ID code: 1CA6, PD0120 *********************************** ************** ****** 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) GA 101 0.021 1 : 2) TA 102 0.021 1 : 3) GA 103 0.062 1 : 4) AA 104 0.027 1 : 5) TA 105 0.026 1 : 6) CA 106 0.043 1 : 7) GA 107 0.021 1 : 8) CA 108 0.027 2 : 1) CB 116 0.015 2 : 2) GB 115 0.048 2 : 3) CB 114 0.046 2 : 4) TB 113 0.025 2 : 5) AB 112 0.021 2 : 6) GB 111 0.037 2 : 7) TB 110 0.029 2 : 8) GB 109 0.047 Strand= 2 Nucleo= 16 Atoms = 324 Units = 16 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 8 levels ... Strand 1 has 8 bases (5'-3'): GTGATCGC Strand 2 has 8 bases (3'-5'): CGCTAGTG FIRST SUM= 78.694 CPTS: 5.540 35.180 16.170 21.804 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 32 STEP 1 SUM= 78.694 DEL= 0.000E+00 STEP 2 SUM= 53.691 DEL= -0.250E+02 STEP 3 SUM= 220.028 DEL= 0.166E+03 STEP 4 SUM= 50.803 DEL= -0.169E+03 STEP 5 SUM= 48.891 DEL= -0.191E+01 STEP 6 SUM= 46.231 DEL= -0.266E+01 STEP 7 SUM= 42.784 DEL= -0.345E+01 STEP 8 SUM= 40.173 DEL= -0.261E+01 STEP 9 SUM= 39.108 DEL= -0.107E+01 STEP 10 SUM= 42.346 DEL= 0.324E+01 STEP 11 SUM= 38.897 DEL= -0.345E+01 STEP 12 SUM= 38.502 DEL= -0.395E+00 STEP 13 SUM= 37.292 DEL= -0.121E+01 STEP 14 SUM= 42.425 DEL= 0.513E+01 STEP 15 SUM= 36.983 DEL= -0.544E+01 STEP 16 SUM= 36.525 DEL= -0.459E+00 STEP 17 SUM= 36.384 DEL= -0.140E+00 STEP 18 SUM= 36.262 DEL= -0.123E+00 STEP 19 SUM= 36.050 DEL= -0.211E+00 STEP 20 SUM= 35.823 DEL= -0.227E+00 STEP 21 SUM= 35.335 DEL= -0.488E+00 STEP 22 SUM= 35.514 DEL= 0.179E+00 STEP 23 SUM= 35.129 DEL= -0.385E+00 STEP 24 SUM= 34.754 DEL= -0.375E+00 STEP 25 SUM= 33.970 DEL= -0.784E+00 STEP 26 SUM= 33.157 DEL= -0.813E+00 STEP 27 SUM= 33.616 DEL= 0.459E+00 STEP 28 SUM= 32.947 DEL= -0.669E+00 STEP 29 SUM= 32.778 DEL= -0.169E+00 STEP 30 SUM= 32.672 DEL= -0.105E+00 STEP 31 SUM= 32.635 DEL= -0.374E-01 STEP 32 SUM= 32.621 DEL= -0.138E-01 STEP 33 SUM= 32.615 DEL= -0.674E-02 STEP 34 SUM= 32.612 DEL= -0.221E-02 STEP 35 SUM= 32.612 DEL= -0.574E-03 STEP 36 SUM= 32.612 DEL= -0.180E-03 STEP 37 SUM= 32.611 DEL= -0.220E-03 STEP 38 SUM= 32.611 DEL= -0.292E-03 STEP 39 SUM= 32.611 DEL= -0.165E-03 STEP 40 SUM= 32.611 DEL= -0.589E-04 STEP 41 SUM= 32.611 DEL= -0.178E-04 STEP 42 SUM= 32.611 DEL= -0.836E-05 STEP 43 SUM= 32.611 DEL= -0.331E-05 STEP 44 SUM= 32.611 DEL= -0.112E-05 STEP 45 SUM= 32.611 DEL= -0.360E-06 STEP 46 SUM= 32.611 DEL= -0.668E-07 STEP 47 SUM= 32.611 DEL= -0.652E-08 STEP 48 SUM= 32.611 DEL= -0.349E-09 STEP 49 SUM= 32.611 DEL= -0.130E-10 STEP 50 SUM= 32.611 DEL= -0.220E-12 STEP 51 SUM= 32.611 DEL= 0.000E+00 STEP 52 SUM= 32.611 DEL= 0.000E+00 STEP 