ID code: 1ZQJ, PDE036 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 20 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 0.044 1 : 2) AA 2 0.142 1 : 3) TA 3 0.052 1 : 4) TA 4 0.216 1 : 5) AA 5 0.199 1 : 6) GA 6 0.116 1 : 7) AA 7 0.230 2 : 1) GB 7 0.184 2 : 2) TB 6 0.313 2 : 3) AB 5 0.287 2 : 4) AB 4 0.076 2 : 5) TB 3 0.139 2 : 6) CB 2 0.144 2 : 7) TB 1 0.194 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= 25.325 CPTS: 2.453 6.709 4.479 11.684 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 25.325 DEL= 0.000E+00 STEP 2 SUM= 17.497 DEL= -0.783E+01 STEP 3 SUM= 39.953 DEL= 0.225E+02 STEP 4 SUM= 15.887 DEL= -0.241E+02 STEP 5 SUM= 14.729 DEL= -0.116E+01 STEP 6 SUM= 13.184 DEL= -0.154E+01 STEP 7 SUM= 13.495 DEL= 0.311E+00 STEP 8 SUM= 12.483 DEL= -0.101E+01 STEP 9 SUM= 11.688 DEL= -0.795E+00 STEP 10 SUM= 10.803 DEL= -0.884E+00 STEP 11 SUM= 10.911 DEL= 0.108E+00 STEP 12 SUM= 10.386 DEL= -0.525E+00 STEP 13 SUM= 10.286 DEL= -0.997E-01 STEP 14 SUM= 10.101 DEL= -0.186E+00 STEP 15 SUM= 9.562 DEL= -0.539E+00 STEP 16 SUM= 19.584 DEL= 0.100E+02 STEP 17 SUM= 9.532 DEL= -0.101E+02 STEP 18 SUM= 9.513 DEL= -0.186E-01 STEP 19 SUM= 9.480 DEL= -0.338E-01 STEP 20 SUM= 9.413 DEL= -0.671E-01 STEP 21 SUM= 9.288 DEL= -0.124E+00 STEP 22 SUM= 9.151 DEL= -0.137E+00 STEP 23 SUM= 9.112 DEL= -0.393E-01 STEP 24 SUM= 9.066 DEL= -0.454E-01 STEP 25 SUM= 9.007 DEL= -0.592E-01 STEP 26 SUM= 8.962 DEL= -0.450E-01 STEP 27 SUM= 8.935 DEL= -0.273E-01 STEP 28 SUM= 8.920 DEL= -0.143E-01 STEP 29 SUM= 8.918 DEL= -0.262E-02 STEP 30 SUM= 8.916 DEL= -0.170E-02 STEP 31 SUM= 8.916 DEL= -0.475E-03 STEP 32 SUM= 8.916 DEL= -0.341E-04 STEP 33 SUM= 8.915 DEL= -0.142E-03 STEP 34 SUM= 8.915 DEL= -0.371E-04 STEP 35 SUM= 8.915 DEL= -0.505E-05 STEP 36 SUM= 8.915 DEL= -0.321E-05 STEP 37 SUM= 8.915 DEL= -0.420E-05 STEP 38 SUM= 8.915 DEL= -0.410E-05 STEP 39 SUM= 8.915 DEL= -0.126E-05 STEP 40 SUM= 8.915 DEL= -0.471E-06 STEP 41 SUM= 8.915 DEL= -0.222E-07 STEP 42 SUM= 8.915 DEL= -0.106E-07 STEP 43 SUM= 8.915 DEL= -0.240E-09 STEP 44 SUM= 8.915 DEL= -0.964E-10 STEP 45 SUM= 8.915 DEL= -0.218E-12 STEP 46 SUM= 8.915 DEL= -0.533E-14 STEP 47 SUM= 8.915 DEL= 0.000E+00 FINAL SUM= 8.915 CPTS: 1.766 5.416 0.653 1.081 GRA=-0.12E-10 0.56E-10-0.27E-10-0.48E-11 0.57E-10-0.22E-10-0.11E-10 0.90E-13 GRA= 0.47E-11-0.38E-10-0.89E-11-0.34E-10-0.12E-09 0.19E-09-0.59E-11 0.14E-10 GRA=-0.52E-10 0.27E-10 0.16E-10 0.49E-11 0.68E-10-0.20E-10 0.75E-11 0.44E-11 GRA=-0.61E-10-0.49E-10 0.12E-10-0.25E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.437 -0.892 -0.114 P: 59.964 35.143 46.879 D: 2.848 2) U: -0.501 -0.854 -0.142 P: 58.441 31.909 46.045 D: 1.010 3) U: -0.473 -0.880 -0.053 P: 56.598 29.270 45.851 D: 1.397 4) U: -0.561 -0.825 -0.067 P: 54.789 26.467 45.961 D: 1.653 5) U: -0.572 -0.813 -0.109 P: 52.939 23.636 45.672 D: 1.270 6) U: -0.614 -0.782 -0.109 P: 50.955 21.368 45.131 D: 0.738 7) U: -0.619 -0.782 -0.073 P: 48.964 18.917 45.041 