ID code: 418D, DR0001 *********************************** ************** ****** 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) GA 1 0.024 1 : 2) UA 2 0.015 1 : 3) GA 3 0.029 1 : 4) CA 4 0.033 1 : 5) AA 5 0.030 1 : 6) CA 6 0.018 2 : 1) CB 14 0.020 2 : 2) AB 13 0.017 2 : 3) CB 12 0.017 2 : 4) GB 11 0.027 2 : 5) UB 10 0.028 2 : 6) GB 9 0.038 Strand= 2 Nucleo= 12 Atoms = 250 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'): GUGCAC Strand 2 has 6 bases (3'-5'): CACGUG FIRST SUM= 60.477 CPTS: 1.858 2.280 6.214 50.124 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 24 STEP 1 SUM= 60.477 DEL= 0.000E+00 STEP 2 SUM= 45.899 DEL= -0.146E+02 STEP 3 SUM= 35.282 DEL= -0.106E+02 STEP 4 SUM= 30.369 DEL= -0.491E+01 STEP 5 SUM= 26.351 DEL= -0.402E+01 STEP 6 SUM= 26.598 DEL= 0.247E+00 STEP 7 SUM= 24.401 DEL= -0.220E+01 STEP 8 SUM= 20.894 DEL= -0.351E+01 STEP 9 SUM= 15.180 DEL= -0.571E+01 STEP 10 SUM= 136.025 DEL= 0.121E+03 STEP 11 SUM= 14.734 DEL= -0.121E+03 STEP 12 SUM= 13.922 DEL= -0.812E+00 STEP 13 SUM= 12.332 DEL= -0.159E+01 STEP 14 SUM= 18.326 DEL= 0.599E+01 STEP 15 SUM= 11.798 DEL= -0.653E+01 STEP 16 SUM= 11.964 DEL= 0.166E+00 STEP 17 SUM= 11.567 DEL= -0.397E+00 STEP 18 SUM= 11.185 DEL= -0.382E+00 STEP 19 SUM= 10.585 DEL= -0.600E+00 STEP 20 SUM= 10.380 DEL= -0.205E+00 STEP 21 SUM= 10.018 DEL= -0.362E+00 STEP 22 SUM= 9.507 DEL= -0.511E+00 STEP 23 SUM= 9.140 DEL= -0.367E+00 STEP 24 SUM= 8.574 DEL= -0.566E+00 STEP 25 SUM= 7.973 DEL= -0.601E+00 STEP 26 SUM= 7.604 DEL= -0.369E+00 STEP 27 SUM= 7.515 DEL= -0.889E-01 STEP 28 SUM= 7.417 DEL= -0.979E-01 STEP 29 SUM= 7.411 DEL= -0.556E-02 STEP 30 SUM= 7.412 DEL= 0.939E-03 STEP 31 SUM= 7.409 DEL= -0.336E-02 STEP 32 SUM= 7.408 DEL= -0.478E-03 STEP 33 SUM= 7.408 DEL= -0.405E-03 STEP 34 SUM= 7.408 DEL= -0.913E-04 STEP 35 SUM= 7.408 DEL= -0.641E-04 STEP 36 SUM= 7.408 DEL= -0.804E-04 STEP 37 SUM= 7.408 DEL= -0.823E-04 STEP 38 SUM= 7.408 DEL= -0.298E-04 STEP 39 SUM= 7.408 DEL= -0.171E-05 STEP 40 SUM= 7.408 DEL= -0.284E-06 STEP 41 SUM= 7.408 DEL= -0.394E-07 STEP 42 SUM= 7.408 DEL= -0.578E-08 STEP 43 SUM= 7.408 DEL= -0.533E-09 STEP 44 SUM= 7.408 DEL= -0.145E-10 STEP 45 SUM= 7.408 DEL= -0.490E-12 STEP 46 SUM= 7.408 DEL= -0.444E-14 STEP 47 SUM= 7.408 DEL= 0.000E+00 FINAL SUM= 7.408 CPTS: 1.326 3.036 2.072 0.973 GRA= 0.75E-09 0.31E-09-0.15E-09-0.11E-09-0.21E-09 0.75E-09 0.44E-10-0.12E-09 GRA=-0.13E-08-0.38E-08-0.15E-10 0.53E-09-0.57E-09 0.11E-07 0.35E-09-0.52E-09 GRA=-0.26E-08-0.99E-08-0.22E-09 0.63E-09-0.32E-09 0.16E-08 0.15E-09-0.29E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: 0.796 -0.544 -0.266 P: -2.594 6.419 9.245 D: 1.598 2) U: 0.876 -0.452 -0.170 P: -0.022 4.890 8.828 D: 0.593 3) U: 0.891 -0.411 -0.195 P: 2.040 4.016 8.648 D: 1.030 