ID code: 8ICR, PDE079 *********************************** ************** ****** 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 0.153 1 : 2) AA 2 0.017 1 : 3) TA 3 0.054 1 : 4) TA 4 0.197 1 : 5) AA 5 0.046 1 : 6) GA 6 0.064 1 : 7) AA 7 0.206 2 : 1) GB 7 0.080 2 : 2) TB 6 0.282 2 : 3) AB 5 0.107 2 : 4) AB 4 0.074 2 : 5) TB 3 0.108 2 : 6) CB 2 0.098 2 : 7) TB 1 0.194 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= 12.811 CPTS: 1.112 3.312 3.863 4.525 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 12.811 DEL= 0.000E+00 STEP 2 SUM= 14.507 DEL= 0.170E+01 STEP 3 SUM= 9.520 DEL= -0.499E+01 STEP 4 SUM= 17.512 DEL= 0.799E+01 STEP 5 SUM= 8.777 DEL= -0.873E+01 STEP 6 SUM= 8.310 DEL= -0.466E+00 STEP 7 SUM= 7.630 DEL= -0.680E+00 STEP 8 SUM= 7.065 DEL= -0.565E+00 STEP 9 SUM= 7.666 DEL= 0.601E+00 STEP 10 SUM= 6.881 DEL= -0.786E+00 STEP 11 SUM= 6.590 DEL= -0.291E+00 STEP 12 SUM= 6.491 DEL= -0.988E-01 STEP 13 SUM= 6.307 DEL= -0.184E+00 STEP 14 SUM= 5.786 DEL= -0.521E+00 STEP 15 SUM= 6.799 DEL= 0.101E+01 STEP 16 SUM= 5.581 DEL= -0.122E+01 STEP 17 SUM= 6.184 DEL= 0.603E+00 STEP 18 SUM= 5.540 DEL= -0.644E+00 STEP 19 SUM= 5.469 DEL= -0.708E-01 STEP 20 SUM= 5.399 DEL= -0.699E-01 STEP 21 SUM= 5.203 DEL= -0.196E+00 STEP 22 SUM= 5.071 DEL= -0.133E+00 STEP 23 SUM= 5.247 DEL= 0.177E+00 STEP 24 SUM= 5.031 DEL= -0.216E+00 STEP 25 SUM= 4.969 DEL= -0.614E-01 STEP 26 SUM= 4.910 DEL= -0.593E-01 STEP 27 SUM= 4.830 DEL= -0.804E-01 STEP 28 SUM= 4.722 DEL= -0.107E+00 STEP 29 SUM= 4.685 DEL= -0.371E-01 STEP 30 SUM= 4.653 DEL= -0.320E-01 STEP 31 SUM= 4.663 DEL= 0.959E-02 STEP 32 SUM= 4.649 DEL= -0.140E-01 STEP 33 SUM= 4.645 DEL= -0.415E-02 STEP 34 SUM= 4.646 DEL= 0.107E-02 STEP 35 SUM= 4.645 DEL= -0.116E-02 STEP 36 SUM= 4.645 DEL= -0.821E-04 STEP 37 SUM= 4.645 DEL= 0.416E-04 STEP 38 SUM= 4.645 DEL= -0.516E-04 STEP 39 SUM= 4.645 DEL= -0.379E-05 STEP 40 SUM= 4.645 DEL= -0.582E-05 STEP 41 SUM= 4.645 DEL= -0.529E-05 STEP 42 SUM= 4.645 DEL= 0.132E-06 STEP 43 SUM= 4.645 DEL= -0.274E-05 STEP 44 SUM= 4.645 DEL= -0.683E-06 STEP 45 SUM= 4.645 DEL= -0.902E-07 STEP 46 SUM= 4.645 DEL= -0.404E-09 STEP 47 SUM= 4.645 DEL= -0.445E-11 STEP 48 SUM= 4.645 DEL= -0.208E-12 STEP 49 SUM= 4.645 DEL= -0.622E-14 STEP 50 SUM= 4.645 DEL= 0.000E+00 FINAL SUM= 4.645 CPTS: 0.804 2.817 0.294 0.730 GRA= 0.10E-09 0.51E-09-0.16E-10-0.55E-11-0.27E-09 0.24E-09 0.46E-10 0.12E-10 GRA=-0.64E-09 0.31E-09-0.11E-09-0.28E-10-0.30E-09-0.41E-09 0.35E-10-0.22E-10 GRA= 0.12E-09 0.48E-09-0.45E-10 0.31E-10-0.22E-09-0.40E-09-0.35E-10-0.64E-10 GRA= 0.15E-09-0.51E-10 0.24E-10 0.46E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.492 -0.851 -0.184 P: 60.090 35.260 47.336 D: 0.667 2) U: -0.538 -0.833 -0.130 P: 58.538 32.407 46.612 D: 0.947 3) U: -0.529 -0.840 -0.122 P: 56.649 29.946 46.294 D: 0.856 4) U: -0.592 -0.794 -0.138 P: 54.830 27.287 46.126 D: 0.316 5) U: -0.602 -0.783 -0.158 P: 52.769 24.430 45.575 D: 1.290 6) U: -0.621 -0.770 -0.149 P: 50.704 22.252 44.921 D: 