ID code: 8ICQ, PDE078 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 26 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 0.067 1 : 2) AA 2 0.031 1 : 3) TA 3 0.031 1 : 4) TA 4 0.241 1 : 5) AA 5 0.074 1 : 6) GA 6 0.046 1 : 7) AA 7 0.261 2 : 1) GB 7 0.089 2 : 2) TB 6 0.203 2 : 3) AB 5 0.184 2 : 4) AB 4 0.030 2 : 5) TB 3 0.139 2 : 6) CB 2 0.132 2 : 7) TB 1 0.227 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= 17.835 CPTS: 1.423 5.105 3.198 8.110 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 17.835 DEL= 0.000E+00 STEP 2 SUM= 13.504 DEL= -0.433E+01 STEP 3 SUM= 24.658 DEL= 0.112E+02 STEP 4 SUM= 12.557 DEL= -0.121E+02 STEP 5 SUM= 12.018 DEL= -0.538E+00 STEP 6 SUM= 11.176 DEL= -0.842E+00 STEP 7 SUM= 10.430 DEL= -0.746E+00 STEP 8 SUM= 9.684 DEL= -0.746E+00 STEP 9 SUM= 8.810 DEL= -0.874E+00 STEP 10 SUM= 13.361 DEL= 0.455E+01 STEP 11 SUM= 8.689 DEL= -0.467E+01 STEP 12 SUM= 8.479 DEL= -0.210E+00 STEP 13 SUM= 8.229 DEL= -0.249E+00 STEP 14 SUM= 7.649 DEL= -0.581E+00 STEP 15 SUM= 9.278 DEL= 0.163E+01 STEP 16 SUM= 7.528 DEL= -0.175E+01 STEP 17 SUM= 7.817 DEL= 0.289E+00 STEP 18 SUM= 7.500 DEL= -0.316E+00 STEP 19 SUM= 7.449 DEL= -0.519E-01 STEP 20 SUM= 7.258 DEL= -0.190E+00 STEP 21 SUM= 9.131 DEL= 0.187E+01 STEP 22 SUM= 7.233 DEL= -0.190E+01 STEP 23 SUM= 7.188 DEL= -0.447E-01 STEP 24 SUM= 7.113 DEL= -0.758E-01 STEP 25 SUM= 7.171 DEL= 0.585E-01 STEP 26 SUM= 7.064 DEL= -0.107E+00 STEP 27 SUM= 6.999 DEL= -0.652E-01 STEP 28 SUM= 6.925 DEL= -0.735E-01 STEP 29 SUM= 6.835 DEL= -0.908E-01 STEP 30 SUM= 6.816 DEL= -0.182E-01 STEP 31 SUM= 6.790 DEL= -0.267E-01 STEP 32 SUM= 6.799 DEL= 0.907E-02 STEP 33 SUM= 6.778 DEL= -0.205E-01 STEP 34 SUM= 6.774 DEL= -0.401E-02 STEP 35 SUM= 6.774 DEL= -0.802E-03 STEP 36 SUM= 6.774 DEL= 0.421E-03 STEP 37 SUM= 6.773 DEL= -0.739E-03 STEP 38 SUM= 6.773 DEL= -0.604E-04 STEP 39 SUM= 6.773 DEL= -0.704E-04 STEP 40 SUM= 6.773 DEL= -0.479E-04 STEP 41 SUM= 6.773 DEL= -0.539E-04 STEP 42 SUM= 6.773 DEL= -0.268E-04 STEP 43 SUM= 6.773 DEL= 0.887E-05 STEP 44 SUM= 6.773 DEL= -0.158E-04 STEP 45 SUM= 6.773 DEL= -0.414E-06 STEP 46 SUM= 6.773 DEL= -0.110E-08 STEP 47 SUM= 6.773 DEL= -0.744E-10 STEP 48 SUM= 6.773 DEL= -0.112E-10 STEP 49 SUM= 6.773 DEL= -0.906E-13 STEP 50 SUM= 6.773 DEL= -0.888E-15 STEP 51 SUM= 6.773 DEL= 0.000E+00 FINAL SUM= 6.773 CPTS: 1.036 4.451 0.265 1.021 GRA=-0.80E-09-0.16E-08 0.14E-10-0.29E-09 0.23E-08 0.11E-08-0.75E-10 0.92E-10 GRA=-0.82E-09-0.12E-08 0.69E-10-0.10E-09 0.42E-09 0.28E-08 0.13E-09 0.37E-09 GRA=-0.14E-09-0.11E-08 0.13E-09-0.12E-09-0.13E-08-0.60E-09 0.21E-10 0.53E-11 GRA= 0.32E-09-0.19E-09-0.21E-09-0.10E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.443 -0.892 -0.084 P: 59.701 35.679 46.923 D: 2.247 2) U: -0.486 -0.864 -0.129 P: 58.083 32.216 46.346 D: 0.751 3) U: -0.503 -0.858 -0.108 P: 56.262 29.693 46.028 D: 0.766 4) U: -0.561 -0.818 -0.125 P: 54.547 27.151 45.896 D: 0.897 5) U: -0.582 -0.805 -0.112 P: 52.645 24.177 45.516 D: 1.324 6) U: -0.601 -0.791 -0.116 