4) U: 0.890 -0.381 -0.252 P: 4.206 2.969 8.298 D: 2.954 5) U: 0.941 -0.150 -0.303 P: 5.965 2.914 7.597 D: 1.233 6) U: 0.897 -0.237 -0.372 P: 8.661 2.598 6.462 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 1 -4.33 -0.01 13.55 -3.14 1 0 2) UA 2 -4.05 0.10 14.88 -4.81 4 -29 3) GA 3 -4.27 0.35 18.77 -6.72 1 15 4) CA 4 -4.66 0.22 22.85 -14.90 3 -15 5) AA 5 -4.67 -0.05 10.02 -11.97 2 29 6) CA 6 -4.72 -0.50 7.54 -13.65 3 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 14 -3.65 -0.10 16.60 -12.09 3 0 2) AB 13 -4.33 0.15 15.30 -5.99 2 29 3) CB 12 -4.54 0.28 17.51 -3.71 3 -15 4) GB 11 -4.83 0.34 18.71 -6.73 1 15 5) UB 10 -4.28 0.91 25.91 -9.79 4 -29 6) GB 9 -4.12 0.87 20.83 -5.42 1 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) G 1-C 14 -3.99 0.04 15.07 4.47 1 0 2) U 2-A 13 -4.19 -0.03 15.09 0.59 4 -29 3) G 3-C 12 -4.40 0.03 18.14 -1.50 1 15 4) C 4-G 11 -4.75 -0.06 20.78 -4.08 3 -15 5) A 5-U 10 -4.47 -0.48 17.96 -1.09 2 29 6) C 6-G 9 -4.42 -0.69 14.19 -4.12 3 0 Average: -4.37 -0.20 16.87 -0.96 --------------------------------- |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) G 1-C 14 -0.68 -0.11 0.13 -3.05 -15.23 -5.34 1 0 2) U 2-A 13 0.28 0.25 0.62 -0.42 -10.79 7.42 4 -29 3) G 3-C 12 0.27 0.63 0.23 1.27 -10.43 10.45 1 15 4) C 4-G 11 0.17 0.56 0.00 4.13 -21.63 4.58 3 -15 5) A 5-U 10 -0.39 0.86 -0.01 -15.89 -21.77 9.85 2 29 6) C 6-G 9 -0.60 0.38 0.85 -13.29 -19.07 6.57 3 0 Average: -0.16 0.43 0.30 -4.54 -16.49 5.59 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/U 2 0.05 0.02 3.27 -2.74 -9.60 43.04 6 3) U 2/G 3 -0.42 0.42 2.04 1.78 0.08 37.95 -9 4) G 3/C 4 -0.58 -0.03 2.31 5.62 -4.80 30.66 5 5) C 4/A 5 0.44 -0.43 1.84 -10.81 16.66 37.54 9 6) A 5/C 6 0.09 -0.70 3.37 -1.43 -8.46 28.37 -6 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 14/A 13 -0.91 0.35 2.77 -5.36 14.03 30.28 -6 3) A 13/C 12 -0.40 -0.04 2.43 0.09 0.28 34.91 9 4) C 12/G 11 -0.48 -0.04 2.54 2.75 -6.40 36.54 5 5) G 11/U 10 1.01 0.73 1.85 9.21 -16.79 32.26 -9 6) U 10/G 9 0.30 0.22 2.50 -4.03 11.16 31.65 6 --------------------------------------- |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) G 1/U 2 -0.43 -0.16 3.02 -4.05 -11.82 36.66 6 3) U 2/G 3 -0.41 0.23 2.23 0.94 -0.10 36.43 -9 4) G 3/C 4 -0.53 0.00 2.42 4.19 0.80 33.60 5 5) C 4/A 5 0.72 -0.58 1.85 -0.80 16.72 34.90 9 6) A 5/C 6 0.19 -0.46 2.93 -2.73 -9.81 30.01 -6 Average: -0.09 -0.19 2.49 -0.49 -0.84 34.32 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 1/U 2 0.18 -2.33 3.34 0.07 1.09 43.71 6 3) U 2/G 3 -0.29 -1.57 2.78 5.29 11.04 35.44 -9 4) G 3/C 4 -0.13 -1.29 3.34 10.72 5.88 25.96 5 5) C 4/A 5 1.29 -2.56 3.56 -1.78 26.31 33.93 9 6) A 5/C 6 0.89 -2.54 3.13 4.59 -4.10 28.78 -6 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 