ID code: 1ZQE, PDE031 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 19 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 0.041 1 : 2) AA 2 0.063 1 : 3) TA 3 0.036 1 : 4) TA 4 0.169 1 : 5) AA 5 0.048 1 : 6) GA 6 0.141 1 : 7) AA 7 0.165 2 : 1) GB 7 0.209 2 : 2) TB 6 0.147 2 : 3) AB 5 0.180 2 : 4) AB 4 0.027 2 : 5) TB 3 0.056 2 : 6) CB 2 0.128 2 : 7) TB 1 0.215 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= 27.947 CPTS: 1.860 8.738 5.876 11.473 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 27.947 DEL= 0.000E+00 STEP 2 SUM= 19.859 DEL= -0.809E+01 STEP 3 SUM= 43.710 DEL= 0.239E+02 STEP 4 SUM= 18.223 DEL= -0.255E+02 STEP 5 SUM= 17.289 DEL= -0.934E+00 STEP 6 SUM= 15.851 DEL= -0.144E+01 STEP 7 SUM= 14.636 DEL= -0.122E+01 STEP 8 SUM= 13.816 DEL= -0.820E+00 STEP 9 SUM= 13.186 DEL= -0.630E+00 STEP 10 SUM= 13.138 DEL= -0.475E-01 STEP 11 SUM= 12.858 DEL= -0.280E+00 STEP 12 SUM= 12.423 DEL= -0.435E+00 STEP 13 SUM= 11.782 DEL= -0.640E+00 STEP 14 SUM= 19.418 DEL= 0.764E+01 STEP 15 SUM= 11.744 DEL= -0.767E+01 STEP 16 SUM= 11.688 DEL= -0.556E-01 STEP 17 SUM= 11.590 DEL= -0.980E-01 STEP 18 SUM= 11.454 DEL= -0.136E+00 STEP 19 SUM= 11.430 DEL= -0.243E-01 STEP 20 SUM= 11.330 DEL= -0.991E-01 STEP 21 SUM= 11.202 DEL= -0.129E+00 STEP 22 SUM= 11.185 DEL= -0.172E-01 STEP 23 SUM= 11.133 DEL= -0.517E-01 STEP 24 SUM= 11.045 DEL= -0.877E-01 STEP 25 SUM= 10.969 DEL= -0.758E-01 STEP 26 SUM= 10.916 DEL= -0.536E-01 STEP 27 SUM= 10.887 DEL= -0.289E-01 STEP 28 SUM= 10.888 DEL= 0.137E-02 STEP 29 SUM= 10.873 DEL= -0.155E-01 STEP 30 SUM= 10.871 DEL= -0.157E-02 STEP 31 SUM= 10.869 DEL= -0.181E-02 STEP 32 SUM= 10.869 DEL= -0.162E-03 STEP 33 SUM= 10.869 DEL= -0.831E-04 STEP 34 SUM= 10.869 DEL= -0.120E-03 STEP 35 SUM= 10.869 DEL= -0.106E-03 STEP 36 SUM= 10.869 DEL= -0.351E-04 STEP 37 SUM= 10.869 DEL= -0.345E-04 STEP 38 SUM= 10.869 DEL= -0.278E-05 STEP 39 SUM= 10.869 DEL= -0.117E-05 STEP 40 SUM= 10.869 DEL= -0.221E-06 STEP 41 SUM= 10.869 DEL= -0.139E-06 STEP 42 SUM= 10.869 DEL= -0.709E-08 STEP 43 SUM= 10.869 DEL= -0.146E-08 STEP 44 SUM= 10.869 DEL= -0.326E-11 STEP 45 SUM= 10.869 DEL= -0.888E-14 STEP 46 SUM= 10.869 DEL= 0.000E+00 STEP 47 SUM= 10.869 DEL= 0.000E+00 STEP 48 SUM= 10.869 DEL= -0.355E-14 STEP 49 SUM= 10.869 DEL= 0.000E+00 FINAL SUM= 10.869 CPTS: 1.639 6.937 0.722 1.571 GRA= 0.97E-13 0.12E-12 0.11E-13-0.11E-13-0.41E-12-0.33E-12-0.24E-13-0.57E-13 GRA= 0.17E-12 0.53E-12 0.48E-13 0.15E-13-0.22E-13-0.20E-12-0.56E-13 0.94E-14 GRA=-0.15E-12 0.12E-12 0.14E-13-0.43E-13-0.74E-13-0.42E-14 0.36E-13 0.26E-13 GRA= 0.23E-12 0.19E-12-0.23E-13-0.22E-14 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.373 -0.921 -0.111 P: 60.149 35.472 46.194 D: 2.996 2) U: -0.469 -0.876 -0.112 P: 58.661 31.684 45.360 D: 1.692 3) U: -0.472 -0.880 -0.042 P: 56.754 29.102 45.285 D: 1.341 4) U: -0.574 -0.817 -0.054 P: 55.042 26.252 45.465 D: 1.568 5) U: -0.587 -0.808 -0.054 P: 53.146 23.514 45.322 D: 2.690 6) U: -0.642 -0.764 -0.065 P: 51.069 21.392 