P: 50.638 21.859 44.820 D: 0.788 7) U: -0.596 -0.799 -0.082 P: 48.567 19.075 44.762 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.82 0.24 12.28 0.67 3 0 2) AA 2 -1.42 0.06 5.61 -3.90 2 30 3) TA 3 -1.42 0.05 6.04 -6.23 4 -24 4) TA 4 -1.76 -0.33 10.15 -2.28 4 -28 5) AA 5 -1.27 -0.12 6.52 -1.58 2 27 6) GA 6 -1.52 -0.33 9.55 -0.46 1 4 7) AA 7 -1.67 -0.04 15.08 6.70 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -1.75 0.24 12.20 -9.54 1 0 2) TB 6 -1.71 -0.04 10.24 -10.95 4 -30 3) AB 5 -1.24 -0.04 6.67 -9.12 2 24 4) AB 4 -1.02 -0.16 3.89 -11.72 2 28 5) TB 3 -1.63 -0.31 8.49 -8.62 4 -27 6) CB 2 -0.79 -0.01 7.68 -12.01 3 -4 7) TB 1 -0.93 -0.17 3.13 -6.06 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 -1.29 0.00 12.24 5.10 3 0 2) A 2-T 6 -1.56 0.05 7.92 3.53 2 30 3) T 3-A 5 -1.33 0.04 6.36 1.45 4 -24 4) T 4-A 4 -1.39 -0.09 7.02 4.72 4 -28 5) A 5-T 3 -1.45 0.10 7.50 3.52 2 27 6) G 6-C 2 -1.16 -0.16 8.61 5.77 1 4 7) A 7-T 1 -1.30 0.07 9.10 6.38 2 0 Average: -1.35 0.00 8.39 4.35 --------------------------------- |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 0.93 0.48 -1.71 0.08 -8.86 11.70 3 0 2) A 2-T 6 0.29 0.02 -0.25 -4.63 -14.85 6.98 2 30 3) T 3-A 5 -0.18 0.01 0.43 -0.63 -15.34 8.39 4 -24 4) T 4-A 4 -0.74 -0.48 0.09 6.26 -14.00 3.31 4 -28 5) A 5-T 3 0.36 -0.43 0.06 -1.97 -10.20 -1.67 2 27 6) G 6-C 2 -0.72 -0.34 -0.09 1.87 -12.47 5.60 1 4 7) A 7-T 1 -0.74 -0.21 0.10 11.95 0.64 -2.40 2 0 Average: -0.11 -0.14 -0.20 1.85 -10.73 4.56 ---------------------------------- |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 -0.84 -0.12 4.59 -10.28 -3.07 22.07 9 3) A 2/T 3 0.32 -0.07 3.45 1.66 -1.37 32.21 7 4) T 3/T 4 -0.40 -0.61 2.89 5.58 7.85 32.28 -4 5) T 4/A 5 0.40 0.35 3.53 -2.05 0.40 39.77 10 6) A 5/G 6 0.02 -0.53 3.04 4.39 0.95 28.14 3 7) G 6/A 7 -0.35 0.50 3.56 3.87 6.05 22.98 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.20 -0.34 3.13 -5.57 -2.92 26.79 -9 3) T 6/A 5 0.79 0.06 2.77 -2.34 0.87 30.80 7 4) A 5/A 4 0.16 0.12 3.23 -1.31 -6.50 37.36 4 5) A 4/T 3 -0.70 -0.29 3.57 6.18 3.39 44.76 10 6) T 3/C 2 1.10 0.62 3.19 0.55 -3.21 20.86 -3 7) C 2/T 1 -0.33 -0.37 3.36 -6.21 7.05 30.98 -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 -0.52 0.11 3.86 -7.93 -0.08 24.43 9 3) A 2/T 3 0.56 -0.07 3.11 -0.34 -1.12 31.51 7 4) T 3/T 4 -0.12 -0.36 3.06 2.13 7.17 34.82 -4 5) T 4/A 5 -0.15 0.32 3.55 2.07 -1.50 42.27 10 6) A 5/G 6 0.56 -0.57 3.12 2.47 2.08 24.50 3 7) G 6/A 7 -0.34 0.44 3.46 -1.17 -0.50 26.98 2 Average: -0.00 -0.02 3.36 -0.46 1.01 30.75 --------------------------------- |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 -0.72 0.20 4.70 -9.41 0.70 21.86 9 3) A 2/T 3 0.59 -0.52 3.51 4.49 1.85 31.69 7 4) T 3/T 4 -0.12 -1.09 3.19 7.99 12.04 31.11 -4 5) T 4/A 5 0.68 -0.22 3.56 -0.53 6.01 39.48 10 6) A 5/G 6 0.16 -0.79 3.17 4.79 4.78 27.85 3 7) G 6/A 7 -0.49 0.56 3.48 2.54 10.82 22.97 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.69 0.15 3.14 -10.18 7.69 24.72 -9 3) T 6/A 5 