ID code: 1D1U, PD0152 *********************************** ************** ****** 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 1 0.012 1 : 2) TA 2 0.045 1 : 3) CA 3 0.037 1 : 4) GA 4 0.064 1 : 5) TA 5 0.032 1 : 6) GA 6 0.020 2 : 1) GB 16 0.022 2 : 2) AB 15 0.016 2 : 3) GB 14 0.023 2 : 4) CB 13 0.010 2 : 5) AB 12 0.015 2 : 6) CB 11 0.011 Strand= 2 Nucleo= 12 Atoms = 243 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'): CTCGTG Strand 2 has 6 bases (3'-5'): GAGCAC FIRST SUM= 29.277 CPTS: 2.580 3.131 6.754 16.812 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 24 STEP 1 SUM= 29.277 DEL= 0.000E+00 STEP 2 SUM= 24.648 DEL= -0.463E+01 STEP 3 SUM= 19.330 DEL= -0.532E+01 STEP 4 SUM= 17.623 DEL= -0.171E+01 STEP 5 SUM= 15.331 DEL= -0.229E+01 STEP 6 SUM= 14.745 DEL= -0.586E+00 STEP 7 SUM= 13.672 DEL= -0.107E+01 STEP 8 SUM= 11.334 DEL= -0.234E+01 STEP 9 SUM= 107.970 DEL= 0.966E+02 STEP 10 SUM= 11.687 DEL= -0.963E+02 STEP 11 SUM= 11.222 DEL= -0.465E+00 STEP 12 SUM= 11.006 DEL= -0.216E+00 STEP 13 SUM= 9.881 DEL= -0.112E+01 STEP 14 SUM= 8.149 DEL= -0.173E+01 STEP 15 SUM= 16.251 DEL= 0.810E+01 STEP 16 SUM= 7.890 DEL= -0.836E+01 STEP 17 SUM= 7.728 DEL= -0.162E+00 STEP 18 SUM= 7.504 DEL= -0.224E+00 STEP 19 SUM= 7.294 DEL= -0.209E+00 STEP 20 SUM= 7.050 DEL= -0.244E+00 STEP 21 SUM= 7.166 DEL= 0.116E+00 STEP 22 SUM= 6.995 DEL= -0.171E+00 STEP 23 SUM= 6.942 DEL= -0.539E-01 STEP 24 SUM= 6.923 DEL= -0.185E-01 STEP 25 SUM= 6.896 DEL= -0.275E-01 STEP 26 SUM= 6.877 DEL= -0.186E-01 STEP 27 SUM= 6.872 DEL= -0.533E-02 STEP 28 SUM= 6.878 DEL= 0.672E-02 STEP 29 SUM= 6.870 DEL= -0.836E-02 STEP 30 SUM= 6.870 DEL= -0.417E-03 STEP 31 SUM= 6.870 DEL= 0.149E-03 STEP 32 SUM= 6.869 DEL= -0.285E-03 STEP 33 SUM= 6.869 DEL= -0.814E-05 STEP 34 SUM= 6.869 DEL= -0.220E-04 STEP 35 SUM= 6.869 DEL= 0.360E-04 STEP 36 SUM= 6.869 DEL= -0.454E-04 STEP 37 SUM= 6.869 DEL= -0.393E-06 STEP 38 SUM= 6.869 DEL= -0.492E-06 STEP 39 SUM= 6.869 DEL= -0.391E-06 STEP 40 SUM= 6.869 DEL= -0.463E-09 STEP 41 SUM= 6.869 DEL= -0.126E-10 STEP 42 SUM= 6.869 DEL= -0.178E-14 STEP 43 SUM= 6.869 DEL= 0.000E+00 FINAL SUM= 6.869 CPTS: 1.920 3.371 0.369 1.210 GRA=-0.25E-09-0.72E-10 0.26E-09-0.27E-09 0.36E-09-0.13E-08-0.18E-10-0.22E-09 GRA= 0.12E-08 0.13E-08-0.25E-09 0.19E-09-0.13E-09 0.24E-09 0.17E-09 0.19E-09 GRA=-0.29E-09 0.84E-10-0.11E-09 0.30E-09-0.72E-10-0.56E-09 0.21E-09-0.36E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.725 -0.617 -0.307 P: -9.066 15.975 17.459 D: 1.945 2) U: -0.745 -0.619 -0.250 P: -11.638 13.444 16.580 D: 1.710 3) U: -0.723 -0.623 -0.299 P: -13.704 11.573 15.517 D: 0.732 4) U: -0.738 -0.625 -0.256 P: -16.212 9.617 14.330 D: 