ID code: 1EZH *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 17 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) TA 1 0.046 1 : 2) AA 2 0.036 1 : 3) AA 3 0.040 1 : 4) CA 4 0.033 1 : 5) GA 5 0.031 1 : 6) GA 6 0.023 1 : 7) TA 7 0.044 1 : 8) TA 8 0.045 1 : 9) AA 9 0.041 2 : 1) AB 18 0.037 2 : 2) TB 17 0.035 2 : 3) TB 16 0.024 2 : 4) GB 15 0.069 2 : 5) CB 14 0.034 2 : 6) CB 13 0.021 2 : 7) AB 12 0.035 2 : 8) AB 11 0.033 2 : 9) TB 10 0.064 Strand= 2 Nucleo= 18 Atoms = 363 Units = 18 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 9 levels ... Strand 1 has 9 bases (5'-3'): TAACGGTTA Strand 2 has 9 bases (3'-5'): ATTGCCAAT FIRST SUM= 126.448 CPTS: 6.270 77.950 6.757 35.471 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 36 STEP 1 SUM= 126.448 DEL= 0.000E+00 STEP 2 SUM= 98.678 DEL= -0.278E+02 STEP 3 SUM= 99.718 DEL= 0.104E+01 STEP 4 SUM= 85.045 DEL= -0.147E+02 STEP 5 SUM= 73.983 DEL= -0.111E+02 STEP 6 SUM= 68.635 DEL= -0.535E+01 STEP 7 SUM= 63.774 DEL= -0.486E+01 STEP 8 SUM= 57.920 DEL= -0.585E+01 STEP 9 SUM= 56.539 DEL= -0.138E+01 STEP 10 SUM= 54.257 DEL= -0.228E+01 STEP 11 SUM= 51.252 DEL= -0.301E+01 STEP 12 SUM= 48.583 DEL= -0.267E+01 STEP 13 SUM= 50.213 DEL= 0.163E+01 STEP 14 SUM= 47.561 DEL= -0.265E+01 STEP 15 SUM= 45.991 DEL= -0.157E+01 STEP 16 SUM= 51.108 DEL= 0.512E+01 STEP 17 SUM= 45.692 DEL= -0.542E+01 STEP 18 SUM= 45.553 DEL= -0.140E+00 STEP 19 SUM= 45.308 DEL= -0.244E+00 STEP 20 SUM= 44.996 DEL= -0.312E+00 STEP 21 SUM= 44.554 DEL= -0.443E+00 STEP 22 SUM= 44.037 DEL= -0.516E+00 STEP 23 SUM= 44.519 DEL= 0.481E+00 STEP 24 SUM= 43.861 DEL= -0.657E+00 STEP 25 SUM= 43.578 DEL= -0.283E+00 STEP 26 SUM= 43.131 DEL= -0.448E+00 STEP 27 SUM= 42.691 DEL= -0.439E+00 STEP 28 SUM= 42.574 DEL= -0.117E+00 STEP 29 SUM= 42.412 DEL= -0.162E+00 STEP 30 SUM= 42.344 DEL= -0.684E-01 STEP 31 SUM= 42.314 DEL= -0.302E-01 STEP 32 SUM= 42.275 DEL= -0.383E-01 STEP 33 SUM= 42.260 DEL= -0.155E-01 STEP 34 SUM= 42.257 DEL= -0.322E-02 STEP 35 SUM= 42.256 DEL= -0.348E-03 STEP 36 SUM= 42.256 DEL= -0.895E-04 STEP 37 SUM= 42.256 DEL= -0.672E-04 STEP 38 SUM= 42.256 DEL= -0.488E-04 STEP 39 SUM= 42.256 DEL= -0.421E-04 STEP 40 SUM= 42.256 DEL= -0.181E-04 STEP 41 SUM= 42.256 DEL= -0.608E-05 STEP 42 SUM= 42.256 DEL= -0.398E-05 