ID code: 1WMQ 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 290 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: 72 A04C1' 94 G05C1' 239 G05C1' 217 A04C1' 73 A04N9 95 G05N9 240 G05N9 218 A04N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.23397*S + -13.66219 Y = -0.14515*S + 22.91786 Z = 0.96135*S + 6.78534 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.23397*S + -13.66219 Y = -0.14515*S + 22.91786 Z = 0.96135*S + 6.78534 >>>>>> HELIX ROTATION: -59.749 DISPLACEMENT: 2.9692 STATISTICS: OVERALL STANDARD DEV.: 2.2572 SIGMA(X): 0.1866, SIGMA(Y): 0.3913, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.0089, SIGMA(ROTATION): 17.530 THERE ARE 6.03 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 0.43640 0.50746 0.74300 64.13 59.51 42.01 -0.69199 -0.71740 0.08060 133.79 135.84 85.38 0.11820 0.50093 0.85738 83.21 59.94 30.98 0.66242 -0.19806 0.72248 48.52 101.42 43.74 0.75446 0.18115 0.63085 41.02 79.56 50.89 0.14713 -0.37423 0.91559 81.54 111.98 23.71 0.63370 0.54374 0.55025 50.68 57.06 56.62 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.68045 -0.50806 0.52807 47.12 120.53 58.13 -0.19296 0.36208 0.91196 101.13 68.77 24.22 0.75580 -0.13799 0.64010 40.90 97.93 50.20 0.65230 0.25885 0.71239 49.28 75.00 44.57 0.16016 -0.44236 0.88242 80.78 116.25 28.06 -0.75649 0.64288 0.12011 139.16 49.99 83.10 0.45229 -0.40974 0.79218 63.11 114.19 37.61 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.69375 -0.62286 0.36162 46.07 128.53 68.80 0.96519 -0.18780 0.18206 15.16 100.82 79.51 0.89652 -0.44283 0.01248 26.30 116.28 89.29 -0.92658 -0.36443 0.09293 157.91 111.37 84.67 -0.88369 -0.46806 0.00425 152.09 117.91 89.76 0.98354 -0.16798 0.06663 10.41 99.67 86.18 0.65075 0.67406 0.34952 49.40 47.62 69.54 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 31 25 112 108 35 80 I= 2 31 0 18 143 139 6 55 I= 3 25 18 0 131 125 16 73 I= 4 112 143 131 0 8 147 144 I= 5 108 139 125 8 0 142 152 I= 6 35 6 16 147 142 0 56 I= 7 80 55 73 144 152 56 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 39.34-12.40 43.97-90.00 0.00 0.00 19.10 51.59 90.00 33.88****** 0.00 -70.19 19.22 18.04 90.00 0.00 0.00 -0.54-24.22-90.00 19.41 0.00 0.00 9.64-29.12-49.92 26.51****** 0.00 47.59 12.27 24.02 -2.85 0.00 0.00 42.13 -9.64 22.49 4.42 0.00 0.00 25.41-33.73-46.06-27.65 0.00 0.00 -48.79 10.94-54.81 -5.58****** 0.00 -9.51-26.13 12.89-90.00 0.00 0.50 -16.53-16.51 47.78-46.77 0.00 0.00 71.89 16.66 56.65 90.00 0.00 0.00 -17.88 50.94 0.00 0.00****** 0.00 -36.24 -8.72 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 31.53 5.32 31.12 1.20 0.92 0.06 6.09 62.77 16.28 29.85 -7.10 1.20-121.68 65.02 37.78 -10.85 6.83 18.06 12.48 -13.15 -0.26 2.67 6.24 3.66 37.02 51.02 -13.12 -7.77 -0.58 115.99 74.50 -83.90 -6.31 9.81 131.93 13.86-131.86 3.16 -1.65 1.57 2.90 31.99 58.00 -90.00 18.67 3.22 -31.57 86.50 32.09 -2.21 7.52 8.20 4.62 6.78 3.45 -8.86 -2.93 -0.51 51.81 -37.68 2.69 -5.85 3.21 -34.75 -38.51 0.53 -3.18 5.11 142.21 19.85 142.14 -1.24 7.52 2.08 6.63 -28.57 61.43 90.00 90.00 -0.59 105.62 81.47 -34.22 -2.49 -7.57 56.63 -5.21 56.46 1.31 1.69 1.56 -5.90 13.85 -75.61 -64.58 -3.64 1.34-109.47 -14.34 71.40 -6.16 -9.75 - - - - - - - 64.12 -15.16 - - - - 59.46 -38.07 -10.78 -6.98 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.