ID code: 1ZQI, PDE035 *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 18 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 0.040 1 : 2) AA 2 0.026 1 : 3) TA 3 0.047 1 : 4) TA 4 0.167 1 : 5) AA 5 0.043 1 : 6) GA 6 0.172 1 : 7) AA 7 0.199 2 : 1) GB 7 0.148 2 : 2) TB 6 0.164 2 : 3) AB 5 0.192 2 : 4) AB 4 0.035 2 : 5) TB 3 0.175 2 : 6) CB 2 0.184 2 : 7) TB 1 0.274 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= 19.112 CPTS: 1.412 5.845 2.483 9.372 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 28 STEP 1 SUM= 19.112 DEL= 0.000E+00 STEP 2 SUM= 13.117 DEL= -0.600E+01 STEP 3 SUM= 29.630 DEL= 0.165E+02 STEP 4 SUM= 11.856 DEL= -0.178E+02 STEP 5 SUM= 12.454 DEL= 0.598E+00 STEP 6 SUM= 11.346 DEL= -0.111E+01 STEP 7 SUM= 10.649 DEL= -0.697E+00 STEP 8 SUM= 10.281 DEL= -0.368E+00 STEP 9 SUM= 9.805 DEL= -0.476E+00 STEP 10 SUM= 9.126 DEL= -0.680E+00 STEP 11 SUM= 17.073 DEL= 0.795E+01 STEP 12 SUM= 9.083 DEL= -0.799E+01 STEP 13 SUM= 9.001 DEL= -0.813E-01 STEP 14 SUM= 8.660 DEL= -0.341E+00 STEP 15 SUM= 8.312 DEL= -0.348E+00 STEP 16 SUM= 8.667 DEL= 0.355E+00 STEP 17 SUM= 8.196 DEL= -0.470E+00 STEP 18 SUM= 8.270 DEL= 0.737E-01 STEP 19 SUM= 8.152 DEL= -0.117E+00 STEP 20 SUM= 8.076 DEL= -0.761E-01 STEP 21 SUM= 7.986 DEL= -0.904E-01 STEP 22 SUM= 8.863 DEL= 0.877E+00 STEP 23 SUM= 7.963 DEL= -0.900E+00 STEP 24 SUM= 7.922 DEL= -0.411E-01 STEP 25 SUM= 7.854 DEL= -0.682E-01 STEP 26 SUM= 7.803 DEL= -0.511E-01 STEP 27 SUM= 7.723 DEL= -0.800E-01 STEP 28 SUM= 7.610 DEL= -0.112E+00 STEP 29 SUM= 7.537 DEL= -0.730E-01 STEP 30 SUM= 7.507 DEL= -0.305E-01 STEP 31 SUM= 7.500 DEL= -0.649E-02 STEP 32 SUM= 7.491 DEL= -0.958E-02 STEP 33 SUM= 7.486 DEL= -0.436E-02 STEP 34 SUM= 7.483 DEL= -0.312E-02 STEP 35 SUM= 7.484 DEL= 0.310E-03 STEP 36 SUM= 7.483 DEL= -0.375E-03 STEP 37 SUM= 7.483 DEL= -0.346E-04 STEP 38 SUM= 7.483 DEL= -0.816E-05 STEP 39 SUM= 7.483 DEL= -0.129E-04 STEP 40 SUM= 7.483 DEL= -0.167E-04 STEP 41 SUM= 7.483 DEL= -0.516E-05 STEP 42 SUM= 7.483 DEL= -0.355E-06 STEP 43 SUM= 7.483 DEL= 0.107E-07 STEP 44 SUM= 7.483 DEL= -0.282E-07 STEP 45 SUM= 7.483 DEL= -0.586E-08 STEP 46 SUM= 7.483 DEL= -0.749E-09 STEP 47 SUM= 7.483 DEL= -0.555E-12 STEP 48 SUM= 7.483 DEL= -0.137E-12 STEP 49 SUM= 7.483 DEL= -0.266E-14 STEP 50 SUM= 7.483 DEL= 0.000E+00 FINAL SUM= 7.483 CPTS: 0.930 5.092 0.267 1.194 GRA=-0.12E-08 0.83E-09 0.18E-09-0.16E-09-0.21E-08-0.10E-08 0.22E-09-0.45E-09 GRA= 0.19E-08 0.27E-08-0.47E-09 0.58E-09-0.21E-08 0.73E-09-0.12E-09-0.12E-09 GRA= 0.20E-08 0.30E-09-0.14E-09 0.56E-09 0.55E-10 0.36E-08 0.25E-10 0.56E-10 GRA=-0.75E-09-0.36E-08-0.16E-10-0.14E-09 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.479 -0.865 -0.149 P: 60.184 35.283 47.551 D: 2.133 2) U: -0.552 -0.823 -0.138 P: 58.446 31.991 46.666 D: 1.538 3) U: -0.570 -0.814 -0.110 P: 56.309 29.549 46.535 D: 0.818 4) U: -0.605 -0.786 -0.126 P: 54.443 27.056 46.425 D: 0.719 5) U: -0.630 -0.761 -0.154 P: 52.252 24.228 45.865 D: 1.913 6) U: -0.626 -0.766 -0.147 P: 50.198 22.066 