ID code: 8ICO, PDE076 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 27 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 0.051 1 : 2) AA 2 0.032 1 : 3) TA 3 0.030 1 : 4) TA 4 0.170 1 : 5) AA 5 0.067 1 : 6) GA 6 0.055 1 : 7) AA 7 0.202 2 : 1) GB 7 0.084 2 : 2) TB 6 0.139 2 : 3) AB 5 0.131 2 : 4) AB 4 0.120 2 : 5) TB 3 0.221 2 : 6) CB 2 0.087 2 : 7) TB 1 0.206 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= 17.495 CPTS: 2.358 4.072 2.788 8.277 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 17.495 DEL= 0.000E+00 STEP 2 SUM= 13.163 DEL= -0.433E+01 STEP 3 SUM= 21.354 DEL= 0.819E+01 STEP 4 SUM= 12.050 DEL= -0.930E+01 STEP 5 SUM= 11.150 DEL= -0.900E+00 STEP 6 SUM= 10.264 DEL= -0.886E+00 STEP 7 SUM= 9.592 DEL= -0.671E+00 STEP 8 SUM= 8.882 DEL= -0.710E+00 STEP 9 SUM= 8.008 DEL= -0.874E+00 STEP 10 SUM= 18.542 DEL= 0.105E+02 STEP 11 SUM= 7.956 DEL= -0.106E+02 STEP 12 SUM= 7.879 DEL= -0.774E-01 STEP 13 SUM= 7.731 DEL= -0.148E+00 STEP 14 SUM= 7.035 DEL= -0.697E+00 STEP 15 SUM= 8.652 DEL= 0.162E+01 STEP 16 SUM= 6.819 DEL= -0.183E+01 STEP 17 SUM= 7.483 DEL= 0.664E+00 STEP 18 SUM= 6.776 DEL= -0.707E+00 STEP 19 SUM= 6.700 DEL= -0.758E-01 STEP 20 SUM= 6.580 DEL= -0.121E+00 STEP 21 SUM= 7.283 DEL= 0.703E+00 STEP 22 SUM= 6.545 DEL= -0.738E+00 STEP 23 SUM= 6.496 DEL= -0.487E-01 STEP 24 SUM= 6.411 DEL= -0.850E-01 STEP 25 SUM= 6.304 DEL= -0.107E+00 STEP 26 SUM= 6.355 DEL= 0.512E-01 STEP 27 SUM= 6.219 DEL= -0.136E+00 STEP 28 SUM= 6.099 DEL= -0.120E+00 STEP 29 SUM= 6.044 DEL= -0.553E-01 STEP 30 SUM= 5.973 DEL= -0.705E-01 STEP 31 SUM= 5.970 DEL= -0.349E-02 STEP 32 SUM= 5.963 DEL= -0.697E-02 STEP 33 SUM= 5.965 DEL= 0.220E-02 STEP 34 SUM= 5.960 DEL= -0.506E-02 STEP 35 SUM= 5.962 DEL= 0.240E-02 STEP 36 SUM= 5.959 DEL= -0.321E-02 STEP 37 SUM= 5.960 DEL= 0.450E-03 STEP 38 SUM= 5.959 DEL= -0.561E-03 STEP 39 SUM= 5.959 DEL= -0.167E-03 STEP 40 SUM= 5.959 DEL= -0.985E-04 STEP 41 SUM= 5.959 DEL= -0.126E-03 STEP 42 SUM= 5.959 DEL= 0.165E-04 STEP 43 SUM= 5.959 DEL= -0.548E-04 STEP 44 SUM= 5.959 DEL= -0.329E-04 STEP 45 SUM= 5.959 DEL= -0.305E-05 STEP 46 SUM= 5.959 DEL= -0.211E-05 STEP 47 SUM= 5.959 DEL= -0.293E-06 STEP 48 SUM= 5.959 DEL= -0.111E-07 STEP 49 SUM= 5.959 DEL= -0.675E-09 STEP 50 SUM= 5.959 DEL= -0.162E-10 STEP 51 SUM= 5.959 DEL= -0.173E-11 STEP 52 SUM= 5.959 DEL= -0.355E-14 STEP 53 SUM= 5.959 DEL= 0.000E+00 FINAL SUM= 5.959 CPTS: 1.374 3.663 0.295 0.627 GRA=-0.19E-09 0.17E-09 0.66E-10-0.60E-10 0.12E-09 0.58E-09-0.29E-09 0.12E-09 GRA=-0.65E-09 0.80E-09 0.28E-09-0.15E-09-0.28E-10-0.72E-09 0.49E-10 0.11E-09 GRA= 0.28E-09 0.13E-08-0.23E-09 0.33E-09 0.43E-09-0.18E-09-0.37E-10-0.22E-09 GRA=-0.18E-09-0.96E-10 0.69E-10 0.38E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.444 -0.882 -0.158 P: 60.373 35.715 47.339 D: 1.758 2) U: -0.501 -0.849 -0.168 P: 58.673 32.465 46.532 D: 0.899 3) U: -0.539 -0.831 -0.136 P: 56.914 29.823 46.205 D: 0.724 4) U: -0.579 -0.798 -0.168 P: 54.982 27.357 46.002 D: 1.253 5) U: -0.608 -0.776 -0.165 P: 52.951 24.379 