ID code: 2VAL *********************************** ************** ****** 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 0.041 1 : 2) CA 2 0.056 1 : 3) GA 3 0.076 1 : 4) GA 4 0.072 1 : 5) GA 5 0.074 1 : 6) AA 6 0.133 1 : 7) AA 7 0.133 2 : 1) AB 7 0.127 2 : 2) AB 6 0.074 2 : 3) GB 5 0.079 2 : 4) GB 4 0.101 2 : 5) GB 3 0.117 2 : 6) CB 2 0.059 2 : 7) GB 1 0.060 Strand= 2 Nucleo= 14 Atoms = 306 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'): GCGGGAA Strand 2 has 7 bases (3'-5'): AAGGGCG FIRST SUM= 783.297 CPTS: 15.261 684.695 2.556 80.785 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 783.297 DEL= 0.000E+00 STEP 2 SUM= 747.970 DEL= -0.353E+02 STEP 3 SUM= 597.268 DEL= -0.151E+03 STEP 4 SUM= 443.691 DEL= -0.154E+03 STEP 5 SUM= 793.573 DEL= 0.350E+03 STEP 6 SUM= 407.830 DEL= -0.386E+03 STEP 7 SUM= 477.922 DEL= 0.701E+02 STEP 8 SUM= 398.785 DEL= -0.791E+02 STEP 9 SUM= 388.253 DEL= -0.105E+02 STEP 10 SUM= 378.945 DEL= -0.931E+01 STEP 11 SUM= 367.275 DEL= -0.117E+02 STEP 12 SUM= 488.163 DEL= 0.121E+03 STEP 13 SUM= 366.396 DEL= -0.122E+03 STEP 14 SUM= 364.790 DEL= -0.161E+01 STEP 15 SUM= 361.246 DEL= -0.354E+01 STEP 16 SUM= 365.075 DEL= 0.383E+01 STEP 17 SUM= 359.368 DEL= -0.571E+01 STEP 18 SUM= 357.813 DEL= -0.155E+01 STEP 19 SUM= 355.029 DEL= -0.278E+01 STEP 20 SUM= 350.521 DEL= -0.451E+01 STEP 21 SUM= 350.903 DEL= 0.382E+00 STEP 22 SUM= 346.797 DEL= -0.411E+01 STEP 23 SUM= 341.678 DEL= -0.512E+01 STEP 24 SUM= 333.779 DEL= -0.790E+01 STEP 25 SUM= 320.941 DEL= -0.128E+02 STEP 26 SUM= 308.825 DEL= -0.121E+02 STEP 27 SUM= 302.922 DEL= -0.590E+01 STEP 28 SUM= 296.526 DEL= -0.640E+01 STEP 29 SUM= 288.166 DEL= -0.836E+01 STEP 30 SUM= 285.756 DEL= -0.241E+01 STEP 31 SUM= 282.387 DEL= -0.337E+01 STEP 32 SUM= 277.966 DEL= -0.442E+01 STEP 33 SUM= 277.374 DEL= -0.592E+00 STEP 34 SUM= 276.384 DEL= -0.990E+00 STEP 35 SUM= 275.331 DEL= -0.105E+01 STEP 36 SUM= 275.206 DEL= -0.125E+00 STEP 37 SUM= 275.006 DEL= -0.200E+00 STEP 38 SUM= 274.760 DEL= -0.246E+00 STEP 39 SUM= 274.567 DEL= -0.193E+00 STEP 40 SUM= 274.393 DEL= -0.174E+00 STEP 41 SUM= 274.160 DEL= -0.233E+00 STEP 42 SUM= 273.967 DEL= -0.193E+00 STEP 43 SUM= 273.696 DEL= -0.271E+00 STEP 44 SUM= 273.441 DEL= -0.254E+00 STEP 45 SUM= 273.614 DEL= 0.173E+00 STEP 46 SUM= 273.339 DEL= -0.275E+00 STEP 47 SUM= 273.247 DEL= -0.919E-01 STEP 48 SUM= 273.137 DEL= -0.110E+00 STEP 49 SUM= 273.057 DEL= -0.797E-01 STEP 50 SUM= 273.009 DEL= -0.485E-01 STEP 51 SUM= 272.976 DEL= -0.321E-01 STEP 52 SUM= 272.946 DEL= -0.306E-01 STEP 53 SUM= 272.902 DEL= -0.441E-01 STEP 54 SUM= 272.851 DEL= -0.506E-01 STEP 55 SUM= 272.794 DEL= -0.573E-01 STEP 56 SUM= 272.761 DEL= -0.326E-01 STEP 57 SUM= 272.711 DEL= -0.502E-01 STEP 58 SUM= 272.655 DEL= -0.560E-01 STEP 59 SUM= 272.612 DEL= -0.426E-01 STEP 60 SUM= 272.546 DEL= -0.666E-01 STEP 