53 SUM= 32.611 DEL= -0.711E-14 STEP 54 SUM= 32.611 DEL= 0.000E+00 FINAL SUM= 32.611 CPTS: 4.933 19.875 6.113 1.690 GRA= 0.29E-10 0.80E-10-0.17E-12-0.94E-11-0.11E-09-0.12E-09 0.75E-12 0.84E-11 GRA= 0.17E-10 0.14E-10 0.82E-11 0.50E-11 0.18E-10 0.58E-11 0.36E-11 0.90E-12 GRA= 0.97E-11 0.19E-10-0.55E-11-0.52E-11 0.63E-12-0.27E-10-0.94E-11-0.11E-11 GRA= 0.23E-10 0.45E-10 0.83E-12 0.81E-13-0.21E-10-0.85E-11 0.47E-11-0.14E-11 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.943 -0.321 0.085 P: 17.221 18.645 3.182 D: 4.701 2) U: -0.892 -0.452 0.034 P: 14.357 17.361 3.693 D: 11.815 3) U: -0.960 -0.065 -0.273 P: 10.248 15.934 3.277 D: 1.152 4) U: -0.951 0.035 -0.308 P: 7.501 15.977 2.114 D: 1.381 5) U: -0.954 0.114 -0.277 P: 4.896 16.683 1.446 D: 0.709 6) U: -0.950 0.186 -0.249 P: 1.615 17.153 0.855 D: 6.418 7) U: -0.936 0.238 -0.258 P: -1.865 17.551 -0.257 D: 6.435 8) U: -0.922 0.314 -0.228 P: -4.763 18.460 -1.039 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GA 101 -1.79 0.93 23.65 -3.45 1 0 2) TA 102 -0.55 0.35 28.16 -11.27 4 -29 3) GA 103 -2.08 0.42 16.78 0.15 1 12 4) AA 104 -1.77 0.36 17.43 -2.05 2 22 5) TA 105 -1.68 -0.09 19.76 -4.39 4 -22 6) CA 106 -1.69 -0.04 20.00 -13.37 3 -10 7) GA 107 -2.80 -0.41 12.35 -8.57 1 13 8) CA 108 -1.16 -0.18 14.91 -10.07 3 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CB 116 -1.72 -0.59 20.34 2.30 3 0 2) GB 115 -3.01 -0.55 19.85 9.33 1 13 3) CB 114 -1.89 -0.02 35.57 -12.33 3 -10 4) TB 113 -1.63 -0.21 22.60 -11.00 4 -22 5) AB 112 -1.85 0.20 16.09 -7.98 2 22 6) GB 111 -2.04 -0.07 15.40 -5.06 1 12 7) TB 110 -0.10 -0.15 16.99 7.92 4 -29 8) GB 109 -1.82 0.13 7.20 11.47 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) G101-C116 -1.75 0.76 21.99 -2.87 1 0 2) T102-G115 -1.78 0.45 24.00 -10.30 4 -29 3) G103-C114 -1.98 0.22 26.18 6.24 1 12 4) A104-T113 -1.70 0.28 20.02 4.47 2 22 5) T105-A112 -1.77 -0.14 17.92 1.80 4 -22 6) C106-G111 -1.87 0.02 17.70 -4.16 3 -10 7) G107-T110 -1.45 -0.13 14.67 -8.25 1 13 8) C108-G109 -1.49 -0.16 11.06 -10.77 3 0 Average: -1.72 0.16 19.19 -2.98 --------------------------------- |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) G101-C116 -0.07 0.33 -0.00 3.31 -1.15 5.67 1 0 2) T102-G115 2.46 -0.20 0.12 8.31 -1.94 6.94 4 -29 3) G103-C114 -0.19 0.40 -0.33 -18.79 -12.17 5.66 1 12 4) A104-T113 -0.14 0.15 -0.36 -5.17 -13.05 6.01 2 22 5) T105-A112 0.17 0.11 -0.38 3.68 -12.37 0.04 4 -22 6) C106-G111 0.35 -0.11 -0.38 4.60 -18.43 -0.68 3 -10 7) G107-T110 -2.70 -0.56 -0.44 -4.64 -0.65 -2.41 1 13 8) C108-G109 0.66 -0.06 0.11 7.71 1.40 4.15 3 0 Average: 0.07 0.01 -0.21 -0.12 -7.29 3.17 