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.92 0.02 7.60 4.71 3 0 2) AA 2 -1.38 -0.14 2.43 -0.21 2 30 3) TA 3 -1.17 -0.25 7.59 -8.28 4 -24 4) TA 4 -1.66 -0.80 7.38 -7.76 4 -28 5) AA 5 -0.96 -0.44 4.52 -0.58 2 27 6) GA 6 -1.38 -0.86 8.37 1.66 1 4 7) AA 7 -1.69 -0.54 13.53 6.94 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -0.42 0.34 14.85 -6.97 1 0 2) TB 6 -0.88 -0.10 7.87 -7.36 4 -30 3) AB 5 -0.80 0.14 1.48 -3.85 2 24 4) AB 4 -0.64 0.13 4.06 -14.47 2 28 5) TB 3 -1.45 0.29 2.57 -10.60 4 -27 6) CB 2 -0.72 0.35 0.60 -11.46 3 -4 7) TB 1 -0.66 0.48 -5.13 -5.95 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 -0.67 -0.16 11.23 5.84 3 0 2) A 2-T 6 -1.13 -0.02 5.15 3.57 2 30 3) T 3-A 5 -0.99 -0.20 4.54 -2.22 4 -24 4) T 4-A 4 -1.15 -0.47 5.72 3.35 4 -28 5) A 5-T 3 -1.20 -0.37 3.55 5.01 2 27 6) G 6-C 2 -1.05 -0.61 4.48 6.56 1 4 7) A 7-T 1 -1.18 -0.51 4.20 6.44 2 0 Average: -1.05 -0.33 5.55 4.08 --------------------------------- |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 -0.49 0.36 -1.45 -7.25 -2.26 18.86 3 0 2) A 2-T 6 -0.50 -0.24 0.14 -5.45 -7.57 4.08 2 30 3) T 3-A 5 -0.37 -0.11 -0.11 6.11 -12.13 8.84 4 -24 4) T 4-A 4 -1.03 -0.67 0.04 3.31 -22.23 -3.28 4 -28 5) A 5-T 3 0.49 -0.14 0.65 1.95 -11.19 -0.71 2 27 6) G 6-C 2 -0.66 -0.51 0.34 7.78 -9.81 -4.30 1 4 7) A 7-T 1 -1.04 -0.06 0.51 18.66 1.00 0.30 2 0 Average: -0.51 -0.20 0.02 3.59 -9.17 3.40 ---------------------------------- |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 -0.82 0.05 4.45 -8.79 -2.18 19.22 9 3) A 2/T 3 0.52 -0.23 3.09 10.31 -10.14 38.94 7 4) T 3/T 4 -0.59 -0.86 3.40 2.41 5.87 26.12 -4 5) T 4/A 5 0.67 0.44 3.70 -2.80 9.79 42.92 10 6) A 5/G 6 -0.27 -0.71 2.89 6.79 1.53 22.08 3 7) G 6/A 7 -0.50 0.42 3.24 4.04 3.50 30.54 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.82 -0.65 2.85 -10.59 -3.14 34.00 -9 3) T 6/A 5 0.40 0.36 3.34 -1.24 5.58 34.18 7 4) A 5/A 4 0.07 0.30 3.25 5.20 -15.97 38.24 4 5) A 4/T 3 -0.85 0.09 3.09 -1.43 1.25 40.35 10 6) T 3/C 2 0.88 0.34 3.20 0.95 -0.15 25.67 -3 7) C 2/T 1 -0.12 0.04 3.07 -6.85 7.30 25.94 -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 -0.82 0.35 3.65 -9.69 0.48 26.61 9 3) A 2/T 3 0.46 -0.29 3.21 4.54 -7.86 36.56 7 4) T 3/T 4 -0.26 -0.58 3.33 3.80 10.92 32.18 -4 5) T 4/A 5 -0.09 0.18 3.39 -2.12 4.27 41.63 10 6) A 5/G 6 0.30 -0.52 3.05 3.87 0.84 23.88 3 7) G 6/A 7 -0.31 0.19 3.15 -1.41 -1.90 28.24 2 Average: -0.12 -0.11 3.30 -0.17 1.12 31.52 --------------------------------- |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 -0.93 0.11 4.51 -9.16 -0.09 18.56 9 3) A 2/T 3 0.81 -0.76 3.10 12.75 -6.55 38.39 7 4) T 3/T 4 0.16 -1.03 3.68 6.03 9.11 24.66 -4 5) T 4/A 5 1.37 -0.26 3.72 0.38 13.63 42.79 10 6) A 5/G 6 -0.06 -0.85 2.95 6.53 4.01 22.12 3 7) G 6/A 7 -0.40 0.15 3.21 1.64 9.06 30.64 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -1.02 0.77 2.74 -14.61 9.23 31.54 -9 3) T 6/A 5 0.15 -0.53 3.39 -4.14 -2.38 33.95 7 4) A 5/A 