61 SUM= 272.456 DEL= -0.896E-01 STEP 62 SUM= 272.439 DEL= -0.170E-01 STEP 63 SUM= 272.407 DEL= -0.321E-01 STEP 64 SUM= 272.313 DEL= -0.938E-01 STEP 65 SUM= 272.257 DEL= -0.567E-01 STEP 66 SUM= 272.219 DEL= -0.377E-01 STEP 67 SUM= 272.193 DEL= -0.257E-01 STEP 68 SUM= 272.182 DEL= -0.117E-01 STEP 69 SUM= 272.177 DEL= -0.447E-02 STEP 70 SUM= 272.174 DEL= -0.269E-02 STEP 71 SUM= 272.174 DEL= -0.944E-03 STEP 72 SUM= 272.173 DEL= -0.959E-03 STEP 73 SUM= 272.172 DEL= -0.406E-03 STEP 74 SUM= 272.172 DEL= -0.296E-03 STEP 75 SUM= 272.172 DEL= -0.188E-03 STEP 76 SUM= 272.172 DEL= -0.943E-04 STEP 77 SUM= 272.171 DEL= -0.138E-03 STEP 78 SUM= 272.171 DEL= -0.143E-03 STEP 79 SUM= 272.171 DEL= -0.134E-03 STEP 80 SUM= 272.171 DEL= -0.104E-03 STEP 81 SUM= 272.171 DEL= -0.644E-04 STEP 82 SUM= 272.171 DEL= -0.453E-04 STEP 83 SUM= 272.171 DEL= -0.306E-04 STEP 84 SUM= 272.171 DEL= -0.178E-04 STEP 85 SUM= 272.171 DEL= -0.941E-05 STEP 86 SUM= 272.171 DEL= -0.493E-05 STEP 87 SUM= 272.171 DEL= -0.230E-05 STEP 88 SUM= 272.171 DEL= -0.866E-06 STEP 89 SUM= 272.171 DEL= -0.380E-06 STEP 90 SUM= 272.171 DEL= -0.250E-06 STEP 91 SUM= 272.171 DEL= -0.120E-06 STEP 92 SUM= 272.171 DEL= -0.330E-07 STEP 93 SUM= 272.171 DEL= -0.797E-08 STEP 94 SUM= 272.171 DEL= -0.346E-08 STEP 95 SUM= 272.171 DEL= -0.163E-08 STEP 96 SUM= 272.171 DEL= -0.432E-09 STEP 97 SUM= 272.171 DEL= -0.603E-10 STEP 98 SUM= 272.171 DEL= -0.472E-11 STEP 99 SUM= 272.171 DEL= -0.284E-12 STEP 100 SUM= 272.171 DEL= 0.000E+00 STEP 101 SUM= 272.171 DEL= 0.568E-13 STEP 102 SUM= 272.171 DEL= -0.568E-13 FINAL SUM= 272.171 CPTS: 10.543 202.562 6.411 52.654 GRA= 0.34E-08 0.18E-07-0.17E-08-0.15E-08-0.97E-08-0.19E-07 0.40E-08-0.88E-09 GRA= 0.35E-08 0.75E-08-0.17E-08-0.14E-08 0.30E-08 0.17E-07-0.76E-09-0.30E-08 GRA= 0.10E-08-0.19E-07 0.17E-08-0.15E-09 0.39E-08-0.13E-07 0.33E-08 0.20E-09 GRA= 0.51E-08 0.34E-07-0.53E-08 0.41E-08 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.893 -0.261 0.368 P: -15.861 8.805 -11.291 D: 52.157 2) U: -0.990 -0.078 0.114 P: -17.456 6.198 -10.472 D: 41.164 3) U: -0.994 -0.090 -0.068 P: -17.844 4.134 -10.271 D: 35.417 4) U: -0.968 -0.097 -0.232 P: -17.466 2.242 -9.800 D: 37.778 5) U: -0.895 -0.066 -0.440 P: -17.736 0.402 -10.093 D: 53.933 6) U: -0.778 -0.041 -0.627 P: -17.506 -1.711 -10.037 D: 51.722 7) U: -0.613 -0.022 -0.789 P: -17.338 -3.986 -10.178 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 1 -19.97 0.23 -15.22 38.10 1 0 2) CA 2 -17.77 3.40 -5.74 41.24 3 -13 3) GA 3 -15.86 5.30 2.42 49.50 1 9 4) GA 4 -12.13 6.95 19.68 48.80 1 1 5) GA 5 -9.99 6.43 30.34 53.62 1 2 6) AA 6 -8.02 5.89 47.21 59.80 2 18 7) AA 7 -7.03 4.62 64.09 65.86 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) AB 7 22.47 7.18 62.61 138.28 2 0 2) AB 6 22.07 0.15 37.44 124.06 2 18 3) GB 5 19.98 -3.90 23.67 115.39 1 2 