ID code: 2BPF, PDE011 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 280 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 G05C1' 30 G06C1' 30 G06C1' 52 C07C1' 52 C07C1' 71 G08C1' 71 G08C1' 93 C09C1' 93 C09C1' 112 C10C1' 112 C10C1' 131 G11C1' 169 G02C1' 150 C01C1' 191 G03C1' 169 G02C1' 213 C04C1' 191 G03C1' 232 G05C1' 213 C04C1' 254 C06C1' 232 G05C1' 272 C07C1' 254 C06C1' 9 G05N9 31 G06N9 31 G06N9 53 C07N1 53 C07N1 72 G08N9 72 G08N9 94 C09N1 94 C09N1 113 C10N1 113 C10N1 132 G11N9 170 G02N9 151 C01N1 192 G03N9 170 G02N9 214 C04N1 192 G03N9 233 G05N9 214 C04N1 255 C06N1 233 G05N9 273 C07N1 255 C06N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.47224*S + -14.16181 Y = 0.37420*S + 47.11880 Z = 0.79810*S + -13.71263 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.47224*S + -14.16181 Y = 0.37420*S + 47.11880 Z = 0.79810*S + -13.71263 >>>>>> HELIX ROTATION: 35.186 DISPLACEMENT: 3.5405 STATISTICS: OVERALL STANDARD DEV.: 1.2859 SIGMA(X): 1.5512, SIGMA(Y): 1.5101, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.5084, SIGMA(ROTATION): 10.532 THERE ARE 10.23 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 0.10736 0.05236 0.99284 83.84 87.00 6.86 0.11700 0.01515 0.99302 83.28 89.13 6.78 0.01125 0.10828 0.99406 89.36 83.78 6.25 -0.03933 -0.00667 0.99920 92.25 90.38 2.29 -0.20856 0.01269 0.97793 102.04 89.27 12.06 -0.18474 -0.09009 0.97865 100.65 95.17 11.86 -0.02325 -0.18171 0.98308 91.33 100.47 10.56 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.15934 -0.11900 0.98003 80.83 96.83 11.47 0.00428 0.16043 0.98704 89.75 80.77 9.24 -0.04560 0.14271 0.98871 92.61 81.80 8.62 -0.00056 -0.21148 0.97738 90.03 102.21 12.21 0.02796 -0.28640 0.95770 88.40 106.64 16.72 -0.08079 -0.15246 0.98500 94.63 98.77 9.94 0.15318 0.25737 0.95410 81.19 75.09 17.43 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.12515 -0.04767 0.99099 82.81 92.73 7.70 0.07453 -0.00430 0.99721 85.73 90.25 4.28 -0.00701 0.01859 0.99980 90.40 88.93 1.14 -0.09900 -0.06263 0.99311 95.68 93.59 6.73 -0.03638 -0.16513 0.98560 92.08 99.50 9.74 -0.07472 -0.09869 0.99231 94.29 95.66 7.11 0.01517 -0.07764 0.99687 89.13 94.45 4.54 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 3 8 12 11 11 6 I= 2 3 0 4 10 11 10 5 I= 3 8 4 0 7 10 7 5 I= 4 12 10 7 0 6 2 6 I= 5 11 11 10 6 0 4 5 I= 6 11 10 7 2 4 0 5 I= 7 6 5 5 6 5 5 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 -3.04 6.14 -1.22 -1.83 -0.00 0.00 -11.47 0.17 13.79 12.28 0.00 NaN -6.51 1.87 5.27 6.14 0.00 0.00 1.14 9.16 2.97 -0.61 0.00 0.00 -3.23 5.35 6.66 -2.76****** 0.00 -1.12 8.54 12.25-16.69 0.00 0.00 1.57 1.66 1.93 9.61 0.00 0.00 10.14 -6.73 3.58 -2.88 0.00 0.00 -1.53 11.96 5.97 1.00****** 0.00 16.72 -0.50 -9.52 2.81************ -2.95 11.48 10.70 0.16 0.00 0.00 3.64 9.23 0.47-28.15 0.00 0.00 1.57 10.44 0.00 0.00****** 0.00 4.40-16.83 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 3.84 1.13 3.67 -0.80 28.79 3.31 0.75 2.21 -7.37 1.39 3.56 -0.71 13.21 8.43 -5.93 -1.26 1.41 4.86 1.96 4.44 -0.69 33.86 3.38 -1.35 0.40 -4.26 1.95 4.45 -0.54 -4.09 -7.66 7.28 -0.24 0.91 7.05 -0.07 7.05 0.28 30.83 3.63 0.02 1.13 -0.09 0.28 7.04 0.38 -11.56 -2.10 3.19 -1.29 0.65 6.90 -4.96 4.80 -0.38 37.62 3.48 -0.43 2.72 6.15 -5.23 4.49 -0.31 -3.92 -8.68 -8.36 -0.50 1.37 4.41 0.56 -4.38 0.40 36.62 3.08 -0.50 2.71 9.34 0.57 -4.36 0.43 10.04 -18.31 -12.28 0.30 0.91 5.30 -3.80 3.69 1.00 33.33 4.12 0.66 6.94 1.52 -3.54 3.94 1.02 -25.02 -6.59 -2.24 0.62 0.68 - - - - - - - 4.04 2.06 - - - - -3.06 -27.26 1.80 0.60 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.