ID code: 1ZQB, PDE028 C ********************************************************************* C FREEHEL98.FOR 1 June 1998 C This is the Fortran program code for helix analysis program FREEHELIX. C For operating instructions, see the separate file FREEHEL98.TEX. This C program is radically changed from the earlier NEWHELIX, deleting the C old RADJ and TADJ, and adding the helix-independent parameters VALL C (total bending), VROL (roll), VTIL (tilt), VTWI (twist), VSLI (slide), C VRIS (rise) and VSHF (shift). This program can be used with DNA C helices of any degree of bending. C Richard E. Dickerson, Oxford C ********************************************************************* TITL CELL 1., 1., 1., 90., 90., 90. BRKH FPUN 0 PMIN 0 PMAX 0 BASE 7 HELX RC1' YC1' HELX RN9 YN1 BROL CYLN TRNG END 1 INPUT FRAC.COORDS. X,Y,Z AND ATOM NAME IN FORMAT: (T31,3F8.3,T20,A1,T25,2A1,T14,3A1) WILL READ 281 ATOMS: PRINT FLAG= 0 CELL CONSTANTS A,B,C,ALPHA,BETA,GAMMA ARE: 1.000 1.000 1.000 90.000 90.000 90.000 COORDINATES IN ORTHONORMAL SYSTEM: PRINT FLAG= 0 ************************************** ATOM PAIRS USED TO DETERMINE THE HELIX AXIS ARE: 8 C01C1' 27 A02C1' 27 A02C1' 48 T03C1' 48 T03C1' 68 T04C1' 68 T04C1' 88 A05C1' 88 A05C1' 109 G06C1' 109 G06C1' 131 A07C1' 169 C02C1' 149 T01C1' 188 T03C1' 169 C02C1' 208 A04C1' 188 T03C1' 229 A05C1' 208 A04C1' 250 T06C1' 229 A05C1' 270 G07C1' 250 T06C1' 9 C01N1 28 A02N9 28 A02N9 49 T03N1 49 T03N1 69 T04N1 69 T04N1 89 A05N9 89 A05N9 110 G06N9 110 G06N9 132 A07N9 170 C02N1 150 T01N1 189 T03N1 170 C02N1 209 A04N9 189 T03N1 230 A05N9 209 A04N9 251 T06N1 230 A05N9 271 G07N9 251 T06N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.55772*S + 20.78273 Y = 0.81588*S + -21.01094 Z = 0.15261*S + 36.37706 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.55772*S + 20.78273 Y = 0.81588*S + -21.01094 Z = 0.15261*S + 36.37706 >>>>>> HELIX ROTATION: 31.943 DISPLACEMENT: 3.3955 STATISTICS: OVERALL STANDARD DEV.: 0.7200 SIGMA(X): 0.8270, SIGMA(Y): 0.8056, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.2376, SIGMA(ROTATION): 6.303 THERE ARE 11.27 RESIDUES PER TURN ***************************************************** THE FOLLOWING DIAMOND LIST HAS BEEN OUTPUT ON UNIT: 12 NORMAL END OF JOB: YOU HAVE GIVEN BIRTH TO A HELIX NUMBER BASE PAIRS = 7 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.15705 0.21407 0.96411 99.04 77.64 15.40 -0.10306 0.18936 0.97649 95.92 79.08 12.45 -0.17803 0.15095 0.97238 100.25 81.32 13.50 -0.07903 -0.06595 0.99469 94.53 93.78 5.91 -0.00957 -0.09900 0.99504 90.55 95.68 5.71 0.02491 -0.15132 0.98817 88.57 98.70 8.82 0.09242 -0.17470 0.98028 84.70 100.06 11.40 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.15327 0.25899 0.95364 98.82 74.99 17.51 -0.18968 -0.01442 0.98174 100.93 90.83 10.97 -0.14725 -0.21081 0.96637 98.47 102.17 14.90 -0.00957 -0.18186 0.98328 90.55 100.48 10.49 0.10215 -0.21290 0.97172 84.14 102.29 13.66 0.29926 0.00018 0.95417 72.59 89.99 17.41 0.01685 -0.01251 0.99978 89.03 90.72 1.20 