ID code: 1MWL, DR0008 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 342 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: 12 C08C1' 32 A09C1' 32 A09C1' 54 C10C1' 54 C10C1' 74 C11C1' 74 C11C1' 94 G12C1' 94 G12C1' 117 G13C1' 117 G13C1' 160 G15C1' 203 A31C1' 183 C30C1' 225 C32C1' 203 A31C1' 245 C33C1' 225 C32C1' 265 G34C1' 245 C33C1' 288 G35C1' 265 G34C1' 331 G37C1' 288 G35C1' 13 C08N1 33 A09N9 33 A09N9 55 C10N1 55 C10N1 75 C11N1 75 C11N1 95 G12N9 95 G12N9 118 G13N9 118 G13N9 161 G15N9 204 A31N9 184 C30N1 226 C32N1 204 A31N9 246 C33N1 226 C32N1 266 G34N9 246 C33N1 289 G35N9 266 G34N9 332 G37N9 289 G35N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.82001*S + 1.99763 Y = -0.56485*S + 0.84328 Z = -0.09233*S + 12.58255 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.82001*S + 1.99763 Y = -0.56485*S + 0.84328 Z = -0.09233*S + 12.58255 >>>>>> HELIX ROTATION: 33.205 DISPLACEMENT: 2.5992 STATISTICS: OVERALL STANDARD DEV.: 2.2571 SIGMA(X): 1.9864, SIGMA(Y): 2.2548, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.7713, SIGMA(ROTATION): 10.690 THERE ARE 10.84 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 0.01681 -0.14413 0.98942 89.04 98.29 8.34 0.22083 -0.23187 0.94735 77.24 103.41 18.67 0.29580 -0.31851 0.90058 72.79 108.57 25.76 0.44941 -0.16967 0.87707 63.29 99.77 28.71 0.41137 -0.00805 0.91143 65.71 90.46 24.30 0.38128 0.14932 0.91232 67.59 81.41 24.17 0.41682 0.15726 0.89528 65.37 80.95 26.46 0.19136 0.29239 0.93696 78.97 73.00 20.45 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.28427 -0.16168 0.94501 73.48 99.30 19.09 0.47291 -0.07735 0.87771 61.78 94.44 28.63 0.47368 -0.01603 0.88055 61.73 90.92 28.29 0.38639 0.02819 0.92191 67.27 88.38 22.79 0.42932 0.23928 0.87088 64.58 76.16 29.44 0.24412 0.32856 0.91239 75.87 70.82 24.16 0.13973 0.35760 0.92336 81.97 69.05 22.58 0.03626 0.28081 0.95908 87.92 73.69 16.45 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.17027 -0.14581 0.97455 80.20 98.38 12.95 0.35866 -0.14383 0.92232 68.98 98.27 22.73 0.39247 -0.14526 0.90822 66.89 98.35 24.74 0.39457 -0.05356 0.91730 66.76 93.07 23.47 0.38500 0.08033 0.91941 67.36 85.39 23.16 0.32597 0.24341 0.91351 70.98 75.91 24.01 0.29309 0.27188 0.91661 72.96 74.22 23.56 0.11366 0.29383 0.94908 83.47 72.91 18.36 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 11 13 14 18 24 25 25 I= 2 11 0 2 5 12 22 24 29 I= 3 13 2 0 5 12 22 24 30 I= 4 14 5 5 0 7 17 19 25 I= 5 18 12 12 7 0 9 12 19 I= 6 24 22 22 17 9 0 2 12 I= 7 25 24 24 19 12 2 0 10 I= 8 25 29 30 25 19 12 10 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 3.59 7.52 11.75 5.07****** 0.00 18.74 3.48 10.89 -4.80****** 0.00 9.69 15.81 1.33 6.44 0.00 0.00 26.54 9.97 1.75 -3.05 0.00 0.00 0.88 25.75 11.78 3.66****** 0.00 20.35 18.78 -0.16 -5.61 NaN 0.00 -3.06 28.52 9.33 -2.04 0.00 0.00 7.05 21.56 12.15 2.65 0.00 0.00 -8.38 22.63 8.30 3.99****** 0.00 4.65 29.00 10.49 -5.48****** 0.00 -12.33 20.45 -1.70 1.21 0.00 0.00 0.23 24.16 6.17 -0.79 0.00 0.00 -24.14 10.18 11.49 9.88****** 0.00 -7.05 21.33 6.61 -3.33************ -18.15 9.11 0.00 0.00 0.00 0.00 -9.86 13.03 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 11.22 -0.27 11.22 -1.67 31.47 3.11 -0.20 4.74 12.03 -0.07 10.86 -1.54 -0.81 -15.16 -3.75 -5.86 -2.45 2.10 1.13 1.77 -1.90 28.79 3.29 0.92 12.40 18.74 1.02 1.65 -1.84 -0.94 -16.87 -4.56 -6.18 -1.27 5.28 -2.65 4.57 -2.12 31.84 3.24 -0.85 21.50 11.65 -2.41 4.68 -2.03 -1.30 -19.49 -5.50 -4.98 -1.18 7.70 0.23 7.69 -1.85 30.88 3.01 -0.07 23.30 2.61 -0.43 7.70 -1.73 12.99 -10.13 -6.80 -6.16 -1.09 9.96 2.70 9.59 -1.80 30.28 3.09 0.68 22.93 -3.08 2.86 9.56 -1.69 -3.03 -13.06 6.18 -6.63 -0.19 2.50 0.78 2.37 -1.33 32.70 3.08 -0.20 23.01 -6.46 0.77 2.37 -1.30 6.59 -12.57 3.15 -6.07 0.59 10.54 3.06 10.09 -1.78 31.87 3.20 0.25 16.58 -16.26 2.99 9.97 -1.68 -6.23 -17.21 9.73 -6.13 1.97 - - - - - - - 11.43 -14.17 - - - - -8.30 3.50 -5.39 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.