ID code: 1ICG, AH0015 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 332 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' 92 C05C1' 92 C05C1' 112 G06C1' 112 G06C1' 135 G07C1' 135 G07C1' 158 C08C1' 198 C02C1' 175 G01C1' 258 C05C1' 198 C02C1' 278 G06C1' 258 C05C1' 301 G07C1' 278 G06C1' 324 C08C1' 301 G07C1' 10 G01N9 33 C02N1 33 C02N1 93 C05N1 93 C05N1 113 G06N9 113 G06N9 136 G07N9 136 G07N9 159 C08N1 199 C02N1 176 G01N9 259 C05N1 199 C02N1 279 G06N9 259 C05N1 302 G07N9 279 G06N9 325 C08N1 302 G07N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.39507*S + 18.63669 Y = -0.41485*S + 0.27865 Z = 0.81965*S + 9.12393 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.39507*S + 18.63669 Y = -0.41485*S + 0.27865 Z = 0.81965*S + 9.12393 >>>>>> HELIX ROTATION: 63.795 DISPLACEMENT: 4.1880 STATISTICS: OVERALL STANDARD DEV.: 5.9689 SIGMA(X): 3.6720, SIGMA(Y): 3.4667, SIGMA(Z)=SIGMA(DISPLACEMENT): 2.6428, SIGMA(ROTATION): 46.525 THERE ARE 5.64 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 0.43339 -0.16411 0.88614 64.32 99.45 27.61 0.41860 -0.06574 0.90579 65.25 93.77 25.07 0.31580 0.06890 0.94632 71.59 86.05 18.86 0.14894 -0.00701 0.98882 81.43 90.40 8.58 0.01835 -0.05044 0.99856 88.95 92.89 3.08 0.00602 -0.22224 0.97497 89.66 102.84 12.85 0.07390 -0.27581 0.95837 85.76 106.01 16.59 0.10959 -0.34351 0.93273 83.71 110.09 21.13 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.48431 0.04958 0.87349 61.03 87.16 29.13 0.26993 0.03227 0.96234 74.34 88.15 15.77 0.19032 0.00341 0.98172 79.03 89.80 10.97 0.16703 -0.02670 0.98559 80.38 91.53 9.74 0.14773 -0.19275 0.97006 81.50 101.11 14.05 0.01393 -0.40513 0.91415 89.20 113.90 23.91 0.10451 -0.48553 0.86795 84.00 119.05 29.78 0.12077 -0.44179 0.88895 83.06 116.22 27.26 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.43999 -0.07625 0.89476 63.90 94.37 26.52 0.34177 -0.00754 0.93975 70.02 90.43 19.99 0.25815 0.05059 0.96478 75.04 87.10 15.25 0.16047 -0.02693 0.98667 80.77 91.54 9.36 0.08974 -0.14993 0.98462 84.85 98.62 10.06 0.04592 -0.27488 0.96038 87.37 105.95 16.18 0.09902 -0.36789 0.92458 84.32 111.59 22.39 0.11351 -0.41243 0.90389 83.48 114.36 25.33 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 7 13 17 21 25 25 27 I= 2 7 0 6 10 16 23 25 26 I= 3 13 6 0 7 15 22 25 28 I= 4 17 10 7 0 8 15 20 22 I= 5 21 16 15 8 0 7 12 15 I= 6 25 23 22 15 7 0 6 9 I= 7 25 25 25 20 12 6 0 2 I= 8 27 26 28 22 15 9 2 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 -19.49 18.76 5.11 2.53 0.00 0.00 -9.33 27.33 6.23-10.70 0.00 -0.00 -22.67 10.14 8.34 5.02 0.00 0.00 -11.97 10.13 3.64 -3.21 0.00 0.00 -17.76 6.13 10.34 -2.15 0.00****** -10.86 1.52 1.68 -1.39****** 0.00 -7.30 -4.47 7.07 3.53 0.00 0.00 -7.67 -5.97 7.53 -5.96 0.00 0.00 2.00 -2.34 9.87 -0.96 0.00 0.00 5.44-12.92 13.41 5.52****** 0.00 12.62 2.33 4.41 -2.27 0.00 0.00 23.52 4.09 6.35 -2.82 0.00 0.00 15.29 6.28 3.79 2.21****** 0.00 26.66 12.29 -0.53 -2.62 0.00 0.00 13.11 16.28 0.00 0.00 0.00 0.00 15.83 21.58 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 7.34 -2.33 6.96 -1.45 31.86 3.44 -0.60 21.42 -14.89 -2.36 6.46 -1.36 -8.18 -10.15 7.53 -0.05 4.79 6.01 1.26 5.88 -1.20 26.97 3.36 0.26 10.50 -16.81 1.34 5.69 -1.15 -4.11 -10.70 -0.65 0.32 2.36 7.26 -3.30 6.47 -1.86 37.21 3.17 -2.04 4.68 -14.48 -3.11 6.45 -1.80 3.26 -6.89 -4.76 0.31 0.54 8.14 -2.17 7.84 -0.82 31.45 3.47 -0.07 -5.80 -7.33 -2.12 7.87 -0.73 -9.11 0.37 -1.50 -2.50 -0.61 7.72 1.33 7.60 -1.49 42.69 2.94 1.46 -8.74 4.95 1.27 7.50 -1.37 12.47 -3.46 -10.61 -2.68 0.56 6.47 -0.32 6.47 -1.75 26.46 3.19 0.01 0.73 16.16 -0.56 6.12 -1.66 4.85 -10.92 1.87 -0.15 0.35 2.93 1.79 2.32 -1.86 31.97 3.35 0.13 8.37 20.62 1.73 2.05 -1.82 -1.14 -11.41 6.72 0.61 -1.76 - - - - - - - 20.07 14.80 - - - - -2.70 5.58 0.05 -4.66 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.