ID code: 9ICL, PDE0101 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 21 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 0.103 1 : 2) AA 3 0.041 1 : 3) TA 4 0.155 1 : 4) CA 5 0.096 1 : 5) TA 6 0.089 1 : 6) GA 7 0.060 2 : 1) GB 6 0.093 2 : 2) TB 5 0.231 2 : 3) AB 4 0.033 2 : 4) GB 3 0.037 2 : 5) AB 2 0.062 2 : 6) CB 1 0.095 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= 21.366 CPTS: 2.378 5.828 2.105 11.054 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 24 STEP 1 SUM= 21.366 DEL= 0.000E+00 STEP 2 SUM= 12.997 DEL= -0.837E+01 STEP 3 SUM= 48.896 DEL= 0.359E+02 STEP 4 SUM= 11.667 DEL= -0.372E+02 STEP 5 SUM= 11.763 DEL= 0.968E-01 STEP 6 SUM= 11.024 DEL= -0.739E+00 STEP 7 SUM= 10.412 DEL= -0.613E+00 STEP 8 SUM= 9.618 DEL= -0.794E+00 STEP 9 SUM= 8.856 DEL= -0.762E+00 STEP 10 SUM= 12.354 DEL= 0.350E+01 STEP 11 SUM= 8.740 DEL= -0.361E+01 STEP 12 SUM= 8.546 DEL= -0.195E+00 STEP 13 SUM= 8.294 DEL= -0.252E+00 STEP 14 SUM= 10.334 DEL= 0.204E+01 STEP 15 SUM= 8.269 DEL= -0.207E+01 STEP 16 SUM= 8.221 DEL= -0.481E-01 STEP 17 SUM= 7.953 DEL= -0.267E+00 STEP 18 SUM= 9.100 DEL= 0.115E+01 STEP 19 SUM= 7.897 DEL= -0.120E+01 STEP 20 SUM= 7.887 DEL= -0.101E-01 STEP 21 SUM= 7.866 DEL= -0.208E-01 STEP 22 SUM= 7.815 DEL= -0.508E-01 STEP 23 SUM= 7.742 DEL= -0.730E-01 STEP 24 SUM= 7.681 DEL= -0.612E-01 STEP 25 SUM= 7.642 DEL= -0.395E-01 STEP 26 SUM= 7.597 DEL= -0.446E-01 STEP 27 SUM= 7.579 DEL= -0.185E-01 STEP 28 SUM= 7.578 DEL= -0.975E-03 STEP 29 SUM= 7.574 DEL= -0.343E-02 STEP 30 SUM= 7.573 DEL= -0.137E-02 STEP 31 SUM= 7.572 DEL= -0.763E-03 STEP 32 SUM= 7.572 DEL= -0.443E-04 STEP 33 SUM= 7.572 DEL= -0.816E-04 STEP 34 SUM= 7.572 DEL= -0.199E-03 STEP 35 SUM= 7.572 DEL= -0.158E-03 STEP 36 SUM= 7.571 DEL= -0.104E-03 STEP 37 SUM= 7.571 DEL= -0.852E-05 STEP 38 SUM= 7.571 DEL= 0.200E-06 STEP 39 SUM= 7.571 DEL= -0.551E-06 STEP 40 SUM= 7.571 DEL= -0.202E-06 STEP 41 SUM= 7.571 DEL= -0.465E-07 STEP 42 SUM= 7.571 DEL= -0.256E-09 STEP 43 SUM= 7.571 DEL= -0.105E-10 STEP 44 SUM= 7.571 DEL= -0.711E-14 STEP 45 SUM= 7.571 DEL= 0.000E+00 FINAL SUM= 7.571 CPTS: 1.641 4.360 0.247 1.323 GRA= 0.87E-09 0.30E-08-0.26E-10 0.12E-08-0.79E-09 0.25E-08-0.11E-09-0.43E-09 GRA=-0.28E-08-0.45E-08-0.22E-10-0.80E-09 0.59E-08 0.19E-08-0.53E-10-0.13E-09 GRA= 0.17E-08-0.82E-09 0.31E-10 0.33E-09-0.41E-08 0.93E-09-0.13E-10 0.43E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.615 -0.782 -0.100 P: 58.971 31.909 47.166 D: 0.801 2) U: -0.641 -0.760 -0.106 P: 56.850 29.179 46.503 D: 2.527 3) U: -0.661 -0.740 -0.125 P: 54.414 26.997 46.462 D: 0.799 4) U: -0.650 -0.747 -0.140 P: 51.962 24.376 46.003 D: 0.877 5) U: -0.650 -0.749 -0.128 P: 49.609 21.967 45.725 D: 2.567 6) U: -0.583 -0.808 -0.091 P: 48.112 19.353 45.385 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 2 -0.48 0.43 6.11 -8.91 3 0 2) AA 3 -0.27 0.61 4.88 -8.37 2 30 3) TA 4 -1.02 0.13 1.91 -8.41 4 -22 4) CA 5 -0.47 0.08 -1.33 -2.28 3 -4 5) TA 6 -0.88 0.03 4.68 -8.17 4 -25 6) GA 7 -0.07 0.05 12.99 -7.04 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 6 -0.80 -0.60 9.12 -0.44 1 0 2) TB 5 -1.30 -0.96 3.46 -0.91 4 -30 3) AB 4 -0.47 -0.46 -0.08 -7.26 2 22 4) GB 3 -0.85 -0.25 6.01 -5.97 1 4 5) AB 2 -0.57 0.12 9.80 -10.16 2 25 6) CB 1 -0.56 -0.22 -3.71 -8.63 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 -0.64 0.52 7.62 -4.24 3 0 2) A 3-T 5 -0.78 0.78 4.17 -3.73 2 30 3) T 4-A 4 -0.75 0.30 0.91 -0.57 4 -22 4) C 5-G 3 -0.66 0.17 2.34 1.85 3 -4 5) T 6-A 2 -0.72 -0.04 7.24 1.00 4 -25 6) G 7-C 1 -0.31 0.14 4.64 0.79 1 0 Average: -0.64 0.31 4.49 -0.82 --------------------------------- |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 0.31 -0.18 -0.09 -3.01 -9.35 4.74 3 0 2) A 3-T 5 1.03 -0.35 0.13 1.43 -9.28 3.23 2 30 3) T 4-A 4 -0.55 -0.33 0.19 1.98 -15.67 8.00 4 -22 4) C 5-G 3 0.38 -0.17 0.13 -7.33 -8.25 1.91 3 -4 5) T 6-A 2 -0.31 0.15 -0.28 -5.12 -18.33 4.38 4 -25 6) G 7-C 1 0.49 -0.18 0.68 16.70 -15.67 4.08 1 0 Average: 0.23 -0.18 0.13 0.78 -12.76 4.39 ---------------------------------- |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 0.17 0.49 3.62 -1.37 2.51 34.96 9 3) A 3/T 4 -0.63 -0.99 3.26 -2.87 1.95 27.81 7 4) T 4/C 5 0.57 -0.15 3.59 -4.22 6.70 38.76 -2 5) C 5/T 6 -0.63 -0.19 3.16 5.76 -6.54 28.44 -3 6) T 6/G 7 1.15 0.31 3.48 3.25 3.46 37.49 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 6/T 5 -0.55 -0.67 3.40 -5.81 -2.44 36.47 -9 3) T 5/A 4 0.96 1.01 3.20 -3.43 -8.34 23.04 7 4) A 4/G 3 -0.36 0.31 3.65 5.10 0.72 44.84 2 5) G 3/A 2 0.06 0.52 3.57 3.55 -3.54 25.96 3 6) A 2/C 1 0.35 -0.64 2.52 -18.57 -0.80 37.80 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 -0.19 0.58 3.51 -3.59 2.47 35.71 9 3) A 3/T 4 0.17 -1.00 3.23 -3.15 5.14 25.43 7 4) T 4/C 5 0.10 -0.23 3.62 0.44 2.99 41.80 -2 5) C 5/T 6 -0.28 -0.36 3.37 4.66 -1.50 27.20 -3 6) T 6/G 7 0.75 0.48 3.00 -7.66 2.13 37.65 -9 Average: 0.11 -0.11 3.34 -1.86 2.25 33.56 --------------------------------- |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 0.39 0.58 3.58 3.90 5.77 34.45 9 3) A 3/T 4 -0.30 -1.10 3.43 1.34 3.57 27.75 7 4) T 4/C 5 0.81 -0.69 3.53 -0.46 6.59 39.04 -2 5) C 5/T 6 -0.41 -0.39 3.23 8.13 -5.51 27.91 -3 6) T 6/G 7 1.44 0.50 3.33 7.69 9.20 36.05 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 6/T 5 -1.01 0.34 3.43 -6.03 6.31 36.04 -9 3) T 5/A 4 0.48 -1.29 3.30 -5.10 8.88 22.75 7 4) A 4/G 3 -1.07 -0.61 3.58 -0.45 1.60 45.01 2 5) G 3/A 2 -0.50 -0.37 3.61 -0.16 6.98 26.09 3 6) A 2/C 1 -0.00 0.40 2.59 -23.81 2.62 34.78 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 -0.32 0.49 3.54 -1.06 6.22 35.33 9 3) A 3/T 4 0.08 -1.21 3.31 -1.75 6.37 25.33 7 4) T 4/C 5 -0.12 -0.61 3.64 -0.56 4.09 42.18 -2 5) C 5/T 6 -0.43 -0.39 3.40 4.16 0.81 27.43 -3 6) T 6/G 7 0.67 0.46 3.00 -8.26 6.47 35.56 -9 Average: -0.03 -0.25 3.38 -1.50 4.79 33.17 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 2/A 3 -0.05 0.31 -0.15 1.97 0.32 1.97 3.52 9 3) A 3/T 4 0.13 -0.51 0.11 1.98 0.53 1.98 3.27 7 4) T 4/C 5 0.01 -0.10 -0.98 0.57 0.11 1.14 3.62 -2 5) C 5/T 6 -0.22 -0.14 -0.25 -0.64 0.26 0.69 3.38 -3 6) T 6/G 7 0.34 0.30 -5.06 2.34 0.45 5.57 3.03 -9 Overall axis bend ... UU= 2.42 PP= 9.08 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 2 0.00 0.00 2) A 3 0.34 -83.59 3) T 4 0.23 123.15 4) C 5 0.38 96.79 5) T 6 0.58 57.05 6) G 7 0.00 0.00 Path length= 16.82 End-to-end= 16.70 Shortening= 0.74 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 2 32.78 -30.20 156.60 33.63 C2'-endo 105.7 102.5 103.8 2)AA 3 27.21 -24.54 153.80 27.93 C2'-endo 107.0 102.3 105.8 3)TA 4 30.21 -4.28 95.65 46.68 O1'-endo 104.9 102.1 103.7 4)CA 5 24.43 -21.82 154.30 24.80 C2'-endo 107.0 104.2 104.6 5)TA 6 41.09 -20.60 117.24 47.17 C1'-exo 104.4 98.4 106.6 6)GA 7 44.41 -31.81 138.35 44.63 C1'-exo 106.0 98.2 105.0 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 -103.32 60.43 129.62 -175.41 -112.77 -62.03 179.52 2)AA 3 -97.72 57.08 133.27 -169.34 -107.30 -46.34 160.87 3)TA 4 -126.45 42.98 93.14 158.87 -68.25 -75.14 -159.41 4)CA 5 -114.77 52.28 129.19 -179.06 -92.09 -86.10 -177.49 5)TA 6 -115.80 67.53 118.45 -162.02 -119.45 -18.54 146.40 6)GA 7 -88.24 19.00 135.40 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 6 26.85 -30.39 175.99 31.20 C2'-endo 107.7 103.4 103.4 2)TB 5 36.37 -18.26 116.01 41.66 C1'-exo 100.7 105.0 103.1 3)AB 4 17.06 0.62 89.10 30.80 O1'-endo 106.5 104.7 104.0 4)GB 3 43.53 -27.58 128.31 46.21 C1'-exo 103.1 98.8 105.1 5)AB 2 24.44 -47.82 208.53 55.24 C3'-exo 105.1 99.2 97.1 6)CB 1 2.53 18.70 59.23 37.20 C4'-exo 106.6 105.3 102.5 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 -109.57 51.75 138.88 ...... ...... ...... ...... 2)TB 5 -121.22 68.53 111.48 -166.50 -98.22 -62.41 178.08 3)AB 4 -128.78 52.29 102.10 175.60 -59.82 -102.94 -178.70 4)GB 3 -104.24 37.70 122.56 -177.06 -111.78 -64.82 174.43 5)AB 2 -82.37 -69.70 -169.42 178.34 -125.83 -22.99 143.39 6)CB 1 -157.57 61.11 85.71 -171.77 -100.48 68.73 173.53