ID code: 1D1U, PD0152 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 6 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 243 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 C01C1' 27 T02C1' 27 T02C1' 47 C03C1' 47 C03C1' 66 G04C1' 66 G04C1' 88 T05C1' 88 T05C1' 108 G06C1' 149 A12C1' 130 C11C1' 170 C13C1' 149 A12C1' 189 G14C1' 170 C13C1' 211 A15C1' 189 G14C1' 232 G16C1' 211 A15C1' 9 C01N1 28 T02N1 28 T02N1 48 C03N1 48 C03N1 67 G04N9 67 G04N9 89 T05N1 89 T05N1 109 G06N9 150 A12N9 131 C11N1 171 C13N1 150 A12N9 190 G14N9 171 C13N1 212 A15N9 190 G14N9 233 G16N9 212 A15N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.82902*S + -11.85262 Y = 0.51403*S + 12.04295 Z = 0.22022*S + 16.50920 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.82902*S + -11.85262 Y = 0.51403*S + 12.04295 Z = 0.22022*S + 16.50920 >>>>>> HELIX ROTATION: 33.839 DISPLACEMENT: 3.2300 STATISTICS: OVERALL STANDARD DEV.: 0.8653 SIGMA(X): 1.6110, SIGMA(Y): 1.4920, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.2578, SIGMA(ROTATION): 4.110 THERE ARE 10.64 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 = 6 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.00734 0.03899 0.99921 90.42 87.77 2.27 -0.09140 -0.10768 0.98998 95.24 96.18 8.12 0.20915 0.05424 0.97638 77.93 86.89 12.48 0.07776 0.07598 0.99407 85.54 85.64 6.24 0.12792 0.10913 0.98576 82.65 83.73 9.68 -0.17955 0.22264 0.95822 100.34 77.14 16.62 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.17058 0.10300 0.97995 80.18 84.09 11.49 0.05360 0.26488 0.96279 86.93 74.64 15.68 -0.07983 0.24318 0.96669 94.58 75.93 14.83 -0.16614 0.19527 0.96657 99.56 78.74 14.86 -0.15183 0.06877 0.98601 98.73 86.06 9.59 -0.19276 0.02075 0.98103 101.11 88.81 11.18 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.02951 0.09485 0.99505 88.31 84.56 5.70 0.03673 0.14884 0.98818 87.90 81.44 8.82 0.03605 0.16990 0.98480 87.93 80.22 10.00 -0.06421 0.15547 0.98575 93.68 81.06 9.68 -0.09007 0.14406 0.98546 95.17 81.72 9.78 -0.21175 0.12486 0.96931 102.22 82.83 14.23 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 I= 1 0 3 4 6 7 14 I= 2 3 0 1 5 7 14 I= 3 4 1 0 5 7 14 I= 4 6 5 5 0 1 8 I= 5 7 7 7 1 0 7 I= 6 14 14 14 8 7 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 2.27 -0.05 -5.15 -8.24 0.00 0.00 4.24 10.66 11.41 -1.54 -0.00 0.00 -0.26 -8.12-11.92 15.77 0.00 0.00 7.93 13.44 6.46 -4.30 0.00 0.00 -11.07 5.69 7.47 1.67****** 0.00 7.57 12.68 5.10 -2.46 0.00 0.00 -5.87 2.11 -3.43 -0.36 0.00 0.00 4.02 14.28 3.98 -6.13 0.00 0.00 -9.24 -2.85 -2.67 18.93****** 0.00 1.32 9.50 3.18 1.72 0.00 0.50 -13.42 9.62 0.00 0.00 0.00 0.00 -1.79 11.03 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 3.15 -1.87 2.53 -0.26 38.48 3.16 0.52 2.55 5.09 1.82 2.53 -0.24 10.90 -2.00 10.72 -2.08 -0.20 1.22 1.07 0.59 -0.33 29.14 3.53 -0.20 7.76 4.17 1.08 0.54 -0.35 -14.73 -8.25 21.62 -1.17 0.37 5.81 -0.24 5.80 0.01 36.75 3.16 -0.37 10.00 0.14 -0.50 5.79 0.06 5.25 -18.67 6.89 -1.11 0.06 1.62 -0.48 1.55 -0.60 32.82 3.46 -0.13 9.68 -0.35 0.44 1.56 -0.62 0.11 -9.95 12.14 -1.37 0.36 7.12 6.53 2.85 0.49 34.41 3.55 0.67 8.81 -4.22 6.60 2.54 0.47 -11.17 -10.72 12.26 -1.54 0.02 - - - - - - - 11.81 -7.83 - - - - -11.64 1.09 -0.98 0.64 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.