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.09735 0.15849 0.98255 95.59 80.88 10.72 -0.16601 0.07101 0.98356 99.56 85.93 10.40 -0.20798 -0.02414 0.97784 102.00 91.38 12.09 -0.06773 -0.14873 0.98655 93.88 98.55 9.41 0.06038 -0.19506 0.97893 86.54 101.25 11.78 0.16812 -0.12000 0.97843 80.32 96.89 11.92 0.09347 -0.12072 0.98828 84.64 96.93 8.78 1 I= 1 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 2 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 3 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 4 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 5 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 6 PS= 90.0000 LS= 90.0000 PL= 90.0000 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 I= 1 0 6 12 17 22 22 19 I= 2 6 0 5 13 20 22 18 I= 3 12 5 0 10 18 22 18 I= 4 17 13 10 0 7 13 9 I= 5 22 20 18 7 0 7 4 I= 6 22 22 22 13 7 0 4 I= 7 19 18 18 9 4 4 0 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 ROLL AND TILT ANGLES STRAND 2 ROLL AND TILT ANGLES TIP INCL ROLL TILT RADJ TADJ TIP INCL ROLL TILT RADJ TADJ -3.56 14.96 -0.12 -3.40 0.00 0.00 -5.67 16.51 15.11 -5.18****** 0.00 -8.52 9.01 2.17 4.31 0.00 0.00 4.16 10.13 11.34 -2.36 0.00 0.00 -11.84 6.39 12.92 4.76****** 0.00 8.23 12.33 4.40 -6.78 0.00 0.00 -1.87 5.60 4.35 0.72 0.00 0.00 5.00 9.20 6.66 -0.06 0.00 0.00 -0.59 5.68 1.09 3.42-27.35 0.00 5.77 12.34 14.32 -8.74 0.00 0.50 -2.85 8.34 2.08 3.53 0.00 0.00 15.29 8.13-12.92 -9.96 0.00 0.00 -5.85 9.75 0.00 0.00****** 0.00 -0.12 1.20 0.00 0.00 0.00 0.00 BEST PLANE THROUGH BOTH BASES VALL VTIL VROL VSLI VTWI VRIS VSHF INCL TIP TILT ROLL SLIDE CUP PROP BUCK X DSP Y DSP 6.37 -0.97 6.30 0.20 21.78 3.58 -0.60 10.17 -3.34 1.26 6.26 0.28 -0.56 2.13 1.59 -0.89 0.25 5.97 2.57 5.39 -0.20 38.56 3.29 0.09 10.36 -0.92 2.44 5.44 -0.17 4.80 -12.68 1.03 -1.53 0.30 10.78 -1.66 10.65 -0.36 36.60 3.29 -0.01 11.69 -3.03 -0.66 10.79 -0.29 -2.20 -20.11 5.83 -1.27 0.44 7.82 0.65 7.80 0.04 31.61 3.43 -0.15 9.33 1.16 0.52 7.81 0.07 3.09 -6.88 3.63 -1.11 0.30 7.53 -2.59 7.07 -0.22 27.29 3.35 0.20 11.27 3.38 -2.47 7.12 -0.17 -6.54 -6.37 6.71 -0.94 0.33 4.32 -2.98 -3.12 0.81 30.20 3.73 -0.50 10.68 5.24 -2.74 -3.29 0.78 -8.77 -18.16 0.18 -0.45 -0.17 - - - - - - - 8.18 -3.16 - - - - -5.74 -8.59 -0.88 0.33 NOTE: Angles are calculated from 5" end to 3" end of strand 1, and signs of angles also are calculated with respect to strand 1. To examine individual strand 2 bases w.r.t. strand 2, reverse signs of Tip and Tilt. For Z-DNA, reverse signs of Incl and X Dsp. Y Dsp is correct as printed. ROLL and TILT are the simple components of base pair normals along minor and major axes of base pairs. They are the values that were calculated in NEWHEL90 and earlier. VALL, VTIL, VROL, VSLI and VTWI are the total angle betw een base pair normal vectors, and the Tilt, Roll, Slide and Twist calculated relative to a set of local axes halfway between each of the long axes, the short axes, and normal vectors for the two base pairs. They are completely independent of the choice of overall helix axis.