14/A 13 -1.26 -1.71 2.69 -10.04 -5.31 30.17 -6 3) A 13/C 12 -0.55 -1.82 3.18 -2.92 9.29 32.89 9 4) C 12/G 11 -0.60 -1.97 3.52 -0.56 17.39 34.02 5 5) G 11/U 10 0.72 -1.94 4.13 4.72 27.91 25.90 -9 6) U 10/G 9 0.48 -1.51 2.90 -7.46 2.03 31.02 6 -------------------------------------- |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) G 1/U 2 -0.57 -2.01 3.08 -5.03 -2.07 37.08 6 3) U 2/G 3 -0.41 -1.68 2.99 1.11 10.44 34.24 -9 4) G 3/C 4 -0.37 -1.61 3.45 5.49 11.98 29.98 5 5) C 4/A 5 1.03 -2.23 3.86 1.52 26.90 30.34 9 6) A 5/C 6 0.66 -1.98 3.06 -1.22 -0.56 30.41 -6 Average: 0.07 -1.90 3.29 0.38 9.34 32.41 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G 1/U 2 -0.23 -0.10 -4.06 -7.93 0.25 8.91 3.02 6 3) U 2/G 3 -0.20 0.17 -2.12 1.99 0.26 2.91 2.25 -9 4) G 3/C 4 -0.19 0.10 1.55 3.38 0.21 3.71 2.43 5 5) C 4/A 5 0.45 -0.16 2.02 13.73 0.48 13.88 1.89 9 6) A 5/C 6 0.14 -0.25 1.05 -6.79 0.29 6.87 2.94 -6 Overall axis bend ... UU= 19.60 PP= 27.43 Duplex Offset L.Dir ... wrt end-to-end vector 1) G 1 0.00 0.00 2) U 2 0.67 66.45 3) G 3 0.99 14.25 4) C 4 1.34 -15.91 5) A 5 0.76 -58.46 6) C 6 0.00 0.00 Path length= 12.54 End-to-end= 12.21 Shortening= 2.62 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 1 -29.82 36.70 2.94 37.69 C3'-endo 106.9 101.7 101.8 2)UA 2 -26.85 37.16 11.03 38.69 C3'-endo 107.4 101.4 102.0 3)GA 3 -28.75 39.52 10.45 41.01 C3'-endo 106.9 101.2 101.5 4)CA 4 -29.22 42.12 13.11 43.94 C3'-endo 106.4 100.6 101.1 5)AA 5 -28.63 43.75 16.24 46.12 C3'-endo 106.2 100.1 100.9 6)CA 6 -21.20 37.45 24.42 41.83 C3'-endo 107.3 101.3 101.8 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 1 178.10 118.08 91.69 -165.76 -54.32 -111.16 -151.92 2)UA 2 -159.22 65.94 87.02 -167.29 -63.79 -81.98 -170.01 3)GA 3 -156.33 49.01 82.26 -150.07 -74.73 -79.04 174.14 4)CA 4 -154.73 59.81 79.09 -146.69 -64.94 -69.88 177.33 5)AA 5 -167.42 55.84 75.47 -151.19 -76.04 -35.32 162.50 6)CA 6 -163.62 50.97 81.43 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 14 -20.00 38.74 28.10 44.52 C3'-endo 106.9 101.4 101.1 2)AB 13 -26.10 39.06 15.48 41.27 C3'-endo 107.1 100.8 101.9 3)CB 12 -27.39 40.61 15.36 42.96 C3'-endo 106.9 100.8 101.1 4)GB 11 -24.65 40.48 20.79 44.03 C3'-endo 106.8 101.0 100.9 5)UB 10 -31.68 39.95 3.92 40.87 C3'-endo 106.4 100.7 101.9 6)GB 9 -35.34 38.54 352.07 39.82 C2'-exo 105.9 100.6 102.4 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 14 -161.73 48.43 77.18 ...... ...... ...... ...... 2)AB 13 -166.09 56.16 80.12 -145.08 -82.79 -27.15 141.23 3)CB 12 -161.19 47.17 78.52 -149.63 -77.90 -58.22 164.32 4)GB 11 -159.01 47.42 79.65 -149.10 -73.65 -63.41 176.28 5)UB 10 -153.80 46.28 85.53 -143.74 -72.88 -76.07 -176.46 6)GB 9 -169.10 76.25 90.41 -151.40 -69.42 -64.92 179.69