ID code: 9ICX, PDE0113 *********************************** ************** ****** 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 2 0.039 1 : 2) AA 3 0.056 1 : 3) TA 4 0.058 1 : 4) CA 5 0.130 1 : 5) TA 6 0.038 1 : 6) GA 7 0.060 2 : 1) GB 6 0.049 2 : 2) TB 5 0.106 2 : 3) AB 4 0.058 2 : 4) GB 3 0.059 2 : 5) AB 2 0.021 2 : 6) CB 1 0.063 Strand= 2 Nucleo= 12 Atoms = 240 Units = 12 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 6 levels ... Strand 1 has 6 bases (5'-3'): CATCTG Strand 2 has 6 bases (3'-5'): GTAGAC FIRST SUM= 24.323 CPTS: 5.509 4.097 4.646 10.072 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 24 STEP 1 SUM= 24.323 DEL= 0.000E+00 STEP 2 SUM= 17.816 DEL= -0.651E+01 STEP 3 SUM= 24.205 DEL= 0.639E+01 STEP 4 SUM= 15.633 DEL= -0.857E+01 STEP 5 SUM= 14.235 DEL= -0.140E+01 STEP 6 SUM= 12.600 DEL= -0.163E+01 STEP 7 SUM= 10.900 DEL= -0.170E+01 STEP 8 SUM= 12.063 DEL= 0.116E+01 STEP 9 SUM= 10.268 DEL= -0.180E+01 STEP 10 SUM= 9.532 DEL= -0.736E+00 STEP 11 SUM= 8.822 DEL= -0.711E+00 STEP 12 SUM= 18.031 DEL= 0.921E+01 STEP 13 SUM= 8.786 DEL= -0.924E+01 STEP 14 SUM= 8.760 DEL= -0.266E-01 STEP 15 SUM= 8.719 DEL= -0.405E-01 STEP 16 SUM= 8.648 DEL= -0.714E-01 STEP 17 SUM= 8.548 DEL= -0.999E-01 STEP 18 SUM= 8.564 DEL= 0.164E-01 STEP 19 SUM= 8.466 DEL= -0.981E-01 STEP 20 SUM= 8.385 DEL= -0.806E-01 STEP 21 SUM= 8.340 DEL= -0.452E-01 STEP 22 SUM= 8.303 DEL= -0.371E-01 STEP 23 SUM= 8.292 DEL= -0.111E-01 STEP 24 SUM= 8.273 DEL= -0.189E-01 STEP 25 SUM= 8.255 DEL= -0.184E-01 STEP 26 SUM= 8.255 DEL= 0.136E-03 STEP 27 SUM= 8.250 DEL= -0.473E-02 STEP 28 SUM= 8.246 DEL= -0.432E-02 STEP 29 SUM= 8.245 DEL= -0.265E-03 STEP 30 SUM= 8.245 DEL= -0.691E-04 STEP 31 SUM= 8.245 DEL= -0.464E-04 STEP 32 SUM= 8.245 DEL= -0.103E-04 STEP 33 SUM= 8.245 DEL= -0.136E-04 STEP 34 SUM= 8.245 DEL= 0.922E-06 STEP 35 SUM= 8.245 DEL= -0.370E-05 STEP 36 SUM= 8.245 DEL= -0.274E-05 STEP 37 SUM= 8.245 DEL= -0.199E-05 STEP 38 SUM= 8.245 DEL= -0.170E-05 STEP 39 SUM= 8.245 DEL= -0.234E-07 STEP 40 SUM= 8.245 DEL= -0.673E-09 STEP 41 SUM= 8.245 DEL= -0.281E-10 STEP 42 SUM= 8.245 DEL= -0.628E-11 STEP 43 SUM= 8.245 DEL= -0.799E-13 STEP 44 SUM= 8.245 DEL= -0.533E-14 STEP 45 SUM= 8.245 DEL= 0.000E+00 FINAL SUM= 8.245 CPTS: 3.177 3.411 0.263 1.394 GRA=-0.69E-09-0.52E-09 0.97E-10-0.14E-09 0.64E-09-0.57E-09 0.76E-10 0.93E-10 GRA= 0.16E-08 0.11E-08-0.78E-10 0.18E-09-0.15E-08 0.43E-09-0.16E-09-0.43E-10 GRA= 0.46E-09-0.49E-09 0.96E-10-0.15E-09 0.11E-09 0.13E-09-0.29E-10 0.19E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.599 -0.792 -0.114 P: 58.871 31.606 47.022 D: 1.292 2) U: -0.625 -0.772 -0.116 P: 57.120 29.098 46.378 D: 2.163 3) U: -0.653 -0.751 -0.099 P: 54.830 27.046 46.244 D: 1.187 