45.391 D: 0.413 6) U: -0.608 -0.780 -0.148 P: 50.780 21.890 44.698 D: 0.912 7) U: -0.625 -0.773 -0.106 P: 48.904 19.414 44.460 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.99 0.71 16.69 -3.83 3 0 2) AA 2 -1.17 0.59 10.52 -7.24 2 30 3) TA 3 -1.73 0.30 8.27 -7.72 4 -24 4) TA 4 -1.82 -0.22 9.38 -6.55 4 -28 5) AA 5 -1.21 0.03 6.71 -2.77 2 27 6) GA 6 -1.31 -0.17 3.48 -1.76 1 4 7) AA 7 -1.38 0.01 14.19 -0.89 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -1.39 -0.07 13.78 -1.95 1 0 2) TB 6 -1.63 -0.38 10.57 -6.91 4 -30 3) AB 5 -1.11 -0.39 8.03 -7.53 2 24 4) AB 4 -0.96 -0.33 3.99 -11.94 2 28 5) TB 3 -1.58 -0.40 8.44 -6.94 4 -27 6) CB 2 -1.22 -0.18 9.02 -6.86 3 -4 7) TB 1 -1.19 -0.33 -1.75 -3.72 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 -1.19 0.39 15.24 -0.94 3 0 2) A 2-T 6 -1.40 0.49 10.55 -0.17 2 30 3) T 3-A 5 -1.42 0.34 8.15 -0.09 4 -24 4) T 4-A 4 -1.39 0.05 6.69 2.69 4 -28 5) A 5-T 3 -1.39 0.21 7.58 2.08 2 27 6) G 6-C 2 -1.27 0.00 6.25 2.55 1 4 7) A 7-T 1 -1.28 0.17 6.22 1.42 2 0 Average: -1.33 0.24 8.67 1.08 --------------------------------- |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 0.39 0.63 -1.39 2.91 -5.78 15.20 3 0 2) A 2-T 6 0.46 0.21 -0.15 -0.05 -14.16 8.83 2 30 3) T 3-A 5 -0.61 -0.09 0.19 0.24 -15.24 0.76 4 -24 4) T 4-A 4 -0.86 -0.55 0.08 5.39 -18.49 1.86 4 -28 5) A 5-T 3 0.38 -0.37 -0.24 -1.73 -9.71 -0.83 2 27 6) G 6-C 2 -0.09 -0.34 -0.00 -5.54 -8.62 -0.97 1 4 7) A 7-T 1 -0.20 -0.32 0.21 15.94 -4.61 -4.17 2 0 Average: -0.08 -0.12 -0.19 2.45 -10.94 2.96 ---------------------------------- |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 -0.33 0.03 4.37 -8.43 -0.32 25.20 9 3) A 2/T 3 -0.46 -0.46 3.35 -0.27 1.86 26.52 7 4) T 3/T 4 -0.07 -0.85 3.07 1.14 4.68 32.73 -4 5) T 4/A 5 0.56 0.41 3.49 -0.65 4.30 43.95 10 6) A 5/G 6 0.00 -0.42 3.48 -3.67 0.10 27.48 3 7) G 6/A 7 -0.13 0.34 3.22 9.72 -1.53 26.67 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.39 -0.45 3.13 -5.48 -8.06 31.57 -9 3) T 6/A 5 0.62 0.15 3.02 -0.56 -2.95 34.59 7 4) A 5/A 4 0.17 0.40 3.17 -4.01 -7.92 31.63 4 5) A 4/T 3 -0.68 -0.23 3.81 6.47 4.48 46.65 10 6) T 3/C 2 0.47 0.44 3.25 0.14 0.99 27.61 -3 7) C 2/T 1 -0.03 -0.32 3.01 -11.76 5.53 29.86 -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 -0.36 0.24 3.75 -6.96 3.87 28.39 9 3) A 2/T 3 0.08 -0.31 3.19 -0.42 2.40 30.55 7 4) T 3/T 4 0.05 -0.63 3.12 -1.44 6.30 32.18 -4 5) T 4/A 5 -0.06 0.32 3.65 2.91 -0.09 45.30 10 6) A 5/G 6 0.24 -0.43 3.37 -1.76 -0.45 27.55 3 7) G 6/A 7 -0.08 0.33 3.11 -1.02 -3.53 28.27 2 Average: -0.02 -0.08 3.37 -1.45 1.42 32.04 --------------------------------- |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 -0.14 0.62 4.44 -5.65 5.77 24.41 9 3) A 2/T 3 -0.18 -0.56 3.62 3.22 6.05 25.61 7 4) T 3/T 4 0.31 -1.35 3.41 5.05 9.54 31.50 -4 5) T 4/A 5 0.89 -0.32 3.52 3.02 10.02 43.49 10 6) A 5/G 6 0.20 -0.71 3.53 -2.49 2.49 27.59 3 7) G 6/A 7 -0.10 0.18 3.18 10.10 2.50 26.60 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.72 0.24 3.20 -8.08 14.11 