.35 -2.44 2.94 1 0 2) C 3-G 60 0.31 0.14 -0.40 10.92 -6.35 2.26 3 -13 3) G 4-C 59 -0.13 -0.06 0.03 -1.51 -6.03 -0.79 1 14 4) T 5-A 58 -0.06 -0.07 -0.11 1.14 -6.03 2.42 4 -29 5) G 6-C 57 -0.16 0.10 0.01 3.08 -11.04 2.49 1 11 6) G 7-C 56 -0.16 0.02 -0.18 -4.41 -9.55 -1.26 1 1 7) G 8-C 55 -0.09 0.01 -0.23 -2.73 -14.96 0.56 1 5 8) C 9-G 54 0.13 0.12 -0.34 3.26 -4.65 0.69 3 -13 9) G 10-C 53 0.07 -0.06 -0.10 3.88 -8.71 -1.89 1 14 10) T 11-A 52 0.10 0.02 -0.41 6.06 -8.19 5.82 4 0 Average: 0.00 0.03 -0.20 1.13 -7.80 1.32 ---------------------------------- |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 0.65 -0.11 2.77 10.63 0.34 24.56 5 3) C 3/G 4 -0.87 0.19 3.68 -12.87 2.95 36.75 8 4) G 4/T 5 0.97 -0.43 3.24 3.78 2.93 28.79 6 5) T 5/G 6 -0.59 0.41 3.48 -2.58 -2.98 35.40 -9 6) G 6/G 7 -0.41 -0.65 3.34 -2.08 0.59 29.22 1 7) G 7/G 8 0.26 0.02 3.14 0.62 4.49 37.12 1 8) G 8/C 9 0.97 -0.26 3.05 7.30 -2.47 28.76 5 9) C 9/G 10 -1.18 0.42 3.43 -5.00 -1.58 35.14 8 10) G 10/T 11 0.97 -0.42 3.10 1.56 -2.68 34.76 6 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 61/G 60 0.37 0.12 2.87 -8.65 -4.25 25.24 5 3) G 60/C 59 -0.43 -0.38 3.25 -0.44 -2.64 39.79 8 4) C 59/A 58 0.91 0.41 3.39 1.13 -2.92 25.59 -6 5) A 58/C 57 -0.49 -0.24 3.35 -4.52 -2.04 35.33 9 6) C 57/C 56 -0.42 0.58 3.53 5.41 0.90 32.97 -1 7) C 56/C 55 0.20 -0.03 3.18 -1.07 -9.90 35.30 -1 8) C 55/G 54 0.75 0.37 3.17 1.31 12.78 28.64 5 9) G 54/C 53 -1.12 -0.60 3.19 -5.62 -2.47 37.72 8 10) C 53/A 52 0.94 0.50 3.42 -0.61 3.20 27.05 -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 0.51 -0.11 2.82 0.99 2.30 24.90 5 3) C 3/G 4 -0.65 0.29 3.46 -6.65 2.80 38.27 8 4) G 4/T 5 0.94 -0.42 3.32 2.45 2.93 27.19 6 5) T 5/G 6 -0.54 0.32 3.42 -3.55 -0.47 35.36 -9 6) G 6/G 7 -0.42 -0.62 3.43 1.66 -0.16 31.09 1 7) G 7/G 8 0.23 0.03 3.16 -0.22 7.19 36.21 1 8) G 8/C 9 0.86 -0.32 3.11 4.30 -7.62 28.70 5 9) C 9/G 10 -1.15 0.51 3.31 -5.31 0.45 36.43 8 10) G 10/T 11 0.96 -0.46 3.26 0.48 -2.94 30.90 6 Average: 0.08 -0.09 3.25 -0.65 0.50 32.12 --------------------------------- |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 0.49 -0.45 2.91 11.28 4.32 23.86 5 3) C 3/G 4 -0.94 -0.44 3.92 -11.45 9.05 36.48 8 4) G 4/T 5 0.76 -1.08 3.43 3.84 5.84 28.53 6 5) T 5/G 6 -0.82 -0.34 3.50 -2.45 1.22 35.30 -9 6) G 6/G 7 -0.51 -1.37 3.53 -1.36 3.50 29.02 1 7) G 7/G 8 0.27 -0.99 3.47 2.10 8.15 36.24 1 8) G 8/C 9 1.01 -0.67 3.05 8.44 1.99 28.76 5 9) C 9/G 10 -0.99 0.05 3.63 -2.78 5.25 34.29 8 10) G 10/T 11 1.31 -0.88 3.21 5.73 3.72 33.67 6 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 61/G 60 0.16 -0.62 3.02 -9.49 7.70 24.66 5 3) G 60/C 59 -1.00 -0.74 3.29 -3.73 6.08 39.32 8 4) C 59/A 58 0.34 -0.88 3.61 -1.41 5.63 25.31 -6 5) A 58/C 57 -1.18 -0.62 3.24 -9.39 4.59 34.41 9 6) C 57/C 56 -1.20 -1.27 3.58 0.08 2.81 33.08 -1 7) C 56/C 55 -0.46 -0.67 3.53 -6.76 15.22 33.36 -1 8) C 55/G 54 0.32 -0.71 3.28 -2.23 -8.11 28.95 5 9) G 54/C 53 -1.28 -0.18 3.26 -7.42 7.37 36.84 8 10) C 53/A 52 0.84 -1.00 3.57 -1.17 -0.44 26.86 -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 0.32 -0.53 2.96 0.94 6.28 24.15 5 3) C 3/G 4 -0.98 -0.60 3.60 -7.61 7.54 37.96 8 4) G 4/T 5 0.56 -0.98 3.53 1.22 5.76 26.95 6 5) T 5/G 6 -1.01 -0.48 3.37 -5.89 2.98 34.89 -9 6) G 6/G 7 -0.85 -1.32 3.58 -0.65 3.15 31.17 1 7) G 7/G 8 -0.10 -0.83 3.52 -2.33 11.69 35.07 1 8) G 8/C 9 0.68 -0.69 3.18 3.09 -3.03 28.91 5 9) C 9/G 10 -1.14 -0.07 3.45 -5.11 6.30 35.56 8 10) G 10/T 11 1.08 -0.93 3.39 2.25 1.70 30.39 6 Average: -0.16 -0.72 3.40 -1.57 4.71 31.67 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 2/C 3 0.25 -0.09 0.51 0.60 0.26 0.79 2.83 5 3) C 3/G 4 -0.33 0.14 -3.58 1.83 0.36 4.02 3.48 8 4) G 4/T 5 0.48 -0.23 2.24 1.23 0.53 2.56 3.36 6 5) T 5/G 6 -0.28 0.13 -2.36 -1.19 0.31 2.65 3.43 -9 6) G 6/G 7 -0.23 -0.27 -0.46 0.98 0.36 1.08 3.45 1 7) G 7/G 8 0.07 0.08 -0.81 6.48 0.11 6.53 3.15 1 8) G 8/C 9 0.40 -0.17 1.90 -4.17 0.43 4.58 3.14 5 9) C 9/G 10 -0.60 0.30 -3.88 2.21 0.67 4.46 3.38 8 10) G 10/T 11 0.51 -0.17 1.64 0.33 0.53 1.68 3.30 6 Overall axis bend ... UU= 4.34 PP= 12.82 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 2 0.00 0.00 2) C 3 0.35 127.58 3) G 4 0.32 31.34 4) T 5 0.48 112.02 5) G 6 0.51 47.46 6) G 7 0.88 26.04 7) G 8 0.61 -15.36 8) C 9 0.13 111.59 9) G 10 0.60 -15.22 10) T 11 0.00 0.00 Path length= 29.53 End-to-end= 29.19 Shortening= 1.16 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 2 34.05 -22.89 131.61 35.19 C1'-exo 104.5 103.5 103.6 2)CA 3 50.09 -37.94 141.27 49.94 C1'-exo 101.4 99.7 101.5 3)GA 4 35.14 -33.67 159.13 36.33 C2'-endo 102.9 104.5 101.8 4)TA 