ID code: 438D, AR0011 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 8 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 338 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 G02C1' 32 G02C1' 55 G03C1' 55 G03C1' 78 C04C1' 78 C04C1' 98 G05C1' 98 G05C1' 121 C06C1' 121 C06C1' 161 C08C1' 201 G11C1' 178 G10C1' 224 G12C1' 201 G11C1' 247 C13C1' 224 G12C1' 267 G14C1' 247 C13C1' 290 C15C1' 267 G14C1' 330 C17C1' 290 C15C1' 10 G01N9 33 G02N9 33 G02N9 56 G03N9 56 G03N9 79 C04N1 79 C04N1 99 G05N9 99 G05N9 122 C06N1 122 C06N1 162 C08N1 202 G11N9 179 G10N9 225 G12N9 202 G11N9 248 C13N1 225 G12N9 268 G14N9 248 C13N1 291 C15N1 268 G14N9 331 C17N1 291 C15N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.05708*S + 36.34453 Y = 0.24966*S + 12.65220 Z = 0.96665*S + -1.12177 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.05708*S + 36.34453 Y = 0.24966*S + 12.65221 Z = 0.96665*S + -1.12177 >>>>>> HELIX ROTATION: 36.554 DISPLACEMENT: 2.5868 STATISTICS: OVERALL STANDARD DEV.: 2.1613 SIGMA(X): 1.6456, SIGMA(Y): 1.6108, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.9616, SIGMA(ROTATION): 10.509 THERE ARE 9.85 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 = 8 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.07584 0.33879 0.93780 94.35 70.20 20.31 -0.18370 0.34264 0.92133 100.59 69.96 22.88 -0.34757 0.20237 0.91555 110.34 78.32 23.72 -0.55573 -0.02021 0.83112 123.76 91.16 33.79 -0.37364 -0.24959 0.89336 111.94 104.45 26.70 -0.34369 -0.28690 0.89418 110.10 106.67 26.60 -0.29860 -0.42604 0.85400 107.37 115.22 31.35 -0.00078 -0.51001 0.86017 90.04 120.66 30.66 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.25237 0.31372 0.91536 104.62 71.72 23.74 -0.41385 0.09195 0.90569 114.45 84.72 25.08 -0.31580 -0.11792 0.94147 108.41 96.77 19.70 -0.40234 -0.28152 0.87113 113.72 106.35 29.41 -0.25141 -0.50571 0.82526 104.56 120.38 34.39 -0.13748 -0.45082 0.88196 97.90 116.80 28.12 -0.00356 -0.29345 0.95597 90.20 107.06 17.07 -0.06650 -0.27064 0.96038 93.81 105.70 16.18 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.16003 0.36310 0.91791 99.21 68.71 23.38 -0.32349 0.28026 0.90378 108.87 73.72 25.34 -0.42912 0.07841 0.89984 115.41 85.50 25.86 -0.45175 -0.16447 0.87685 116.86 99.47 28.73 -0.32029 -0.38109 0.86728 108.68 112.40 29.86 -0.21712 -0.39129 0.89429 102.54 113.03 26.58 -0.11715 -0.38674 0.91472 96.73 112.75 23.83 -0.04272 -0.39033 0.91968 92.45 112.97 23.12 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 I= 7 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 8 I= 1 0 10 22 35 44 44 44 44 I= 2 10 0 13 26 38 39 40 42 I= 3 22 13 0 14 27 29 32 35 I= 4 35 26 14 0 14 18 23 27 I= 5 44 38 27 14 0 6 11 16 I= 6 44 39 29 18 6 0 5 10 I= 7 44 40 32 23 11 5 0 4 I= 8 44 42 35 27 16 10 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 4.87 19.67 5.72 2.37****** 0.00 15.11 17.87 13.24 -8.69****** 0.00 -4.34 22.42 12.25 2.25 0.00 0.00 15.15 19.50 5.83-12.02 0.00 0.00 -4.34 23.27 11.84 13.02****** 0.00 12.47 15.00 8.98 5.70 NaN 0.00 -7.44 32.74 16.99 -1.16 0.00 0.00 9.41 27.58 15.68 0.14 0.00 0.00 -7.85 25.34 2.43 1.28****** 0.00 6.81 33.52 4.74 -5.50****** 0.00 -18.80 18.11 1.85 8.20 0.00 0.00 -6.02 27.36 8.50 -8.31 0.00 0.00 -26.65 15.28 10.31 14.62****** 0.00 -7.19 15.39 -1.98 -3.28************ -27.62 12.28 0.00 0.00 0.00 0.00 -15.88 3.03 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 10.55 -1.04 10.50 -1.85 37.73 3.26 0.01 21.02 9.77 -1.16 10.49 -1.76 -0.98 -10.25 -1.13 -5.06 -1.87 13.08 -1.42 13.01 -1.23 28.25 3.31 -0.34 24.95 4.13 -2.56 12.91 -1.18 -5.65 -19.54 -2.10 -5.69 -1.01 14.07 1.27 14.02 -1.37 31.25 3.27 0.05 25.52 3.92 2.41 13.90 -1.26 2.75 -16.96 -7.76 -6.16 -0.30 14.57 0.77 14.55 -1.93 30.97 2.98 0.45 28.64 2.14 0.82 14.65 -1.77 13.12 -16.86 -5.01 -5.81 0.66 6.14 -2.11 5.77 -1.46 30.87 3.33 -0.35 29.84 -0.74 -1.82 5.66 -1.38 -0.07 -14.70 8.12 -4.80 0.82 5.85 0.29 5.85 -1.19 27.29 3.42 -0.09 23.94 -10.87 0.26 5.74 -1.13 -9.79 -12.86 8.04 -5.00 0.93 4.28 3.01 3.04 -1.37 40.67 3.47 0.25 17.65 -15.50 2.84 3.19 -1.31 -8.16 -19.46 -1.75 -5.38 1.19 - - - - - - - 7.15 -21.86 - - - - -11.78 -9.91 -4.88 2.75 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.