4) GB 4 17.92 -4.38 14.56 111.71 1 1 5) GB 3 15.18 -5.44 -8.54 109.28 1 9 6) CB 2 12.83 -5.82 -26.44 104.09 3 -13 7) GB 1 10.92 -5.65 -43.40 100.94 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 1-A 7 1.25 -3.47 23.70 -50.09 1 0 2) C 2-A 6 2.15 1.63 15.85 -41.41 3 -13 3) G 3-G 5 2.06 4.60 13.05 -32.94 1 9 4) G 4-G 4 2.89 5.67 17.12 -31.46 1 1 5) G 5-G 3 2.60 5.94 10.90 -27.83 1 2 6) A 6-C 2 2.40 5.86 10.38 -22.15 2 18 7) A 7-G 1 1.95 5.13 10.35 -17.54 2 0 Average: 2.19 3.62 14.48 -31.92 --------------------------------- |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-A 7 -42.44 7.41 -3.93 -77.83 176.38 50.07 1 0 2) C 2-A 6 -39.85 3.56 -7.06 -43.18 165.31 95.79 3 -13 3) G 3-G 5 -35.84 1.40 -6.34 -21.25 164.89 132.71 1 9 4) G 4-G 4 -30.06 2.57 -6.66 5.12 160.51 164.54 1 1 5) G 5-G 3 -25.16 0.99 -6.83 38.88 162.90 194.81 1 2 6) A 6-C 2 -20.85 0.06 -8.45 73.65 163.89 217.78 2 18 7) A 7-G 1 -17.95 -1.02 -11.25 107.49 166.80 235.27 2 0 Average: -30.31 2.14 -7.22 11.84 165.81 155.85 ---------------------------------- |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 2.17 5.48 0.64 22.58 16.70 23.61 5 3) C 2/G 3 2.00 3.92 0.93 8.91 18.71 18.14 8 4) G 3/G 4 3.64 3.62 -0.42 18.48 8.75 21.63 1 5) G 4/G 5 0.42 0.02 0.42 -1.40 9.02 15.26 1 6) G 5/A 6 1.50 -2.62 -0.92 13.15 -6.00 10.62 2 7) A 6/A 7 0.47 -3.49 -1.34 13.97 -6.96 5.71 4 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) A 7/A 6 -0.42 -9.33 3.76 -12.07 -27.78 -22.10 4 3) A 6/G 5 -2.01 -6.08 0.21 -13.02 -19.12 -18.79 2 4) G 5/G 4 -2.14 -2.45 -0.11 -7.89 -13.13 -10.20 1 5) G 4/G 3 -4.48 -1.60 0.59 -35.16 -6.63 -15.01 1 6) G 3/C 2 -2.81 1.69 0.70 -21.62 6.99 -12.35 8 7) C 2/G 1 -2.43 2.40 1.45 -19.87 9.87 -11.78 5 --------------------------------------- |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 0.87 7.40 2.20 5.25 22.24 0.76 5 3) C 2/G 3 -0.00 5.00 0.57 -2.06 18.91 -0.33 8 4) G 3/G 4 0.75 3.03 -0.27 5.29 10.94 5.72 1 5) G 4/G 5 -2.03 0.81 0.51 -18.28 7.83 0.12 1 6) G 5/A 6 -0.65 -2.16 -0.11 -4.23 -6.50 -0.87 2 7) A 6/A 7 -0.98 -2.95 0.06 -2.95 -8.41 -3.03 4 Average: -0.34 1.86 0.49 -2.83 7.50 0.40 --------------------------------- |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 0.71 -2.20 3.17 6.30 2.01 36.21 5 3) C 2/G 3 -0.78 -2.00 3.54 -0.86 12.59 25.30 8 4) G 3/G 4 0.96 -2.25 3.31 1.39 4.79 33.88 1 5) G 4/G 5 -0.35 -2.57 3.25 2.02 7.28 27.52 1 6) G 5/A 6 0.92 -2.36 3.13 4.94 7.61 30.14 2 7) A 6/A 7 0.22 -2.54 3.19 3.96 6.16 29.12 4 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) A 7/A 6 -0.44 -2.91 3.27 -6.80 8.84 35.83 4 3) A 6/G 5 0.10 -2.28 3.08 -5.91 4.33 28.82 2 4) G 5/G 4 0.07 -2.49 3.25 -2.81 3.81 20.75 1 5) G 4/G 3 -0.48 -2.11 3.27 -2.09 5.77 38.23 1 6) G 3/C 2 -0.30 -1.55 3.41 -2.32 9.43 32.72 8 7) C 2/G 1 0.17 -1.94 3.21 -4.34 7.67 31.80 5 -------------------------------------- |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 0.33 -1.02 0.60 -4.01 -5.53 98.45 5 3) C 2/G 3 -0.04 0.13 1.20 4.12 -2.04 133.93 8 4) G 3/G 4 0.04 -0.88 2.28 0.27 -1.16 125.76 1 5) G 4/G 5 -0.34 -0.62 2.62 0.72 -0.26 120.32 1 6) G 5/A 6 -0.36 -0.99 3.50 -0.74 -1.73 103.02 2 7) A 6/A 7 -0.25 -0.49 3.67 -0.85 -2.62 71.11 4 Average: -0.10 -0.64 2.31 -0.08 -2.22 108.76 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 1/C 2 -0.02 2.30 13.10 13.56 2.30 18.83 3.16 5 3) C 2/G 3 0.09 2.03 0.74 10.44 2.03 10.47 2.11 8 4) G 3/G 4 -0.08 1.97 1.22 9.45 1.97 9.53 1.99 1 5) G 4/G 5 -1.73 0.54 -12.06 4.20 1.81 12.77 1.88 1 6) G 5/A 6 -0.46 -2.07 -3.71 -12.18 2.12 12.73 2.13 2 7) A 6/A 7 -0.53 -2.22 -2.91 -13.02 2.28 13.34 2.29 4 Overall axis bend ... UU= 74.73 PP= 39.92 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 1 0.00 0.00 2) C 2 1.41 34.12 3) G 3 1.55 16.07 4) G 4 1.24 -17.05 5) G 5 1.01 -21.28 6) A 6 0.54 -39.43 7) A 7 0.00 0.00 Path length= 13.55 End-to-end= 12.92 Shortening= 4.65 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 1 -30.57 50.83 23.69 56.92 C3'-endo 103.1 102.5 91.4 2)CA 2 -19.93 50.47 36.24 62.17 C4'-exo 102.5 103.0 95.4 3)GA 3 -26.54 46.25 21.39 50.07 C3'-endo 107.6 97.1 102.7 4)GA 4 -22.19 41.96 25.13 45.94 C3'-endo 105.2 102.9 101.4 5)GA 5 -24.36 40.61 21.57 44.31 C3'-endo 104.6 101.1 101.4 6)AA 6 -31.45 48.67 17.59 52.12 C3'-endo 106.0 97.1 99.0 7)AA 7 -35.79 44.06 4.70 45.61 C3'-endo 102.4 102.9 97.7 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 -175.26 62.55 73.10 -169.92 -63.92 -73.36 172.82 2)CA 2 -163.07 51.54 82.12 -153.28 -83.17 -71.49 168.03 3)GA 3 -170.23 61.79 69.89 -149.35 -67.78 -75.90 176.82 4)GA 4 -173.38 59.87 82.01 -152.04 -75.21 -80.32 -175.12 5)GA 5 -168.27 59.44 79.57 -156.26 -59.45 -70.44 170.74 6)AA 6 -165.90 61.89 63.44 -163.47 -52.26 -81.85 -178.75 7)AA 7 -162.32 60.27 70.11 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)AB 7 -26.36 41.23 18.59 43.48 C3'-endo 100.3 106.6 97.1 2)AB 6 -42.78 47.68 356.67 49.90 C2'-exo 107.4 95.6 99.7 3)GB 5 -38.53 54.62 10.78 55.96 C3'-endo 102.3 97.0 98.2 4)GB 4 -37.33 51.28 7.63 51.51 C3'-endo 101.8 99.6 100.0 5)GB 3 -31.34 41.32 5.63 41.83 C3'-endo 105.8 100.6 103.0 6)CB 2 -13.65 35.45 36.26 43.31 C4'-exo 105.1 101.1 105.4 7)GB 1 -39.72 48.88 354.11 48.13 C2'-exo 100.7 96.9 105.0 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)AB 7 -150.32 26.16 62.02 ...... ...... ...... ...... 2)AB 6 -160.58 51.46 80.07 179.13 -25.07 -58.31 178.01 3)GB 5 -168.90 64.50 69.47 177.64 -47.04 -77.03 -179.26 4)GB 4 -174.80 63.83 64.15 -151.36 -68.24 -87.29 -171.13 5)GB 3 -171.96 54.97 80.39 -149.24 -73.54 -83.61 -174.00 6)CB 2 -163.98 44.95 78.13 -140.01 -97.58 -52.92 160.66 7)GB 1 -164.71 50.67 81.62 -175.95 -54.59 -55.65 163.24