5 49.87 -31.71 129.30 51.70 C1'-exo 101.0 99.7 102.0 5)GA 6 32.67 -25.03 141.09 32.69 C1'-exo 104.5 104.9 103.7 6)GA 7 41.10 -34.88 149.59 41.11 C2'-endo 102.4 103.1 101.0 7)GA 8 28.38 -37.68 190.42 39.64 C3'-exo 106.4 103.4 99.0 8)CA 9 48.90 -33.02 133.96 49.13 C1'-exo 101.9 101.0 101.0 9)GA 10 34.58 -33.48 161.53 35.96 C2'-endo 104.6 103.5 102.4 10)TA 11 35.22 -16.37 114.56 40.56 C1'-exo 104.4 103.7 103.6 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 -101.57 52.14 123.90 179.50 -92.77 -69.69 170.38 2)CA 3 -94.35 55.37 138.37 -139.19 -175.53 -64.65 151.81 3)GA 4 -127.36 49.04 143.74 -165.54 -86.27 -79.64 174.24 4)TA 5 -108.69 49.97 130.35 -138.63 -174.12 -55.04 139.73 5)GA 6 -124.57 48.31 130.61 -170.29 -96.86 -67.20 179.97 6)GA 7 -118.37 52.31 138.26 -166.14 -118.44 27.46 -177.58 7)GA 8 -97.19 -50.57 163.79 177.14 -89.47 -73.30 173.43 8)CA 9 -100.28 55.01 133.39 -130.82 -175.46 -68.60 154.48 9)GA 10 -111.28 48.01 144.45 -169.13 -93.71 -70.72 169.15 10)TA 11 -115.29 56.02 112.36 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 61 40.51 -23.65 123.95 43.28 C1'-exo 102.6 103.2 102.3 2)GB 60 27.42 -12.37 113.11 32.20 C1'-exo 105.5 105.5 104.1 3)CB 59 36.35 -25.41 133.49 37.25 C1'-exo 102.5 104.7 103.4 4)AB 58 17.81 11.37 76.14 49.64 O1'-endo 104.1 104.8 101.4 5)CB 57 32.14 -8.14 100.56 44.98 O1'-endo 102.9 104.9 103.1 6)CB 56 36.73 -34.07 156.31 37.48 C2'-endo 102.2 104.7 101.2 7)CB 55 -22.64 34.73 19.00 37.99 C3'-endo 107.9 103.8 100.6 8)GB 54 45.41 -34.25 139.51 45.71 C1'-exo 101.1 101.9 102.0 9)CB 53 35.67 -31.12 151.95 35.76 C2'-endo 103.5 104.9 101.9 10)AB 52 22.29 -18.00 144.75 22.31 C2'-endo 106.2 106.4 105.1 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 61 -119.40 65.22 122.21 ...... ...... ...... ...... 2)GB 60 -120.79 55.16 113.77 -165.67 -93.91 -68.99 162.02 3)CB 59 -121.51 57.91 126.59 -167.23 -97.87 -71.46 168.71 4)AB 58 -127.30 33.65 81.35 166.39 -78.76 -65.43 175.92 5)CB 57 -132.49 53.59 105.72 -167.19 -135.77 13.23 106.50 6)CB 56 -120.09 58.94 141.19 -166.95 -88.29 -71.02 165.68 7)CB 55 -152.45 -165.45 82.99 -154.44 -75.37 -58.49 168.25 8)GB 54 -100.25 53.31 134.94 -124.48 -171.45 72.84 -124.72 9)CB 53 -118.22 55.57 135.84 -164.36 -91.47 -74.44 174.67 10)AB 52 -125.09 54.83 129.05 -169.38 -109.64 -51.58 171.49