ID code: 2V7R 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 293 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: 9 G01C1' 32 C02C1' 32 C02C1' 52 G03C1' 52 G03C1' 115 G06C1' 115 G06C1' 138 G07C1' 138 G07C1' 158 C66C1' 198 A68C1' 178 C67C1' 220 A69C1' 198 A68C1' 242 C70C1' 220 A69C1' 262 G71C1' 242 C70C1' 285 C72C1' 262 G71C1' 10 G01N9 33 C02N1 33 C02N1 53 G03N9 53 G03N9 116 G06N9 116 G06N9 139 G07N9 139 G07N9 159 C66N1 199 A68N9 179 C67N1 221 A69N9 199 A68N9 243 C70N1 221 A69N9 263 G71N9 243 C70N1 286 C72N1 263 G71N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.75466*S + -3.92163 Y = 0.42183*S + 9.32110 Z = 0.50254*S + -1.93493 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.75466*S + -3.92163 Y = 0.42183*S + 9.32110 Z = 0.50254*S + -1.93493 >>>>>> HELIX ROTATION: 43.659 DISPLACEMENT: 1.6013 STATISTICS: OVERALL STANDARD DEV.: 4.0041 SIGMA(X): 2.1155, SIGMA(Y): 2.3767, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.8695, SIGMA(ROTATION): 23.023 THERE ARE 8.25 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 -0.55960 -0.22593 0.79737 124.03 103.06 37.12 -0.61847 -0.19765 0.76054 128.20 101.40 40.49 -0.54397 -0.39059 0.74266 122.95 112.99 42.04 -0.50858 -0.51287 0.69160 120.57 120.86 46.24 -0.34767 -0.58465 0.73302 110.34 125.78 42.86 -0.23599 -0.56720 0.78905 103.65 124.56 37.90 -0.12585 -0.48015 0.86811 97.23 118.70 29.76 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.58332 -0.29342 0.75739 125.68 107.06 40.76 -0.50840 -0.37722 0.77411 120.56 112.16 39.28 -0.38378 -0.58059 0.71807 112.57 125.49 44.10 -0.16972 -0.66866 0.72394 99.77 131.96 43.62 -0.16337 -0.59469 0.78718 99.40 126.49 38.08 -0.09498 -0.50337 0.85883 95.45 120.22 30.81 -0.07877 -0.40032 0.91298 94.52 113.60 24.08 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.57912 -0.25130 0.77554 125.39 104.55 39.15 -0.55529 -0.29640 0.77705 123.73 107.24 39.01 -0.47128 -0.46674 0.74837 118.12 117.82 41.55 -0.34519 -0.57764 0.73972 110.19 125.28 42.29 -0.26164 -0.59373 0.76094 105.17 126.42 40.45 -0.19376 -0.53122 0.82478 101.17 122.09 34.43 -0.11322 -0.44423 0.88873 96.50 116.37 27.29 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 2 13 23 27 27 29 I= 2 2 0 11 20 24 25 27 I= 3 13 11 0 9 14 16 22 I= 4 23 20 9 0 5 10 17 I= 5 27 24 14 5 0 6 14 I= 6 27 25 16 10 6 0 7 I= 7 29 27 22 17 14 7 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 31.05 18.26 -1.09 3.58 0.00****** 35.74 16.97 4.10 -4.97 0.00 0.00 13.49 37.30 11.92 0.56 0.00 0.00 23.96 29.05 13.67 -1.82 0.00 0.00 -0.18 42.04 5.46 4.86 0.00****** 14.16 40.66 13.18 -2.26****** 0.00 -23.93 36.70 9.56 3.39 0.00 0.00 -2.51 43.51 0.03 -4.26 0.00 0.00 -35.83 20.27 6.06 2.31 0.00****** -25.37 26.33 6.01 -2.60****** 0.00 -36.94 7.33 7.10 3.82 0.00 0.00 -27.93 11.98 5.80 -1.49 0.00 0.00 -29.55 -3.22 0.00 0.00************ -24.05 -1.20 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 2.92 -1.96 2.17 -1.79 31.92 3.37 -0.32 18.28 33.22 -1.74 2.35 -1.76 -5.80 -4.69 -0.27 -7.66 0.05 11.02 -0.51 11.01 -1.58 31.13 3.02 -0.44 32.49 19.16 -0.46 10.94 -1.46 6.24 -10.49 -6.08 -6.10 0.93 9.65 1.44 9.54 -1.03 32.01 3.20 0.20 40.96 5.81 1.53 9.54 -0.89 2.48 -14.35 0.17 -4.96 1.56 5.03 -0.73 4.97 -1.15 34.70 3.18 -0.03 39.14 -13.48 0.55 4.85 -1.06 0.82 -21.42 2.65 -3.62 1.86 6.43 -1.23 6.31 -1.70 30.39 3.24 -0.34 23.30 -30.95 -1.18 5.16 -1.61 0.28 -10.48 3.47 -3.69 1.68 7.72 2.23 7.40 -1.91 29.48 3.34 0.63 8.16 -33.18 2.26 6.42 -1.82 -1.61 -8.99 3.75 -5.10 1.29 - - - - - - - -2.80 -27.12 - - - - -5.50 2.14 -5.62 1.70 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.