45.174 D: 0.362 7) U: -0.629 -0.768 -0.124 P: 48.073 19.408 44.890 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -0.60 0.93 14.96 1.67 3 0 2) AA 2 -1.16 0.71 8.58 -1.60 2 30 3) TA 3 -1.36 0.53 5.10 -7.82 4 -24 4) TA 4 -1.30 -0.00 8.05 -3.38 4 -28 5) AA 5 -0.73 0.17 4.64 -2.22 2 27 6) GA 6 -1.31 -0.17 8.63 -2.03 1 4 7) AA 7 -1.26 0.10 12.80 1.39 2 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 7 -1.02 -0.37 13.83 -3.21 1 0 2) TB 6 -1.36 -0.83 11.88 -6.85 4 -30 3) AB 5 -0.63 -0.47 8.00 -8.71 2 24 4) AB 4 -0.96 -0.54 5.36 -7.32 2 28 5) TB 3 -1.41 -0.42 9.11 -6.82 4 -27 6) CB 2 -0.39 -0.28 3.47 -9.23 3 -4 7) TB 1 -0.58 -0.34 0.33 -5.61 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 -0.81 0.65 14.39 2.44 3 0 2) A 2-T 6 -1.26 0.77 10.23 2.62 2 30 3) T 3-A 5 -1.00 0.50 6.55 0.44 4 -24 4) T 4-A 4 -1.13 0.27 6.71 1.97 4 -28 5) A 5-T 3 -1.07 0.30 6.88 2.30 2 27 6) G 6-C 2 -0.85 0.06 6.05 3.60 1 4 7) A 7-T 1 -0.92 0.22 6.56 3.50 2 0 Average: -1.01 0.39 8.20 2.41 --------------------------------- |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 0.42 0.56 -1.13 1.13 -1.54 14.37 3 0 2) A 2-T 6 0.20 -0.12 -0.12 -3.30 -8.45 1.84 2 30 3) T 3-A 5 -0.73 0.06 0.19 -2.90 -16.53 10.25 4 -24 4) T 4-A 4 -0.34 -0.54 -0.19 2.69 -10.70 -2.63 4 -28 5) A 5-T 3 0.68 -0.25 -0.30 -4.47 -9.04 -0.26 2 27 6) G 6-C 2 -0.92 -0.45 -0.04 5.17 -11.26 -3.31 1 4 7) A 7-T 1 -0.68 -0.24 0.04 12.47 -4.22 -2.73 2 0 Average: -0.20 -0.14 -0.22 1.54 -8.82 2.50 ---------------------------------- |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 -0.92 -0.03 4.31 -8.04 1.32 20.28 9 3) A 2/T 3 0.18 -0.45 3.37 -1.89 -5.09 33.72 7 4) T 3/T 4 -0.05 -0.76 2.92 3.66 7.07 33.30 -4 5) T 4/A 5 0.61 0.24 3.56 -1.90 3.28 41.74 10 6) A 5/G 6 -0.40 -0.61 3.17 3.55 -0.06 18.14 3 7) G 6/A 7 -0.06 0.42 3.45 3.36 2.35 32.65 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -0.70 -0.65 3.30 -3.61 -8.23 32.81 -9 3) T 6/A 5 1.11 0.63 3.06 -2.29 -2.99 25.31 7 4) A 5/A 4 -0.45 0.16 3.29 -1.94 -1.25 46.18 4 5) A 4/T 3 -0.41 0.05 3.68 5.27 -1.61 39.38 10 6) T 3/C 2 1.20 0.40 2.91 -6.09 -2.16 21.19 -3 7) C 2/T 1 -0.30 -0.21 3.37 -3.94 4.69 32.07 -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 -0.81 0.31 3.81 -5.82 4.77 26.54 9 3) A 2/T 3 0.65 -0.54 3.21 -2.09 -1.05 29.51 7 4) T 3/T 4 -0.25 -0.46 3.11 0.86 4.16 39.74 -4 5) T 4/A 5 0.10 0.09 3.62 1.69 2.44 40.56 10 6) A 5/G 6 0.40 -0.50 3.04 -1.27 1.05 19.67 3 7) G 6/A 7 -0.18 0.31 3.41 -0.29 -1.17 32.36 2 Average: -0.02 -0.13 3.37 -1.15 1.70 31.40 --------------------------------- |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 -1.17 0.59 4.36 -7.63 5.48 18.92 9 3) A 2/T 3 0.12 -0.74 3.53 1.02 -0.96 33.37 7 4) T 3/T 4 0.05 -1.19 3.14 6.82 10.59 32.42 -4 5) T 4/A 5 0.71 -0.13 3.61 0.27 7.72 41.35 10 6) A 5/G 6 -0.29 -0.56 3.27 4.16 2.01 17.92 3 7) G 6/A 7 -0.07 0.27 3.44 3.42 8.20 32.36 2 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 7/T 6 -1.28 0.64 3.25 -6.62 15.04 30.76 -9 3) T 6/A 5 