STEP 43 SUM= 42.256 DEL= -0.397E-05 STEP 44 SUM= 42.256 DEL= -0.191E-05 STEP 45 SUM= 42.256 DEL= -0.424E-06 STEP 46 SUM= 42.256 DEL= -0.663E-07 STEP 47 SUM= 42.256 DEL= -0.213E-07 STEP 48 SUM= 42.256 DEL= -0.639E-08 STEP 49 SUM= 42.256 DEL= -0.602E-09 STEP 50 SUM= 42.256 DEL= -0.285E-10 STEP 51 SUM= 42.256 DEL= -0.300E-11 STEP 52 SUM= 42.256 DEL= -0.348E-12 STEP 53 SUM= 42.256 DEL= -0.213E-13 STEP 54 SUM= 42.256 DEL= 0.000E+00 FINAL SUM= 42.256 CPTS: 4.109 32.155 2.075 3.917 GRA= 0.15E-07 0.15E-07-0.33E-09-0.14E-08-0.27E-07-0.20E-07 0.22E-09 0.13E-08 GRA= 0.34E-08 0.24E-08 0.48E-09 0.15E-08 0.57E-08-0.14E-08 0.25E-09-0.20E-09 GRA=-0.67E-08 0.22E-08-0.26E-08-0.10E-08 0.18E-08-0.53E-08 0.36E-08 0.51E-09 GRA= 0.46E-08 0.41E-08-0.29E-08-0.75E-09-0.10E-08 0.11E-07 0.30E-08-0.15E-08 GRA=-0.23E-08-0.63E-08-0.14E-08 0.13E-08 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: 0.892 -0.449 -0.055 P: 14.006 20.831 30.488 D: 27.608 2) U: 0.932 -0.356 -0.072 P: 17.057 19.414 29.697 D: 2.565 3) U: 0.959 -0.283 0.031 P: 20.262 18.341 29.344 D: 3.073 4) U: 0.974 -0.211 0.080 P: 23.799 17.021 29.184 D: 1.875 5) U: 0.989 0.023 0.144 P: 27.260 16.546 29.670 D: 1.558 6) U: 0.984 0.090 0.151 P: 30.794 17.199 30.209 D: 1.027 7) U: 0.990 0.053 0.134 P: 34.176 17.345 30.338 D: 3.071 8) U: 0.990 0.071 0.119 P: 37.407 17.508 31.568 D: 1.480 9) U: 0.995 0.027 0.097 P: 40.699 17.783 31.467 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) TA 1 -4.60 3.40 17.37 -3.59 4 0 2) AA 2 -0.64 2.93 20.89 -7.54 2 28 3) AA 3 -0.60 2.39 12.19 -22.32 2 23 4) CA 4 -1.03 1.55 2.73 -12.24 3 -14 5) GA 5 -1.12 1.22 -2.05 -2.63 1 9 6) GA 6 -0.69 0.80 -3.28 -9.41 1 6 7) TA 7 -1.12 0.49 -2.98 -9.38 4 -23 8) TA 8 -0.08 0.40 -1.90 -8.59 4 -28 9) AA 9 -0.14 0.73 4.82 -3.05 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) AB 18 2.18 -3.16 18.55 6.89 2 0 2) TB 17 -1.00 -2.65 3.90 7.82 4 -28 3) TB 16 -0.82 -2.28 -1.08 -3.71 4 -23 4) GB 15 -0.78 -1.41 5.07 -0.64 1 14 5) CB 14 -1.00 -1.15 4.47 -4.24 3 -9 6) CB 13 -0.55 -0.71 4.05 -11.88 3 -6 7) AB 12 -0.57 -0.28 7.52 -3.44 2 23 8) AB 11 0.20 -0.34 10.94 -3.83 2 28 9) TB 10 -0.42 -0.67 5.71 -7.04 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) T 1-A 18 -1.21 3.28 17.96 -5.24 4 0 2) A 2-T 17 -0.82 