0.569 7) U: -0.623 -0.775 -0.108 P: 48.591 19.482 44.639 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.68 0.69 5.26 -7.32 3 0 2) AA 2 -1.04 0.52 9.24 -6.63 2 30 3) TA 3 -1.18 0.46 8.79 -12.56 4 -24 4) TA 4 -1.40 -0.01 10.58 -5.40 4 -28 5) AA 5 -1.09 0.10 6.44 -3.30 2 27 6) GA 6 -1.55 -0.30 9.26 -2.85 1 4 7) AA 7 -1.31 0.03 14.07 -1.12 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -1.38 -0.19 14.94 -4.97 1 0 2) TB 6 -1.62 -0.50 10.90 -6.00 4 -30 3) AB 5 -1.07 -0.42 4.79 -8.05 2 24 4) AB 4 -1.18 -0.50 5.17 -8.62 2 28 5) TB 3 -1.49 -0.48 6.50 -7.13 4 -27 6) CB 2 -0.73 -0.22 5.04 -7.83 3 -4 7) TB 1 -1.01 -0.30 -0.33 -4.66 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 -1.03 0.44 10.10 -1.17 3 0 2) A 2-T 6 -1.33 0.51 10.07 -0.32 2 30 3) T 3-A 5 -1.12 0.44 6.79 -2.26 4 -24 4) T 4-A 4 -1.29 0.25 7.88 1.61 4 -28 5) A 5-T 3 -1.29 0.29 6.47 1.91 2 27 6) G 6-C 2 -1.14 -0.04 7.15 2.49 1 4 7) A 7-T 1 -1.16 0.17 6.87 1.77 2 0 Average: -1.19 0.29 7.90 0.58 --------------------------------- |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 0.70 0.49 -0.23 -9.67 -12.28 18.49 3 0 2) A 2-T 6 0.57 0.02 -0.33 -1.66 -12.63 10.59 2 30 3) T 3-A 5 -0.10 0.04 0.22 4.00 -20.61 10.93 4 -24 4) T 4-A 4 -0.22 -0.51 -0.20 5.41 -14.02 -1.43 4 -28 5) A 5-T 3 0.40 -0.39 -0.13 -0.06 -10.44 -2.00 2 27 6) G 6-C 2 -0.82 -0.52 -0.20 4.22 -10.68 -7.28 1 4 7) A 7-T 1 -0.31 -0.27 0.05 14.41 -5.78 -6.08 2 0 Average: 0.03 -0.16 -0.12 2.38 -12.35 3.31 ---------------------------------- |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 -0.61 -0.06 3.27 5.41 4.58 21.57 9 3) A 2/T 3 0.13 -0.14 3.38 -0.01 -6.60 35.56 7 4) T 3/T 4 -0.38 -0.67 3.01 3.78 11.25 29.23 -4 5) T 4/A 5 0.32 0.19 3.60 -3.60 3.43 39.07 10 6) A 5/G 6 -0.36 -0.71 3.02 3.94 -0.40 20.11 3 7) G 6/A 7 0.18 0.51 3.61 3.15 0.02 32.32 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.48 -0.41 3.37 -2.60 -4.92 29.47 -9 3) T 6/A 5 0.81 0.16 2.83 -5.67 -1.38 35.22 7 4) A 5/A 4 -0.26 0.12 3.43 2.36 -4.65 41.59 4 5) A 4/T 3 -0.31 -0.06 3.53 1.87 0.15 39.64 10 6) T 3/C 2 0.86 0.58 3.08 -0.33 0.16 25.39 -3 7) C 2/T 1 -0.34 -0.27 3.37 -7.04 4.87 31.12 -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 -0.54 0.17 3.32 1.41 4.75 25.52 9 3) A 2/T 3 0.47 -0.15 3.11 -2.84 -2.61 35.39 7 4) T 3/T 4 -0.32 -0.39 3.22 3.07 7.95 35.41 -4 5) T 4/A 5 0.00 0.13 3.56 -0.87 1.64 39.36 10 6) A 5/G 6 0.25 -0.65 3.05 1.80 -0.28 22.75 3 7) G 6/A 7 -0.08 0.39 3.49 -1.95 -2.42 31.72 2 Average: -0.04 -0.08 3.29 0.10 1.51 31.69 --------------------------------- |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 -0.43 0.07 3.44 8.34 7.01 20.13 9 3) A 2/T 3 0.39 -0.28 3.45 5.73 -0.86 34.77 7 4) T 3/T 4 -0.01 -0.82 3.34 8.34 15.71 27.45 -4 5) T 4/A 5 0.57 -0.16 3.65 -0.52 8.98 38.69 10 6) A 5/G 6 -0.15 -0.75 3.15 5.00 2.38 19.81 3 7) G 6/A 7 0.32 0.38 3.57 4.16 6.34 31.95 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.94 0.36 3.43 -5.64 11.45 27.51 -9 3) T 6/A 5 0.21 -0.59 2.97 -9.53 6.05 34.19 7 4) A 5/A 4 -1.06 -0.65 3.47 -3.70 8.21 41.02 4 5) A 4/T 3 -1.10 -0.48 3.52 -3.49 3.87 39.20 10 6) T 3/C 2 0.28 -0.76 3.23 -3.61 2.31 25.10 -3 7) C 2/T 1 -0.76 -0.04 3.30 -10.27 -3.37 30.32 -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 -0.66 0.24 3.45 1.64 10.06 23.97 9 3) A 2/T 3 0.26 -0.43 3.20 -1.57 3.30 34.64 7 4) T 3/T 4 -0.51 -0.71 3.44 2.14 12.24 34.70 -4 5) T 4/A 5 -0.27 -0.33 3.66 -1.98 6.40 39.23 10 6) A 5/G 6 0.07 -0.75 3.15 0.70 2.18 22.55 3 7) G 6/A 7 -0.22 0.13 3.46 -2.78 1.06 31.47 2 Average: -0.22 -0.31 3.39 -0.31 5.87 31.09 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.24 0.10 1.44 3.89 0.26 4.15 3.33 9 3) A 2/T 3 0.27 -0.09 0.43 -0.67 0.28 0.79 3.12 7 4) T 3/T 4 -0.16 -0.20 1.99 4.08 0.25 4.54 3.23 -4 5) T 4/A 5 0.00 0.08 0.54 1.33 0.08 1.44 3.57 10 6) A 5/G 6 0.11 -0.31 1.13 -0.85 0.33 1.42 3.07 3 7) G 6/A 7 -0.06 0.18 -1.67 -1.71 0.19 2.39 3.50 2 Overall axis bend ... UU= 9.73 PP= 11.75 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.51 -22.51 3) T 3 0.39 -50.66 4) T 4 0.46 -40.82 5) A 5 0.46 -88.08 6) G 6 0.21 177.65 7) A 7 0.00 0.00 Path length= 19.80 End-to-end= 19.71 Shortening= 0.48 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 37.17 -38.19 171.63 40.67 C2'-endo 108.9 99.8 100.5 2)AA 2 32.33 -33.66 169.16 35.28 C2'-endo 106.8 102.0 102.4 3)TA 3 35.89 -15.99 113.25 42.70 C1'-exo 105.0 101.0 106.2 4)TA 4 42.94 -23.34 120.42 47.39 C1'-exo 101.2 101.8 102.9 5)AA 5 25.67 -33.54 187.21 34.67 C3'-exo 106.5 102.4 102.5 6)GA 6 45.58 -32.07 134.97 46.71 C1'-exo 102.9 99.2 104.7 7)AA 7 15.45 -3.84 101.14 21.48 O1'-endo 108.8 104.4 106.2 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 -64.05 148.09 149.42 160.79 -114.77 -47.45 -175.86 2)AA 2 -88.28 45.65 143.69 179.26 -125.36 -48.03 158.36 3)TA 3 -119.83 57.38 112.23 -160.52 -100.93 -50.88 158.12 4)TA 4 -118.92 59.45 111.68 178.18 -91.35 -66.31 -159.34 5)AA 5 -105.68 48.73 148.28 176.53 -88.24 -109.10 -175.35 6)GA 6 -104.01 70.09 137.58 -98.86 160.95 -20.05 109.70 7)AA 7 -98.44 14.40 109.91 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 -12.34 2.31 277.61 18.23 O1'-exo 108.6 105.0 105.2 2)TB 6 42.44 -46.90 171.93 48.03 C2'-endo 103.5 98.7 100.4 3)AB 5 24.25 -8.08 104.84 32.37 O1'-endo 104.6 104.3 105.9 4)AB 4 20.98 -14.90 135.68 21.30 C1'-exo 106.2 106.4 103.6 5)TB 3 40.89 -26.21 129.77 42.57 C1'-exo 104.7 100.1 104.5 6)CB 2 39.46 -44.70 174.95 45.62 C2'-endo 103.6 100.7 99.6 7)TB 1 9.46 14.43 68.83 40.26 C4'-exo 105.2 105.1 103.3 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 -119.65 -83.85 121.31 ...... ...... ...... ...... 2)TB 6 -108.62 -90.96 160.39 -135.14 -114.63 34.60 -158.12 3)AB 5 -119.01 38.60 103.62 169.13 -105.44 79.53 168.48 4)AB 4 -122.07 63.80 114.23 -164.14 -84.24 -57.70 169.81 5)TB 3 -99.66 39.37 124.44 178.56 -105.74 -59.63 167.94 6)CB 2 -94.61 45.91 154.89 -160.85 -126.15 -61.51 169.20 7)TB 1 -143.69 43.26 88.27 175.06 -62.86 -58.00 -174.18