0.41 -0.51 3.31 -5.58 7.34 24.24 7 4) A 5/A 4 -1.21 -0.42 3.29 -8.01 6.57 44.95 4 5) A 4/T 3 -1.18 -0.39 3.69 0.36 6.47 39.18 10 6) T 3/C 2 0.65 -0.43 3.09 -8.89 4.41 20.10 -3 7) C 2/T 1 -0.85 0.07 3.29 -7.92 -3.47 31.39 -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 -1.24 0.62 3.80 -6.77 10.20 24.88 9 3) A 2/T 3 0.26 -0.63 3.39 -2.06 3.36 29.04 7 4) T 3/T 4 -0.55 -0.78 3.26 -0.68 8.84 38.87 -4 5) T 4/A 5 -0.23 -0.27 3.72 0.32 7.10 40.42 10 6) A 5/G 6 0.17 -0.48 3.12 -2.38 3.12 19.05 3 7) G 6/A 7 -0.46 0.16 3.37 -2.13 2.23 32.25 2 Average: -0.34 -0.23 3.45 -2.28 5.81 30.75 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 -0.36 0.19 -1.66 4.59 0.41 4.88 3.83 9 3) A 2/T 3 0.38 -0.27 1.59 1.13 0.47 1.95 3.25 7 4) T 3/T 4 -0.12 -0.23 0.71 2.63 0.26 2.72 3.12 -4 5) T 4/A 5 0.04 0.06 1.52 2.12 0.08 2.60 3.62 10 6) A 5/G 6 0.18 -0.26 -0.45 -0.26 0.32 0.52 3.06 3 7) G 6/A 7 -0.11 0.15 -0.80 -1.07 0.18 1.34 3.41 2 Overall axis bend ... UU= 10.37 PP= 13.70 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.73 -17.95 3) T 3 0.41 -32.53 4) T 4 0.47 -26.49 5) A 5 0.42 -76.86 6) G 6 0.18 -177.59 7) A 7 0.00 0.00 Path length= 20.29 End-to-end= 20.14 Shortening= 0.71 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 12.54 -27.56 214.16 34.35 C3'-exo 108.8 104.0 101.5 2)AA 2 32.44 -26.37 145.79 32.64 C2'-endo 105.7 102.8 104.5 3)TA 3 42.17 -24.32 124.02 45.48 C1'-exo 103.9 100.2 104.9 4)TA 4 51.87 -31.89 128.10 53.89 C1'-exo 100.2 99.3 101.4 5)AA 5 18.27 -28.34 200.15 31.67 C3'-exo 110.3 100.9 103.2 6)GA 6 39.10 -32.33 146.30 39.63 C2'-endo 105.4 100.3 106.0 7)AA 7 20.88 -18.44 155.78 21.08 C2'-endo 110.1 103.3 105.4 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 -51.79 165.71 155.20 136.21 -99.21 -74.11 -169.79 2)AA 2 -98.97 71.71 131.59 160.32 -108.53 -56.56 176.53 3)TA 3 -120.07 63.47 126.16 -158.82 -113.54 -41.89 153.09 4)TA 4 -123.27 47.61 117.56 -170.91 -98.57 -64.21 -161.31 5)AA 5 -104.09 42.08 147.53 179.93 -89.87 -88.38 -172.54 6)GA 6 -101.22 58.85 137.22 -107.39 177.24 -27.63 127.99 7)AA 7 -84.23 9.76 126.61 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 7 -6.99 -11.43 248.07 31.20 C4'-endo 107.6 105.3 103.6 2)TB 6 35.06 -39.76 178.81 41.52 C2'-endo 108.3 100.0 100.6 3)AB 5 33.67 -20.69 127.67 35.18 C1'-exo 105.4 103.0 103.1 4)AB 4 46.61 -28.18 125.54 49.94 C1'-exo 100.5 100.3 103.6 5)TB 3 49.69 -32.76 131.47 51.38 C1'-exo 101.6 98.4 103.3 6)CB 2 29.40 -36.70 182.51 37.21 C3'-exo 104.1 103.5 101.7 7)TB 1 24.98 2.92 86.76 47.29 O1'-endo 105.7 102.3 104.2 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 7 -109.30 -98.39 146.98 ...... ...... ...... ...... 2)TB 6 -109.16 -92.17 154.95 -145.43 -124.80 56.54 -159.85 3)AB 5 -106.70 9.87 113.58 166.06 -99.71 76.70 171.77 4)AB 4 -126.00 56.21 126.76 -152.52 -111.34 -28.25 165.35 5)TB 3 -96.32 50.20 126.60 -171.78 -128.48 -47.67 154.68 6)CB 2 -102.52 29.15 145.19 -170.54 -110.65 -63.48 169.23 7)TB 1 -140.54 51.00 91.24 -163.15 -91.56 -30.30 173.21