ID code: 1EM0, DD0027 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 240 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: 27 C02C1' 46 T03C1' 46 T03C1' 66 A04C1' 66 A04C1' 87 G05C1' 87 G05C1' 109 G06C1' 166 T09C1' 147 C08C1' 186 A10C1' 166 T09C1' 207 G11C1' 186 A10C1' 229 G12C1' 207 G11C1' 28 C02N1 47 T03N1 47 T03N1 67 A04N9 67 A04N9 88 G05N9 88 G05N9 110 G06N9 167 T09N1 148 C08N1 187 A10N9 167 T09N1 208 G11N9 187 A10N9 230 G12N9 208 G11N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.40029*S + 27.80823 Y = -0.14908*S + 14.95882 Z = 0.90418*S + 14.77745 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.40029*S + 27.80823 Y = -0.14908*S + 14.95883 Z = 0.90418*S + 14.77745 >>>>>> HELIX ROTATION: 31.616 DISPLACEMENT: 3.8615 STATISTICS: OVERALL STANDARD DEV.: 1.6514 SIGMA(X): 1.0935, SIGMA(Y): 1.5017, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.6145, SIGMA(ROTATION): 16.631 THERE ARE 11.39 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 0.02076 0.24607 0.96903 88.81 75.75 14.30 0.03807 0.25448 0.96633 87.82 75.26 14.91 -0.03152 0.14588 0.98880 91.81 81.61 8.58 -0.08120 0.13881 0.98699 94.66 82.02 9.25 0.12831 0.24507 0.96098 82.63 75.81 16.06 0.12912 0.25622 0.95796 82.58 75.15 16.67 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.04943 0.17829 0.98274 92.83 79.73 10.66 -0.09020 0.10178 0.99071 95.18 84.16 7.82 0.03553 0.09236 0.99509 87.96 84.70 5.68 -0.07581 0.14760 0.98614 94.35 81.51 9.55 0.05463 0.42563 0.90325 86.87 64.81 25.41 -0.22691 0.01416 0.97381 103.12 89.19 13.14 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.02015 0.20313 0.97894 91.15 78.28 11.78 -0.03314 0.15500 0.98736 91.90 81.08 9.12 -0.00084 0.13238 0.99120 90.05 82.39 7.61 -0.08075 0.15295 0.98493 94.63 81.20 9.96 0.10373 0.30810 0.94568 84.05 72.06 18.97 -0.03651 0.13436 0.99026 92.09 82.28 8.00 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 2 4 4 9 4 I= 2 2 0 2 2 12 1 I= 3 4 2 0 4 12 2 I= 4 4 2 4 0 14 2 I= 5 9 12 12 14 0 13 I= 6 4 1 2 2 13 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 -14.25 -1.15 -0.08 -1.10 0.00 0.00 -10.26 2.86 3.20 3.81 0.00 -0.00 -9.23-11.61 0.55 7.39 0.00 0.00 -7.81 -0.19 6.10 -3.90 0.00 0.00 -5.27 -6.76 -2.83 0.52 0.00****** -0.47 -5.66 -6.52 -2.90 -0.02 0.00 -1.83 -9.07 13.47 1.77 0.00 0.00 -1.37 -9.45 15.36 -8.94 0.00 0.00 15.74 -3.12 0.60 -0.23 0.00 0.00 21.42-13.02-29.45 -4.75 -0.03 0.00 16.10 4.24 0.00 0.00 0.00 0.00 -1.87-13.00 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 2.90 1.71 2.34 0.69 43.46 3.26 0.78 1.19 -11.72 1.72 2.28 0.70 7.44 -3.99 4.00 1.82 0.72 2.27 0.03 2.27 0.84 21.23 3.65 -0.34 -4.66 -7.82 -0.08 2.26 0.85 -10.31 -1.45 11.44 2.30 -0.02 4.74 -0.94 -4.65 0.98 44.27 3.45 0.68 -6.83 -3.34 -0.99 -4.63 0.94 -1.51 -4.80 1.13 1.67 0.47 14.03 -1.56 13.94 0.20 31.89 3.85 -0.94 -9.84 -1.54 -1.35 13.88 0.33 -9.75 -0.46 -0.38 2.55 0.32 13.07 -2.73 -12.79 -0.10 26.88 3.87 0.99 -6.50 17.74 -3.12 -12.51 -0.24 -6.92 -5.80 -10.13 2.21 -0.09 - - - - - - - -3.63 7.13 - - - - 18.18 -17.06 3.71 -1.39 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.