2.79 12.40 -7.68 2 28 3) A 3-T 16 -0.71 2.34 5.56 -9.31 2 23 4) C 4-G 15 -0.91 1.48 3.90 -5.80 3 -14 5) G 5-C 14 -1.06 1.19 1.21 0.81 1 9 6) G 6-C 13 -0.62 0.76 0.39 1.23 1 6 7) T 7-A 12 -0.84 0.39 2.27 -2.97 4 -23 8) T 8-A 11 0.06 0.37 4.52 -2.38 4 -28 9) A 9-T 10 -0.28 0.70 5.26 2.00 2 0 Average: -0.71 1.48 5.94 -3.26 --------------------------------- |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) T 1-A 18 -6.78 0.24 -0.89 -1.17 3.31 33.13 4 0 2) A 2-T 17 0.36 0.28 -0.05 16.99 0.28 0.68 2 28 3) A 3-T 16 0.22 0.12 -0.22 13.27 -26.02 6.04 2 23 4) C 4-G 15 -0.25 0.14 -0.16 -2.34 -12.88 -0.26 3 -14 5) G 5-C 14 -0.12 0.06 0.05 -6.52 -6.87 -1.10 1 9 6) G 6-C 13 -0.15 0.09 -0.18 -7.33 -21.29 2.85 1 6 7) T 7-A 12 -0.55 0.22 -0.27 -10.51 -12.82 -7.94 4 -23 8) T 8-A 11 -0.27 0.07 -0.34 -12.84 -12.42 3.32 4 -28 9) A 9-T 10 0.28 0.06 -0.57 -0.89 -10.09 5.32 2 0 Average: -0.81 0.14 -0.29 -1.26 -10.98 4.67 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) T 1/A 2 4.47 -0.20 3.83 -1.90 -6.36 40.66 10 3) A 2/A 3 0.31 -0.59 3.31 -14.47 -19.45 41.44 4 4) A 3/C 4 -0.48 -1.39 3.78 -14.39 11.23 24.63 -6 5) C 4/G 5 -0.25 -0.28 3.65 -11.19 22.05 35.13 8 6) G 5/G 6 0.85 -0.57 3.49 -0.21 -3.04 34.76 1 7) G 6/T 7 -0.77 -0.43 3.33 -0.88 -2.02 27.49 6 8) T 7/T 8 1.85 -0.06 3.33 2.08 -0.09 46.48 -4 9) T 8/A 9 -0.49 0.54 3.16 3.97 6.19 38.09 10 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) A 18/T 17 -2.66 0.24 2.99 -20.06 3.33 73.11 10 3) T 17/T 16 0.45 0.44 3.48 -10.74 -6.86 36.09 -4 4) T 16/G 15 -0.01 1.41 3.71 1.22 1.91 30.93 6 5) G 15/C 14 -0.37 0.20 3.45 -7.01 -16.04 35.97 8 6) C 14/C 13 0.87 0.59 3.72 0.60 -11.38 30.81 -1 7) C 13/A 12 -0.37 0.56 3.41 2.30 10.49 38.28 -6 8) A 12/A 11 1.58 -0.08 3.40 4.41 0.49 35.22 4 9) A 11/T 10 -1.04 -0.54 3.39 -7.97 -3.85 36.09 10 --------------------------------------- |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) T 1/A 2 0.91 -0.22 3.41 -10.98 -4.85 56.89 10 3) A 2/A 3 0.38 -0.52 3.39 -12.60 -6.30 38.77 4 4) A 3/C 4 -0.25 -1.40 3.74 -6.59 4.66 27.78 -6 5) C 4/G 5 -0.31 -0.24 3.55 -9.10 19.04 35.55 8 6) G 5/G 6 0.86 -0.58 3.61 0.20 4.17 32.79 1 7) G 6/T 7 -0.57 -0.50 3.37 0.71 -6.26 32.89 6 8) T 7/T 8 1.72 0.01 3.36 3.24 -0.29 40.85 -4 9) T 8/A 9 -0.76 0.54 3.27 -2.00 5.02 37.09 10 Average: 0.25 -0.36 3.46 -4.64 1.90 37.82 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) T 1/A 2 2.38 -0.88 3.71 1.30 7.83 38.98 10 3) A 2/A 3 -0.66 -0.01 3.48 -3.20 -6.52 43.43 4 4) A 3/C 4 -0.08 -1.33 4.05 -6.43 14.19 27.67 -6 5) C 4/G 5 -0.56 -1.00 3.85 -6.63 21.70 36.71 8 6) G 5/G 6 0.58 -1.19 3.49 3.48 -4.32 34.74 1 7) G 6/T 7 -0.53 -1.04 3.36 3.59 -3.53 27.12 6 8) T 7/T 8 1.87 -0.65 3.09 9.04 -2.06 45.61 -4 9) T 8/A 9 -0.61 0.48 3.20 7.43 6.92 37.61 10 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) A 18/T 17 -4.98 1.10 3.73 -7.96 9.40 74.62 10 3) T 17/T 16 -0.93 -1.00 3.23 -9.09 6.92 36.68 -4 4) T 16/G 15 -1.16 -1.65 3.58 -0.19 -0.86 30.85 6 5) G 15/C 14 -1.27 -0.49 3.52 -8.50 18.77 34.72 8 6) C 14/C 13 -0.16 -0.78 3.87 -3.68 13.36 30.42 -1 7) C 13/A 12 -1.16 -0.49 3.35 -2.97 -6.19 38.30 -6 8) A 12/A 11 1.12 0.47 3.46 2.04 5.04 35.15 4 9) A 11/T 10 -1.58 0.88 3.20 -11.10 8.68 34.94 10 -------------------------------------- |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) T 1/A 2 -1.15 0.58 3.27 -3.24 9.21 56.56 10 3) A 2/A 3 -0.80 -0.52 3.38 -6.09 0.15 38.84 4 4) A 3/C 4 -0.64 -1.49 3.85 -3.48 6.60 29.97 -6 5) C 4/G 5 -0.93 -0.74 3.71 -7.60 20.28 35.76 8 6) G 5/G 6 0.23 -0.99 3.69 -0.02 4.55 33.22 1 7) G 6/T 7 -0.85 -0.76 3.37 0.35 -4.95 32.85 6 8) T 7/T 8 1.49 -0.12 3.33 5.51 1.38 40.77 -4 9) T 8/A 9 -1.07 0.70 3.22 -1.79 8.22 36.32 10 Average: -0.47 -0.42 3.48 -2.04 5.68 38.04 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) T 1/A 2 0.51 0.27 -5.42 -2.41 0.58 5.93 3.46 10 3) A 2/A 3 0.28 -0.06 -5.77 -4.67 0.28 7.42 3.40 4 4) A 3/C 4 -0.04 -0.54 -4.93 1.16 0.55 5.07 3.78 -6 5) C 4/G 5 -0.16 0.06 -6.41 12.43 0.17 13.98 3.53 8 6) G 5/G 6 0.42 -0.15 1.02 3.74 0.45 3.88 3.63 1 7) G 6/T 7 -0.34 -0.13 -1.17 -2.06 0.37 2.37 3.39 6 8) T 7/T 8 0.81 0.03 0.99 -0.88 0.81 1.33 3.46 -4 9) T 8/A 9 -0.42 0.21 -2.74 0.65 0.47 2.82 3.31 10 Overall axis bend ... UU= 29.56 PP= 31.54 Duplex Offset L.Dir ... wrt end-to-end vector 1) T 1 0.00 0.00 2) A 2 1.40 134.66 3) A 3 2.24 91.43 4) C 4 3.15 61.32 5) G 5 3.05 20.51 6) G 6 1.93 -11.86 7) T 7 1.48 -30.17 8) T 8 0.68 -131.82 9) A 9 0.00 0.00 Path length= 27.95 End-to-end= 26.88 Shortening= 3.80 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)TA 