29.97 -9 3) T 6/A 5 0.00 -0.48 3.23 -4.74 8.47 33.48 7 4) A 5/A 4 -0.53 -0.67 3.29 -9.12 10.98 30.15 4 5) A 4/T 3 -1.55 -0.33 3.69 -1.37 0.85 46.72 10 6) T 3/C 2 -0.08 -0.62 3.37 -3.15 3.18 27.26 -3 7) C 2/T 1 -0.35 -0.11 2.97 -14.16 -3.49 28.97 -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 -0.49 0.44 3.83 -6.39 10.01 27.15 9 3) A 2/T 3 -0.11 -0.52 3.39 -0.71 7.42 29.75 7 4) T 3/T 4 -0.11 -1.01 3.36 -2.04 10.36 31.08 -4 5) T 4/A 5 -0.32 -0.32 3.73 0.79 5.45 45.49 10 6) A 5/G 6 0.05 -0.66 3.45 -2.83 2.84 27.51 3 7) G 6/A 7 -0.22 0.03 3.07 -1.96 -0.77 27.79 2 Average: -0.20 -0.34 3.47 -2.19 5.89 31.46 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.15 0.15 -2.26 3.09 0.21 3.83 3.76 9 3) A 2/T 3 0.10 -0.16 1.98 2.33 0.19 3.06 3.19 7 4) T 3/T 4 0.02 -0.34 0.02 3.51 0.34 3.51 3.14 -4 5) T 4/A 5 -0.05 0.16 2.02 0.52 0.17 2.09 3.66 10 6) A 5/G 6 0.11 -0.22 -0.44 -0.91 0.25 1.01 3.37 3 7) G 6/A 7 -0.06 0.16 -0.99 -2.40 0.17 2.59 3.12 2 Overall axis bend ... UU= 12.49 PP= 12.38 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.56 -20.45 3) T 3 0.58 -31.73 4) T 4 0.41 -35.95 5) A 5 0.45 -92.55 6) G 6 0.24 176.68 7) A 7 0.00 0.00 Path length= 20.23 End-to-end= 20.14 Shortening= 0.46 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 19.04 -29.29 199.74 32.39 C3'-exo 109.9 102.6 102.0 2)AA 2 37.40 -36.57 162.98 39.24 C2'-endo 106.0 101.2 102.6 3)TA 3 38.15 -21.63 122.29 41.96 C1'-exo 104.6 100.7 106.8 4)TA 4 47.25 -21.96 115.99 53.32 C1'-exo 102.3 99.9 102.6 5)AA 5 10.38 -20.09 209.34 23.63 C3'-exo 107.7 104.7 104.0 6)GA 6 47.24 -31.05 131.59 48.38 C1'-exo 102.4 100.1 103.9 7)AA 7 15.59 -9.82 129.35 16.17 C1'-exo 109.9 104.1 106.7 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 -47.90 152.91 149.44 150.82 -112.06 -25.94 167.88 2)AA 2 -90.49 36.06 142.54 -171.32 -139.15 -32.36 141.14 3)TA 3 -114.18 50.70 121.85 -160.24 -119.74 -38.65 144.83 4)TA 4 -126.21 52.64 106.79 -177.15 -97.51 -58.75 -162.63 5)AA 5 -105.53 37.80 138.86 168.26 -75.70 -121.95 -168.42 6)GA 6 -121.34 80.40 134.10 -105.70 167.73 -7.75 111.38 7)AA 7 -94.32 4.95 119.33 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 14.04 -27.28 209.23 32.05 C3'-exo 108.9 103.5 103.1 2)TB 6 40.29 -41.56 168.79 43.47 C2'-endo 104.4 101.8 99.5 3)AB 5 40.56 -30.08 138.62 41.09 C1'-exo 103.2 101.5 103.1 4)AB 4 40.00 -28.63 137.86 40.02 C1'-exo 104.3 102.3 102.4 5)TB 3 39.13 -32.90 147.24 39.03 C2'-endo 103.8 104.7 102.1 6)CB 2 35.29 -48.59 191.33 50.88 C3'-exo 105.6 99.3 97.4 7)TB 1 31.16 -16.12 117.34 35.44 C1'-exo 102.9 105.6 103.8 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 -99.79 -58.21 159.89 ...... ...... ...... ...... 2)TB 6 -112.30 -73.58 159.63 -158.33 -101.25 18.29 -157.70 3)AB 5 -105.15 34.02 124.80 -173.80 -127.42 58.88 179.01 4)AB 4 -124.21 50.86 125.94 -158.64 -95.27 -56.06 175.22 5)TB 3 -85.04 28.58 137.87 -156.95 -138.36 -50.95 156.35 6)CB 2 -85.89 16.40 166.60 -157.21 -137.02 -44.37 152.45 7)TB 1 -140.73 45.08 112.67 -163.37 -94.31 -25.83 -172.10