4) U: -0.622 -0.771 -0.137 P: 52.171 24.154 45.799 D: 1.069 5) U: -0.631 -0.769 -0.105 P: 49.945 21.737 45.644 D: 2.535 6) U: -0.576 -0.815 -0.065 P: 48.538 19.111 45.437 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 2 -0.72 0.35 -1.26 -4.15 3 0 2) AA 3 -0.56 0.44 4.21 -3.30 2 30 3) TA 4 -1.06 0.10 6.17 -8.55 4 -22 4) CA 5 -0.72 -0.16 -2.45 1.33 3 -4 5) TA 6 -0.95 -0.27 5.24 -8.44 4 -25 6) GA 7 -0.24 -0.09 15.60 -5.11 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 6 -0.67 -0.39 16.01 -3.35 1 0 2) TB 5 -1.31 -0.76 5.34 -1.85 4 -30 3) AB 4 -0.61 -0.10 1.30 -10.00 2 22 4) GB 3 -0.82 0.06 9.80 -7.95 1 4 5) AB 2 -0.83 0.38 14.21 -13.43 2 25 6) CB 1 -0.74 0.06 0.74 -7.32 3 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 2-G 6 -0.70 0.37 7.37 -0.40 3 0 2) A 3-T 5 -0.93 0.60 4.78 -0.72 2 30 3) T 4-A 4 -0.83 0.10 3.73 0.72 4 -22 4) C 5-G 3 -0.77 -0.11 3.67 4.64 3 -4 5) T 6-A 2 -0.89 -0.33 9.73 2.50 4 -25 6) G 7-C 1 -0.49 -0.07 8.17 1.10 1 0 Average: -0.77 0.09 6.24 1.31 --------------------------------- |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 2-G 6 -0.05 -0.04 0.10 -17.27 -7.49 4.33 3 0 2) A 3-T 5 0.76 -0.33 0.14 -1.13 -5.15 -5.87 2 30 3) T 4-A 4 -0.45 0.01 -0.28 4.87 -18.56 4.32 4 -22 4) C 5-G 3 0.10 -0.10 0.21 -12.24 -6.63 3.95 3 -4 5) T 6-A 2 -0.12 0.10 -0.39 -8.98 -21.87 -0.18 4 -25 6) G 7-C 1 0.50 -0.03 0.41 14.85 -12.43 6.05 1 0 Average: 0.12 -0.06 0.03 -3.32 -12.02 2.10 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 2/A 3 0.03 0.38 3.13 5.51 2.77 33.98 9 3) A 3/T 4 -0.27 -0.75 2.83 3.91 -4.27 29.49 7 4) T 4/C 5 0.39 -0.44 4.20 -11.34 11.12 39.98 -2 5) C 5/T 6 -0.52 -0.25 2.97 7.74 -11.66 27.52 -3 6) T 6/G 7 1.03 0.54 3.35 5.91 4.87 40.82 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 6/T 5 -0.78 -0.68 3.09 -10.64 -0.43 44.18 -9 3) T 5/A 4 0.94 1.08 3.25 -2.09 -9.14 19.29 7 4) A 4/G 3 -0.16 0.34 3.70 5.77 0.80 40.36 2 5) G 3/A 2 -0.30 0.45 3.58 4.47 -3.58 31.64 3 6) A 2/C 1 0.41 -0.67 2.55 -17.92 4.58 34.59 9 --------------------------------------- |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 2/A 3 -0.38 0.53 3.11 -2.56 1.60 39.08 9 3) A 3/T 4 0.33 -0.92 3.04 0.91 2.44 24.39 7 4) T 4/C 5 0.11 -0.39 3.95 -2.79 5.16 40.17 -2 5) C 5/T 6 -0.41 -0.35 3.28 6.10 -4.04 29.58 -3 6) T 6/G 7 0.72 0.60 2.95 -6.01 0.15 37.70 -9 Average: 0.08 -0.10 3.27 -0.87 1.06 34.18 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 2/A 3 -0.06 0.08 3.16 7.43 3.58 33.57 9 3) A 3/T 4 -0.10 -0.86 2.98 6.81 -1.44 28.75 7 4) T 4/C 5 0.75 -1.03 4.20 -8.37 11.82 40.88 -2 5) C 5/T 6 -0.27 -0.51 3.01 9.24 -10.66 27.24 -3 6) T 6/G 7 1.38 0.64 3.24 9.98 11.93 39.18 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 6/T 5 -1.19 0.46 3.11 -11.80 8.45 42.82 -9 3) T 5/A 4 0.46 -1.25 3.42 -4.02 10.11 18.97 7 4) A 4/G 3 -0.80 -0.45 3.69 -0.98 3.04 40.40 2 5) G 3/A 2 -0.86 -0.21 3.57 -1.50 9.91 31.74 3 6) A 2/C 1 0.17 0.55 2.63 -23.20 0.07 30.90 9 -------------------------------------- |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 2/A 3 -0.62 0.27 3.14 -2.18 6.01 38.19 9 3) A 3/T 4 0.20 -1.04 3.15 1.38 4.31 23.83 7 4) T 4/C 5 -0.05 -0.70 4.02 -4.86 7.34 40.65 -2 5) C 5/T 6 -0.53 -0.38 3.29 3.97 -0.38 30.44 -3 6) T 6/G 7 0.74 0.61 2.95 -6.84 6.41 35.15 -9 Average: -0.06 -0.25 3.31 -1.71 4.74 33.65 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 2/A 3 -0.14 0.30 0.03 1.92 0.33 1.92 3.13 9 3) A 3/T 4 0.23 -0.42 1.95 0.99 0.48 2.19 3.08 7 4) T 4/C 5 0.04 -0.18 -2.73 1.24 0.18 3.00 3.95 -2 5) C 5/T 6 -0.28 -0.14 0.05 -1.90 0.31 1.90 3.29 -3 6) T 6/G 7 0.32 0.35 -4.45 1.54 0.48 4.71 2.99 -9 Overall axis bend ... UU= 3.34 PP= 10.38 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 2 0.00 0.00 2) A 3 0.43 -75.96 3) T 4 0.28 170.01 4) C 5 0.48 119.30 5) T 6 0.59 68.87 6) G 7 0.00 0.00 Path length= 16.43 End-to-end= 16.29 Shortening= 0.86 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 2 32.85 -25.02 140.30 33.30 C1'-exo 105.6 102.2 105.5 2)AA 3 25.66 -23.92 155.56 26.56 C2'-endo 105.7 103.6 105.9 3)TA 4 27.11 -1.83 93.08 44.00 O1'-endo 107.5 100.0 105.9 4)CA 5 36.87 -35.01 159.49 38.45 C2'-endo 106.6 99.2 104.6 5)TA 6 36.50 -21.52 125.40 38.90 C1'-exo 106.8 99.8 106.4 6)GA 7 38.56 -34.67 156.23 39.31 C2'-endo 107.4 99.2 104.3 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CA 2 -115.54 74.92 131.06 -179.74 -114.59 -52.41 -175.37 2)AA 3 -98.75 57.79 134.90 -179.50 -96.53 -55.49 160.64 3)TA 4 -125.03 53.85 94.81 163.93 -73.82 -66.31 -159.64 4)CA 5 -112.80 42.25 147.81 -156.67 -119.26 -62.30 164.27 5)TA 6 -112.71 51.84 119.82 -163.73 -118.13 -15.46 152.10 6)GA 7 -76.10 13.64 139.44 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 6 29.68 -33.93 174.86 34.50 C2'-endo 106.2 102.6 104.0 2)TB 5 40.64 -29.08 136.89 40.74 C1'-exo 102.2 103.6 102.3 3)AB 4 39.11 -30.82 144.81 39.05 C2'-endo 105.1 101.2 103.3 4)GB 3 42.43 -34.52 148.74 42.41 C2'-endo 106.8 98.1 103.3 5)AB 2 16.28 -37.86 215.40 47.81 C3'-exo 106.6 101.4 98.8 6)CB 1 7.94 7.37 73.07 25.36 O1'-endo 108.9 105.3 105.2 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 6 -92.51 20.85 143.23 ...... ...... ...... ...... 2)TB 5 -109.98 43.89 123.27 -159.92 -125.15 -29.66 168.00 3)AB 4 -106.84 26.28 138.75 -163.98 -102.10 -71.27 170.86 4)GB 3 -86.99 25.62 144.79 -171.72 -135.78 -36.04 169.54 5)AB 2 -78.07 -47.25 179.49 166.43 -94.92 -46.71 -175.86 6)CB 1 -147.04 68.09 99.08 -154.76 -115.48 43.18 -176.16