44.881 D: 0.582 7) U: -0.637 -0.768 -0.074 P: 48.634 18.486 44.811 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.26 -0.10 15.33 4.13 3 0 2) AA 2 -0.92 -0.31 3.13 3.72 2 30 3) TA 3 -0.88 -0.27 3.36 -4.74 4 -24 4) TA 4 -1.35 -0.68 2.77 4.18 4 -28 5) AA 5 -0.68 -0.62 2.52 3.45 2 27 6) GA 6 -1.34 -1.06 11.40 3.97 1 4 7) AA 7 -1.20 -0.80 11.14 9.92 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -0.77 0.39 8.47 -8.35 1 0 2) TB 6 -1.10 -0.08 9.54 -9.59 4 -30 3) AB 5 -0.49 0.19 2.36 -9.97 2 24 4) AB 4 -0.61 0.10 5.60 -13.46 2 28 5) TB 3 -1.40 0.17 2.11 -12.48 4 -27 6) CB 2 -0.35 0.55 0.64 -14.98 3 -4 7) TB 1 -0.65 0.51 5.13 -12.39 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 -0.52 -0.24 11.90 6.24 3 0 2) A 2-T 6 -1.01 -0.12 6.34 6.65 2 30 3) T 3-A 5 -0.69 -0.23 2.86 2.62 4 -24 4) T 4-A 4 -0.98 -0.39 4.19 8.82 4 -28 5) A 5-T 3 -1.04 -0.40 2.31 7.96 2 27 6) G 6-C 2 -0.84 -0.81 6.02 9.47 1 4 7) A 7-T 1 -0.93 -0.65 8.13 11.15 2 0 Average: -0.86 -0.41 5.96 7.56 --------------------------------- |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 0.52 0.30 -1.86 6.86 -4.22 18.70 3 0 2) A 2-T 6 0.18 -0.39 -0.36 -6.41 -5.87 4.46 2 30 3) T 3-A 5 -0.39 -0.08 0.25 1.00 -14.71 16.44 4 -24 4) T 4-A 4 -0.73 -0.58 -0.01 -2.83 -9.28 2.25 4 -28 5) A 5-T 3 0.73 -0.45 0.92 0.42 -9.03 1.34 2 27 6) G 6-C 2 -0.99 -0.51 0.33 10.76 -11.01 -6.00 1 4 7) A 7-T 1 -0.55 -0.29 0.02 6.00 -2.48 0.05 2 0 Average: -0.18 -0.29 -0.10 2.26 -8.08 5.32 ---------------------------------- |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 -1.06 0.00 4.89 -14.97 5.00 18.45 9 3) A 2/T 3 0.49 -0.15 3.48 4.23 -8.53 38.87 7 4) T 3/T 4 -0.69 -0.66 3.19 2.91 14.85 27.85 -4 5) T 4/A 5 0.62 0.10 3.79 0.61 -0.47 41.92 10 6) A 5/G 6 -0.48 -0.83 2.68 12.95 0.12 14.67 3 7) G 6/A 7 -0.02 0.38 3.63 -0.22 6.60 35.83 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.72 -0.69 3.38 -1.70 -6.65 32.69 -9 3) T 6/A 5 1.06 0.46 2.87 -3.18 -0.31 26.89 7 4) A 5/A 4 -0.35 0.16 3.44 6.75 -9.42 42.04 4 5) A 4/T 3 -0.84 0.03 2.87 -2.64 0.73 42.83 10 6) T 3/C 2 1.23 0.77 3.27 2.61 -2.10 22.01 -3 7) C 2/T 1 -0.46 -0.16 3.94 4.54 1.94 29.78 -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 -0.89 0.35 4.14 -8.34 5.83 25.57 9 3) A 2/T 3 0.78 -0.31 3.17 0.52 -4.11 32.88 7 4) T 3/T 4 -0.52 -0.41 3.32 4.83 12.14 34.94 -4 5) T 4/A 5 -0.11 0.04 3.33 -1.01 -0.60 42.37 10 6) A 5/G 6 0.38 -0.80 2.97 7.78 1.11 18.34 3 7) G 6/A 7 -0.24 0.27 3.79 2.16 2.33 32.80 2 Average: -0.10 -0.14 3.45 0.99 2.78 31.15 --------------------------------- |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 -1.28 0.62 4.90 -15.46 8.07 16.43 9 3) A 2/T 3 0.69 -0.52 3.50 4.54 -6.25 38.85 7 4) T 3/T 4 -0.44 -1.06 3.33 3.60 15.75 27.71 -4 5) T 4/A 5 0.80 -0.45 3.87 -2.09 1.45 41.81 10 6) A 5/G 6 -0.46 -0.78 2.71 11.92 1.96 15.49 3 7) G 6/A 7 0.12 0.21 3.73 -4.45 13.19 34.96 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -1.11 0.65 3.31 -7.15 11.27 30.85 -9 3) T 6/A 5 0.63 -0.49 