0.28 -0.41 2.98 -7.47 3.73 29.50 7 4) A 5/A 4 -0.46 -0.58 3.35 -7.95 9.78 36.12 4 5) A 4/T 3 -1.47 -0.33 3.42 -1.92 1.56 44.90 10 6) T 3/C 2 0.44 -0.61 3.44 -3.13 6.10 20.48 -3 7) C 2/T 1 -0.85 0.25 3.26 -10.78 -3.95 29.73 -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 -0.77 0.18 3.90 -9.52 4.24 23.48 9 3) A 2/T 3 0.40 -0.44 3.24 -1.44 3.19 30.81 7 4) T 3/T 4 -0.26 -0.82 3.26 -0.06 11.34 33.82 -4 5) T 4/A 5 -0.40 -0.27 3.58 -1.25 3.79 42.46 10 6) A 5/G 6 0.32 -0.71 3.28 0.85 5.51 24.27 3 7) G 6/A 7 -0.68 0.40 3.37 -4.27 3.55 26.68 2 Average: -0.23 -0.27 3.44 -2.62 5.27 30.25 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.24 0.07 -3.61 1.50 0.25 3.91 3.87 9 3) A 2/T 3 0.32 -0.06 1.23 0.96 0.33 1.56 3.13 7 4) T 3/T 4 -0.06 -0.24 1.47 3.90 0.24 4.16 3.07 -4 5) T 4/A 5 -0.09 0.14 1.59 -0.29 0.16 1.61 3.55 10 6) A 5/G 6 0.27 -0.32 1.36 -0.17 0.41 1.37 3.14 3 7) G 6/A 7 -0.20 0.21 -1.66 -1.11 0.29 2.00 3.47 2 Overall axis bend ... UU= 10.29 PP= 13.87 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.61 -4.85 3) T 3 0.50 -38.55 4) T 4 0.47 -47.47 5) A 5 0.55 -87.88 6) G 6 0.36 177.11 7) A 7 0.00 0.00 Path length= 20.23 End-to-end= 20.11 Shortening= 0.59 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 14.91 -29.93 211.18 36.35 C3'-exo 110.4 101.5 102.5 2)AA 2 35.28 -33.78 161.54 36.74 C2'-endo 106.8 101.1 102.8 3)TA 3 39.21 -20.26 118.25 44.46 C1'-exo 103.7 100.9 105.6 4)TA 4 53.57 -39.93 140.99 53.25 C1'-exo 100.8 98.3 100.4 5)AA 5 17.79 -23.40 189.39 24.71 C3'-exo 109.8 102.7 104.3 6)GA 6 46.11 -30.46 131.35 47.76 C1'-exo 103.7 98.4 105.6 7)AA 7 -1.46 0.20 276.14 2.20 O1'-exo 111.2 104.7 106.6 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 -50.07 154.37 158.51 138.18 -98.87 -46.13 -172.15 2)AA 2 -90.73 46.99 139.76 -179.69 -121.38 -36.48 147.93 3)TA 3 -124.24 58.47 117.10 -151.81 -128.47 -16.85 138.73 4)TA 4 -106.70 28.03 125.19 -163.16 -115.74 -62.61 179.95 5)AA 5 -117.09 47.51 135.72 -176.10 -81.78 -94.46 -176.80 6)GA 6 -110.33 60.99 133.06 -108.00 176.19 -6.36 129.65 7)AA 7 -87.21 -17.49 124.93 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 -2.89 -9.35 243.08 21.12 C4'-endo 109.1 105.6 104.0 2)TB 6 34.52 -39.18 174.56 40.13 C2'-endo 106.7 99.5 103.9 3)AB 5 38.76 -21.93 120.83 43.13 C1'-exo 101.6 102.8 104.2 4)AB 4 19.31 2.69 86.35 37.63 O1'-endo 105.4 103.9 104.8 5)TB 3 47.83 -26.93 122.50 52.33 C1'-exo 101.6 97.8 104.8 6)CB 2 37.81 -44.86 178.64 45.44 C2'-endo 103.2 101.5 99.3 7)TB 1 22.99 -0.58 91.16 39.62 O1'-endo 105.1 103.8 105.1 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 7 -121.14 -113.36 138.47 ...... ...... ...... ...... 2)TB 6 -110.60 -69.86 155.09 -146.31 -106.86 55.43 -147.49 3)AB 5 -115.24 62.56 109.66 -163.36 -122.47 44.53 -171.91 4)AB 4 -140.93 73.41 100.05 -157.60 -80.05 -76.23 170.00 5)TB 3 -108.93 43.86 118.29 -166.11 -124.40 -66.00 150.04 6)CB 2 -93.04 29.60 154.19 -160.12 -137.77 -30.41 132.55 7)TB 1 -139.07 42.68 98.29 -165.32 -94.36 -26.04 169.17