1 43.56 -28.85 131.46 44.90 C1'-exo 102.9 100.5 103.0 2)AA 2 49.41 -36.52 140.01 49.30 C1'-exo 101.8 99.4 100.9 3)AA 3 31.68 -32.43 168.73 34.25 C2'-endo 106.3 102.8 101.2 4)CA 4 45.01 -34.28 141.82 44.89 C1'-exo 102.2 101.1 101.0 5)GA 5 31.74 -34.59 174.59 36.05 C2'-endo 106.8 102.3 100.8 6)GA 6 36.53 -31.70 153.38 36.67 C2'-endo 105.1 102.4 101.5 7)TA 7 34.20 -18.29 119.73 37.70 C1'-exo 103.5 104.8 101.8 8)TA 8 35.51 -27.12 142.06 35.38 C1'-exo 104.4 103.6 101.8 9)AA 9 7.51 -27.28 224.53 39.06 C4'-endo 106.8 103.1 102.4 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)TA 1 -102.45 61.81 122.86 -175.11 -90.18 -63.39 170.33 2)AA 2 -111.81 58.06 132.67 -77.87 175.84 -102.02 151.40 3)AA 3 -111.66 53.70 139.53 -166.88 -86.35 -77.39 175.19 4)CA 4 -115.06 50.68 129.49 -164.19 -107.28 -88.06 -170.88 5)GA 5 -107.54 47.09 141.29 174.39 -92.58 -63.73 -171.62 6)GA 6 -109.30 50.61 133.47 -157.26 -116.11 -71.86 158.23 7)TA 7 -127.65 62.47 111.33 179.71 -89.63 -53.68 171.34 8)TA 8 -119.11 55.58 128.07 -174.04 -101.03 -56.33 -146.85 9)AA 9 -78.65 27.04 160.43 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)AB 18 27.28 -32.14 180.21 33.16 C3'-exo 107.2 102.4 102.3 2)TB 17 39.57 -30.05 142.29 39.19 C1'-exo 103.6 103.5 100.5 3)TB 16 21.39 -0.60 90.65 36.78 O1'-endo 105.3 106.0 101.9 4)GB 15 28.90 -31.66 174.80 32.94 C2'-endo 107.1 103.0 101.6 5)CB 14 -24.10 30.49 7.35 31.84 C3'-endo 106.6 105.4 99.6 6)CB 13 -4.40 21.71 48.24 33.91 C4'-exo 107.2 105.9 100.5 7)AB 12 27.59 -33.39 182.93 34.55 C3'-exo 106.5 103.1 100.8 8)AB 11 44.12 -34.38 144.02 43.88 C2'-endo 103.2 100.9 101.3 9)TB 10 30.74 -30.64 164.94 32.72 C2'-endo 106.8 101.8 103.4 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)AB 18 -95.26 53.70 148.83 ...... ...... ...... ...... 2)TB 17 -119.28 58.80 130.60 -174.79 -85.05 -56.99 175.87 3)TB 16 -146.25 64.09 93.18 -167.76 -82.51 -69.23 172.83 4)GB 15 -113.99 61.91 140.83 -168.45 -87.21 -71.31 164.08 5)CB 14 -143.78 62.68 88.29 -164.69 -64.58 -70.74 -178.23 6)CB 13 -137.22 61.67 85.48 -170.64 -75.68 -82.73 176.10 7)AB 12 -94.05 28.12 145.17 -176.11 -92.41 -79.89 163.30 8)AB 11 -84.34 53.51 136.14 -79.05 156.63 -84.72 164.61 9)TB 10 -108.38 -176.72 142.03 -155.38 -80.27 -76.80 165.28