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G101/T102 1.11 -0.88 3.23 0.23 -15.22 38.17 6 3) T102/G103 -1.81 0.16 4.27 -9.64 40.26 26.57 -9 4) G103/A104 0.63 -0.01 2.96 4.96 2.04 27.26 2 5) A104/T105 -0.06 -0.95 2.73 6.81 -4.34 24.60 7 6) T105/C106 -0.23 0.26 3.35 2.80 -12.59 37.83 -2 7) C106/G107 -0.69 -0.38 3.62 -5.83 2.28 25.80 8 8) G107/C108 1.59 0.21 3.41 0.24 -5.71 42.79 5 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C116/G115 -1.42 0.35 3.11 -4.78 14.43 36.89 5 3) G115/C114 0.84 0.44 4.73 17.46 -50.50 27.85 8 4) C114/T113 0.58 -0.25 2.98 -8.65 -2.92 26.91 -2 5) T113/A112 -0.38 0.91 2.74 -2.04 5.02 30.56 7 6) A112/G111 -0.41 -0.47 3.36 1.87 6.53 38.55 2 7) G111/T110 2.36 -0.07 3.68 3.40 15.51 27.53 -9 8) T110/G109 -1.77 0.29 2.86 -12.11 7.75 36.23 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) G101/T102 -0.15 -0.62 3.17 -2.28 -14.83 37.53 6 3) T102/G103 -0.49 -0.14 4.50 3.91 45.38 27.21 -9 4) G103/A104 0.60 0.12 2.97 -1.85 2.48 27.09 2 5) A104/T105 -0.22 -0.93 2.73 2.39 -4.68 27.58 7 6) T105/C106 -0.32 0.36 3.36 2.34 -9.56 38.19 -2 7) C106/G107 0.84 -0.16 3.65 -1.22 -6.62 26.66 8 8) G107/C108 -0.09 -0.04 3.14 -5.94 -6.73 39.51 5 Average: 0.02 -0.20 3.36 -0.38 0.78 31.97 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G101/T102 0.98 -0.13 3.34 4.30 2.49 37.17 6 3) T102/G103 -1.41 1.41 5.24 -7.50 47.84 14.70 -9 4) G103/A104 0.47 0.03 3.26 5.59 9.64 24.81 2 5) A104/T105 0.03 -0.72 3.07 8.04 3.48 23.61 7 6) T105/C106 0.31 0.34 3.34 8.34 0.73 35.95 -2 7) C106/G107 0.21 -0.39 3.80 -0.70 9.40 26.18 8 8) G107/C108 2.18 -0.48 3.20 6.77 4.37 42.06 5 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C116/G115 -1.36 -0.79 3.40 -0.59 -1.40 37.49 5 3) G115/C114 0.46 1.18 6.83 19.33 59.07 12.54 8 4) C114/T113 -0.01 0.99 3.11 -12.86 15.51 19.33 -2 5) T113/A112 -0.82 -0.85 3.06 -6.55 5.29 28.79 7 6) A112/G111 -0.72 0.05 3.28 -2.36 4.02 38.07 2 7) G111/T110 2.32 0.65 3.58 4.01 -7.45 27.12 -9 8) T110/G109 -1.13 -0.26 3.20 -5.39 -0.02 37.86 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) G101/T102 -0.21 -0.40 3.36 1.77 0.65 37.38 6 3) T102/G103 -0.46 1.23 5.89 5.82 53.39 13.82 -9 4) G103/A104 0.25 0.53 3.21 -3.48 13.05 22.31 2 5) A104/T105 -0.40 -0.78 3.08 0.77 4.56 26.29 7 6) T105/C106 -0.21 0.19 3.35 3.01 2.37 37.23 -2 7) C106/G107 1.24 0.14 3.57 1.75 1.00 26.66 8 8) G107/C108 0.53 -0.37 3.15 0.68 2.20 39.93 5 Average: 0.11 0.08 3.66 1.48 11.03 29.09 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) G101/T102 -0.13 -0.30 -4.29 -7.40 0.33 8.55 3.18 6 3) T102/G103 -0.28 0.09 1.74 28.84 0.30 28.90 4.37 -9 4) G103/A104 0.32 0.05 4.31 