4 -0.37 -0.72 3.34 -1.09 17.25 38.65 4 5) A 4/T 3 -1.28 -0.59 2.99 -9.81 1.26 38.96 10 6) T 3/C 2 0.40 -0.73 3.33 -3.90 0.76 25.40 -3 7) C 2/T 1 -0.35 -0.43 3.05 -10.60 -8.11 24.67 -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 -0.95 0.49 3.64 -11.37 4.85 25.37 9 3) A 2/T 3 0.49 -0.62 3.25 4.41 -4.03 36.18 7 4) T 3/T 4 -0.12 -0.88 3.50 2.63 13.30 31.76 -4 5) T 4/A 5 -0.00 -0.45 3.50 -4.68 7.34 41.38 10 6) A 5/G 6 0.19 -0.78 3.10 1.34 2.31 23.89 3 7) G 6/A 7 -0.37 -0.15 3.13 -4.42 0.41 28.40 2 Average: -0.13 -0.40 3.35 -2.01 4.03 31.16 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.36 0.21 -3.62 2.75 0.42 4.54 3.67 9 3) A 2/T 3 0.32 -0.12 5.15 -2.07 0.34 5.55 3.22 7 4) T 3/T 4 -0.10 -0.31 2.62 5.35 0.32 5.95 3.34 -4 5) T 4/A 5 -0.04 0.08 0.06 2.61 0.09 2.61 3.39 10 6) A 5/G 6 0.15 -0.28 2.93 -0.71 0.32 3.02 3.06 3 7) G 6/A 7 -0.18 0.09 -1.12 -1.79 0.20 2.11 3.16 2 Overall axis bend ... UU= 12.46 PP= 17.93 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.75 -24.83 3) T 3 0.64 -59.47 4) T 4 0.59 -45.47 5) A 5 0.64 -86.14 6) G 6 0.34 -149.91 7) A 7 0.00 0.00 Path length= 19.85 End-to-end= 19.69 Shortening= 0.80 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 18.97 -20.40 170.15 21.08 C2'-endo 106.5 104.9 104.6 2)AA 2 7.40 -5.19 134.65 7.58 C1'-exo 108.2 105.9 105.8 3)TA 3 19.52 -9.27 115.70 22.41 C1'-exo 108.7 104.0 106.2 4)TA 4 38.07 -24.12 132.68 38.10 C1'-exo 109.0 100.5 103.8 5)AA 5 3.70 -8.13 213.47 9.99 C3'-exo 109.8 104.2 106.0 6)GA 6 38.94 -27.65 136.29 39.50 C1'-exo 104.5 101.2 104.3 7)AA 7 13.14 -7.18 119.96 14.76 C1'-exo 107.4 104.8 105.9 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 -74.76 166.04 132.87 148.57 -99.96 -73.71 -172.15 2)AA 2 -118.41 68.04 123.20 -176.91 -99.85 -40.36 161.51 3)TA 3 -119.99 48.35 114.14 -151.59 -102.24 -50.48 151.96 4)TA 4 -109.67 51.15 117.87 -172.23 -99.89 -77.70 -177.43 5)AA 5 -121.17 61.71 126.63 -170.32 -82.78 -63.55 173.03 6)GA 6 -103.35 47.16 135.61 -127.44 -175.75 -30.25 123.34 7)AA 7 -106.26 32.43 115.30 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 -4.09 -9.98 245.19 23.99 C4'-endo 107.7 104.8 105.3 2)TB 6 35.26 -33.26 160.98 36.54 C2'-endo 108.0 100.2 103.9 3)AB 5 23.64 -7.08 103.90 30.85 O1'-endo 107.5 104.9 103.6 4)AB 4 0.46 5.30 58.05 10.23 C4'-exo 109.3 104.5 105.9 5)TB 3 31.60 -19.13 126.43 33.39 C1'-exo 107.2 102.1 106.6 6)CB 2 19.86 -12.31 127.28 20.94 C1'-exo 107.6 104.5 105.4 7)TB 1 14.40 -0.86 92.63 23.30 O1'-endo 108.9 105.4 104.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 7 -125.00 -157.92 142.13 ...... ...... ...... ...... 2)TB 6 -125.81 -83.20 150.04 -160.95 -114.98 110.77 -154.68 3)AB 5 -138.37 71.76 92.14 -160.46 -97.43 42.83 -161.01 4)AB 4 -126.45 69.53 108.73 -138.80 -87.01 -64.30 146.07 5)TB 3 -121.46 50.24 117.28 -178.41 -103.55 -71.16 174.91 6)CB 2 -119.81 45.13 113.59 -162.16 -102.27 -51.17 151.86 7)TB 1 -136.16 34.09 102.65 -164.56 -102.85 -29.42 146.99