3.08 -7.46 3.42 25.84 7 4) A 5/A 4 -0.92 -0.39 3.42 -2.36 12.29 42.06 4 5) A 4/T 3 -1.25 -0.57 2.73 -11.73 2.15 41.22 10 6) T 3/C 2 0.56 -1.01 3.49 -2.64 2.50 22.01 -3 7) C 2/T 1 -1.11 0.12 3.79 -2.67 -0.37 29.93 -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 -1.21 0.63 4.09 -11.10 9.21 23.64 9 3) A 2/T 3 0.64 -0.50 3.28 -1.03 -0.88 32.52 7 4) T 3/T 4 -0.65 -0.70 3.39 0.47 14.22 35.03 -4 5) T 4/A 5 -0.26 -0.49 3.36 -6.92 1.88 41.62 10 6) A 5/G 6 0.09 -0.87 3.04 4.65 2.17 18.75 3 7) G 6/A 7 -0.49 0.16 3.78 -3.47 6.42 32.89 2 Average: -0.31 -0.30 3.49 -2.90 5.50 30.74 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.40 0.22 -2.77 5.42 0.45 6.09 4.15 9 3) A 2/T 3 0.45 -0.19 4.00 -0.07 0.49 4.00 3.21 7 4) T 3/T 4 -0.23 -0.25 3.51 5.94 0.34 6.89 3.33 -4 5) T 4/A 5 -0.05 0.04 0.86 0.25 0.06 0.89 3.33 10 6) A 5/G 6 0.17 -0.39 4.08 -0.40 0.42 4.10 3.00 3 7) G 6/A 7 -0.15 0.12 0.04 0.64 0.19 0.65 3.79 2 Overall axis bend ... UU= 17.69 PP= 21.16 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 1.06 -19.63 3) T 3 0.87 -55.30 4) T 4 0.95 -55.65 5) A 5 0.92 -92.49 6) G 6 0.43 -136.44 7) A 7 0.00 0.00 Path length= 20.82 End-to-end= 20.57 Shortening= 1.22 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 6.43 -18.61 221.14 25.46 C4'-endo 108.3 104.0 103.9 2)AA 2 27.99 -28.32 166.66 29.99 C2'-endo 107.5 102.9 103.7 3)TA 3 24.38 -17.14 134.99 24.98 C1'-exo 106.5 103.9 105.2 4)TA 4 41.79 -23.98 125.03 44.43 C1'-exo 105.3 100.2 101.9 5)AA 5 29.75 -29.81 164.53 31.72 C2'-endo 106.7 102.1 103.8 6)GA 6 41.36 -30.40 139.96 41.31 C1'-exo 105.0 101.1 102.9 7)AA 7 26.35 -15.44 124.38 28.53 C1'-exo 107.4 102.7 104.2 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 -53.62 161.34 143.46 139.67 -93.88 -57.50 -174.37 2)AA 2 -104.72 58.00 139.31 176.81 -115.79 -37.49 167.56 3)TA 3 -117.46 42.94 122.52 -166.20 -92.96 -55.76 172.27 4)TA 4 -122.26 46.53 117.65 173.07 -91.64 -71.39 -173.48 5)AA 5 -116.65 62.46 137.26 -168.03 -94.29 -58.81 172.83 6)GA 6 -101.49 39.88 132.40 -118.91 -177.57 -23.61 118.60 7)AA 7 -101.88 24.76 118.23 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 -15.00 -5.78 260.57 35.71 O1'-exo 107.0 103.6 103.6 2)TB 6 19.35 -26.00 190.35 27.30 C3'-exo 108.3 103.1 103.3 3)AB 5 35.10 -14.02 109.51 43.80 C1'-exo 104.0 101.3 103.3 4)AB 4 30.20 -18.64 127.03 32.16 C1'-exo 106.4 102.1 104.4 5)TB 3 40.39 -25.65 130.14 41.64 C1'-exo 105.3 101.6 103.3 6)CB 2 39.30 -29.86 141.30 39.48 C1'-exo 105.4 101.0 103.4 7)TB 1 20.64 0.14 90.18 36.86 O1'-endo 106.4 103.4 103.0 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 -120.61 -110.89 145.01 ...... ...... ...... ...... 2)TB 6 -121.14 -92.52 143.94 -160.23 -94.27 69.56 -163.68 3)AB 5 -128.44 52.47 106.04 -163.87 -111.95 56.79 -164.42 4)AB 4 -122.41 60.09 121.95 -151.00 -99.52 -58.27 154.76 5)TB 3 -119.29 44.55 123.99 -173.64 -114.46 -50.61 160.85 6)CB 2 -118.24 48.38 130.73 -165.92 -104.05 -57.72 169.11 7)TB 1 -132.04 46.11 97.42 -172.01 -90.61 -34.34 157.00