4.25 0.32 6.05 2.98 2 5) A104/T105 -0.15 -0.50 4.48 -2.01 0.52 4.91 2.78 7 6) T105/C106 -0.23 0.20 2.56 -3.61 0.30 4.42 3.37 -2 7) C106/G107 0.42 -0.01 1.81 -2.53 0.42 3.11 3.67 8 8) G107/C108 -0.05 -0.01 -2.32 -4.21 0.05 4.81 3.14 5 Overall axis bend ... UU= 41.50 PP= 47.55 Duplex Offset L.Dir ... wrt end-to-end vector 1) G101 0.00 0.00 2) T102 1.64 7.84 3) G103 3.00 -26.98 4) A104 2.70 -64.75 5) T105 1.96 -87.49 6) C106 1.51 -118.07 7) G107 0.96 -155.94 8) C108 0.00 0.00 Path length= 23.49 End-to-end= 22.39 Shortening= 4.70 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GA 101 22.74 -35.15 198.06 37.71 C3'-exo 106.7 103.2 101.6 2)TA 102 -8.89 22.44 37.36 28.76 C4'-exo 107.4 105.1 103.5 3)GA 103 20.08 -27.45 189.74 28.30 C3'-exo 106.6 104.3 103.8 4)AA 104 20.44 1.68 87.53 38.31 O1'-endo 105.2 105.2 103.5 5)TA 105 24.55 -7.21 103.09 33.22 O1'-endo 105.7 104.9 104.6 6)CA 106 28.84 -26.28 154.66 29.50 C2'-endo 105.4 104.0 104.4 7)GA 107 36.04 -20.63 123.60 38.70 C1'-exo 105.0 102.8 104.3 8)CA 108 33.57 -21.21 128.45 35.08 C1'-exo 105.0 103.6 104.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GA 101 -99.02 169.14 158.71 -166.95 -103.83 -38.69 171.33 2)TA 102 -110.30 7.23 95.79 -171.58 -81.06 -81.92 -150.44 3)GA 103 -87.40 63.15 147.73 -178.59 -81.37 -87.87 174.87 4)AA 104 -106.73 59.68 99.09 165.68 -95.78 -29.59 165.02 5)TA 105 -116.15 34.23 110.30 -176.90 -113.81 -37.69 161.37 6)CA 106 -105.81 51.40 132.29 -165.51 -98.38 -49.10 169.02 7)GA 107 -106.17 31.77 121.98 -176.58 -96.02 -60.75 156.78 8)CA 108 -127.86 74.34 -2.72 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CB 116 7.36 13.22 67.39 35.09 C4'-exo 106.4 106.0 102.9 2)GB 115 31.92 -30.48 159.79 33.15 C2'-endo 106.0 102.7 103.8 3)CB 114 -0.63 20.82 54.37 36.62 C4'-exo 106.6 105.4 102.1 4)TB 113 17.75 2.39 86.06 34.72 O1'-endo 105.5 105.7 103.9 5)AB 112 35.49 -37.25 168.80 38.85 C2'-endo 105.8 101.2 102.4 6)GB 111 26.82 -36.25 189.23 37.48 C3'-exo 106.6 102.1 102.1 7)TB 110 37.96 -36.11 160.08 39.34 C2'-endo 105.2 101.2 102.8 8)GB 109 24.69 -36.20 194.89 38.24 C3'-exo 106.6 102.6 101.5 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CB 116 -131.52 48.88 78.64 ...... ...... ...... ...... 2)GB 115 -92.20 66.39 138.80 176.73 -96.66 -54.38 167.58 3)CB 114 -104.50 29.65 92.57 -166.66 -78.62 -89.29 -157.88 4)TB 113 -108.06 7.37 95.63 -149.60 -109.10 -44.77 149.69 5)AB 112 -95.43 52.62 148.20 -154.93 -124.79 -22.42 145.25 6)GB 111 -83.47 7.09 161.17 174.59 -114.96 -55.60 175.60 7)TB 110 -85.20 47.80 148.98 -83.51 148.63 -54.92 159.96 8)GB 109 -85.52 149.26 159.61 156.67 -89.22 -71.62 -157.24