1.158 5) U: -0.766 -0.590 -0.255 P: -18.465 7.223 13.496 D: 1.325 6) U: -0.779 -0.604 -0.169 P: -21.042 5.646 12.662 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.88 -0.55 -6.35 -4.50 3 0 2) TA 2 -0.96 -0.26 -17.23 -5.74 4 -17 3) CA 3 -0.56 -0.52 -6.01 -9.99 3 -10 4) GA 4 -0.71 -0.10 -6.06 -2.66 1 14 5) TA 5 -0.83 -0.52 -5.57 -4.47 4 -29 6) GA 6 -0.44 -0.52 5.50 -9.07 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 16 -0.91 0.62 4.20 2.99 1 0 2) AB 15 -0.27 0.62 6.07 -4.74 2 17 3) GB 14 -1.07 0.55 2.60 -11.48 1 10 4) CB 13 -1.28 0.47 7.91 -9.20 3 -14 5) AB 12 -1.65 0.90 8.56 -6.85 2 29 6) CB 11 -1.36 0.71 8.65 -3.68 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 1-G 16 -0.90 -0.58 -1.08 -3.74 3 0 2) T 2-A 15 -0.61 -0.44 -5.58 -0.50 4 -17 3) C 3-G 14 -0.82 -0.53 -1.71 0.75 3 -10 4) G 4-C 13 -1.00 -0.29 0.92 3.27 1 14 5) T 5-A 12 -1.24 -0.71 1.50 1.19 4 -29 6) G 6-C 11 -0.90 -0.61 7.07 -2.69 1 0 Average: -0.91 -0.53 0.19 -0.29 --------------------------------- |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 16 0.03 0.07 -0.34 -10.56 -1.51 0.67 3 0 2) T 2-A 15 -0.68 0.36 0.77 -23.30 -10.48 9.09 4 -17 3) C 3-G 14 0.50 0.03 0.12 -8.61 -21.47 9.32 3 -10 4) G 4-C 13 0.57 0.36 0.13 -13.97 -11.86 8.45 1 14 5) T 5-A 12 0.82 0.37 0.75 -14.14 -11.32 0.71 4 -29 6) G 6-C 11 0.92 0.19 0.20 -3.15 -12.75 8.85 1 0 Average: 0.36 0.23 0.27 -12.29 -11.57 6.18 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/T 2 0.25 0.28 4.26 -14.16 -0.16 38.99 -3 3) T 2/C 3 0.20 -0.45 2.65 13.37 -6.45 36.01 -2 4) C 3/G 4 -0.38 0.61 3.39 -0.03 9.93 37.34 8 5) G 4/T 5 -0.42 -0.75 3.67 -1.28 0.09 29.62 6 6) T 5/G 6 0.69 0.23 2.84 16.09 -4.00 40.73 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 16/A 15 0.96 0.01 3.15 -1.42 -8.81 30.58 3 3) A 15/G 14 -0.99 0.12 3.30 -1.32 -4.54 35.77 2 4) G 14/C 13 -0.44 -0.27 3.37 5.34 -0.32 38.21 8 5) C 13/A 12 -0.68 0.76 3.06 -1.12 0.44 37.36 -6 6) A 12/C 11 0.59 -0.42 3.39 5.11 2.58 32.59 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 1/T 2 0.60 0.14 3.70 -7.79 4.32 34.79 -3 3) T 2/C 3 -0.39 -0.29 2.97 6.02 -0.96 35.89 -2 4) C 3/G 4 -0.41 0.44 3.38 2.65 5.12 37.78 8 5) G 4/T 5 -0.55 -0.75 3.36 -1.20 -0.18 33.49 6 6) T 5/G 6 0.64 0.32 3.12 10.60 -3.29 36.66 -9 Average: -0.02 -0.03 3.31 2.06 1.00 35.72 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/T 2 1.00 -1.16 4.09 -10.10 -7.76 39.75 -3 3) T 2/C 3 0.65 -1.36 2.39 17.47 -13.33 33.22 -2 4) C 3/G 4 0.21 -0.22 3.42 4.23 5.65 37.22 8 5) G 4/T 5 -0.05 -1.45 3.59 0.61 -2.76 29.69 6 6) T 5/G 6 1.25 -0.20 2.76 20.09 -3.85 39.11 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 16/A 15 1.20 -0.09 3.24 -2.00 11.09 30.48 3 3) A 15/G 14 -0.97 -0.36 3.18 -5.97 7.05 35.42 2 4) G 14/C 13 -0.75 -0.20 3.38 -1.90 3.86 38.09 8 5) C 13/A 12 -0.66 -1.23 3.28 -6.26 4.84 36.21 -6 6) A 12/C 11 0.71 0.11 3.44 2.15 2.56 32.42 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 1/T 2 1.09 -0.57 3.67 -5.58 1.51 36.15 -3 3) T 2/C 3 -0.09 -0.84 2.89 6.53 -2.39 35.50 -2 4) C 3/G 4 -0.27 -0.17 3.42 1.10 4.99 37.76 8 5) G 4/T 5 -0.38 -1.30 3.44 -2.70 1.21 33.33 6 6) T 5/G 6 1.01 -0.06 3.11 11.27 -0.39 35.95 -9 Average: 0.27 -0.59 3.30 2.12 0.99 35.74 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/T 2 0.32 0.00 -3.29 1.08 0.32 3.46 3.71 -3 3) T 2/C 3 -0.19 -0.20 2.15 -2.21 0.27 3.08 2.98 -2 4) C 3/G 4 -0.23 0.19 0.03 2.60 0.30 2.60 3.39 8 5) G 4/T 5 -0.31 -0.33 -1.77 1.91 0.45 2.60 3.39 6 6) T 5/G 6 0.29 0.23 5.02 0.59 0.37 5.06 3.13 -9 Overall axis bend ... UU= 8.52 PP= 12.77 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) T 2 0.31 169.75 3) C 3 0.30 92.20 4) G 4 0.26 -0.28 5) T 5 0.49 18.18 6) G 6 0.00 0.00 Path length= 16.62 End-to-end= 16.53 Shortening= 0.55 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 33.82 -32.40 160.56 35.13 C2'-endo 105.8 102.4 103.4 2)TA 2 -5.22 25.31 47.17 37.90 C4'-exo 108.6 102.7 103.0 3)CA 3 -15.36 28.98 28.02 33.71 C3'-endo 108.8 102.6 102.8 4)GA 4 -18.85 31.63 22.56 35.07 C3'-endo 108.6 102.2 102.8 5)TA 5 -14.41 30.98 32.37 37.42 C3'-endo 108.3 102.3 102.7 6)GA 6 -23.40 38.28 20.67 41.65 C3'-endo 107.3 101.2 101.7 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 -122.98 -64.63 141.80 -160.97 -110.20 -56.31 151.03 2)TA 2 -156.49 58.27 84.51 178.42 -46.40 -154.43 151.18 3)CA 3 -159.98 145.59 89.60 -133.93 -92.03 -63.06 146.04 4)GA 4 -149.27 62.97 89.43 -173.87 -58.71 -79.76 -179.63 5)TA 5 -149.21 61.68 84.62 -164.75 -66.65 -74.36 173.90 6)GA 6 -129.95 55.45 76.26 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 16 32.70 -32.80 164.73 34.74 C2'-endo 105.8 102.7 103.1 2)AB 15 38.78 -33.39 151.34 39.05 C2'-endo 105.1 101.3 103.4 3)GB 14 32.66 -32.38 163.43 34.52 C2'-endo 106.0 102.4 103.5 4)CB 13 29.01 -31.40 171.24 32.39 C2'-endo 106.4 103.1 103.5 5)AB 12 36.03 -35.53 162.98 37.95 C2'-endo 105.5 101.6 103.1 6)CB 11 37.12 -34.60 158.27 38.18 C2'-endo 105.6 101.3 103.2 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 16 -108.45 50.57 145.15 ...... ...... ...... ...... 2)AB 15 -98.30 41.70 137.93 -160.60 -141.17 -62.61 166.06 3)GB 14 -104.00 50.24 140.74 -172.94 -100.02 -55.55 175.20 4)CB 13 -89.61 -56.96 144.40 165.52 -105.43 -45.17 178.04 5)AB 12 -144.48 -176.81 145.31 -156.82 -109.67 37.64 143.82 6)CB 11 -98.90 44.27 143.02 -146.19 -179.78 109.61 -118.86