ID code: 1KD3, AR0036 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 10 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 420 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 G02C1' 32 G02C1' 75 C04C1' 75 C04C1' 95 A05C1' 95 A05C1' 117 C06C1' 117 C06C1' 137 A07C1' 137 A07C1' 159 G08C1' 159 G08C1' 182 C09C1' 182 C09C1' 202 C10C1' 242 G02C1' 219 G01C1' 285 C04C1' 242 G02C1' 305 A05C1' 285 C04C1' 327 C06C1' 305 A05C1' 347 A07C1' 327 C06C1' 369 G08C1' 347 A07C1' 392 C09C1' 369 G08C1' 412 C10C1' 392 C09C1' 10 G01N9 33 G02N9 33 G02N9 76 C04N1 76 C04N1 96 A05N9 96 A05N9 118 C06N1 118 C06N1 138 A07N9 138 A07N9 160 G08N9 160 G08N9 183 C09N1 183 C09N1 203 C10N1 243 G02N9 220 G01N9 286 C04N1 243 G02N9 306 A05N9 286 C04N1 328 C06N1 306 A05N9 348 A07N9 328 C06N1 370 G08N9 348 A07N9 393 C09N1 370 G08N9 413 C10N1 393 C09N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.68455*S + -10.36062 Y = -0.68306*S + 15.86824 Z = 0.25460*S + 70.43055 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.68455*S + -10.36062 Y = -0.68306*S + 15.86824 Z = 0.25460*S + 70.43055 >>>>>> HELIX ROTATION: 49.568 DISPLACEMENT: 3.7758 STATISTICS: OVERALL STANDARD DEV.: 3.1644 SIGMA(X): 3.7550, SIGMA(Y): 4.2568, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.5507, SIGMA(ROTATION): 29.705 THERE ARE 7.26 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 = 10 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.35540 0.30951 0.88198 110.82 71.97 28.12 -0.38024 0.29549 0.87641 112.35 72.81 28.79 -0.35837 0.20985 0.90969 111.00 77.89 24.54 -0.21830 0.18263 0.95864 102.61 79.48 16.54 -0.16380 0.00771 0.98646 99.43 89.56 9.44 -0.07210 -0.07617 0.99448 94.13 94.37 6.02 -0.10758 -0.03175 0.99369 96.18 91.82 6.44 -0.28564 -0.04169 0.95743 106.60 92.39 16.78 -0.31294 0.00622 0.94975 108.24 89.64 18.24 -0.41341 -0.16935 0.89466 114.42 99.75 26.54 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.42184 0.17154 0.89030 114.95 80.12 27.09 -0.31836 -0.03591 0.94729 108.56 92.06 18.69 -0.28733 0.04720 0.95667 106.70 87.29 16.93 -0.12263 0.02903 0.99203 97.04 88.34 7.24 -0.07616 0.08627 0.99336 94.37 85.05 6.61 -0.18632 -0.00553 0.98247 100.74 90.32 10.74 -0.22593 -0.20217 0.95293 103.06 101.66 17.65 -0.35749 -0.21180 0.90958 110.95 102.23 24.55 -0.37728 -0.29193 0.87888 112.17 106.97 28.49 -0.34884 -0.31315 0.88332 110.42 108.25 27.95 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.37431 0.25152 0.89254 111.98 75.43 26.81 -0.33797 0.16747 0.92614 109.75 80.36 22.16 -0.30143 0.10580 0.94760 107.54 83.93 18.63 -0.14547 0.04410 0.98838 98.36 87.47 8.74 -0.08300 0.04600 0.99549 94.76 87.36 5.44 -0.08315 -0.04205 0.99565 94.77 92.41 5.35 -0.13724 -0.04818 0.98937 97.89 92.76 8.36 -0.29630 -0.11110 0.94861 107.24 96.38 18.45 -0.33734 -0.16973 0.92596 109.71 99.77 22.19 -0.37297 -0.24560 0.89475 111.90 104.22 26.52 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 I= 8 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 9 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 9 10 I= 1 0 5 9 18 21 24 22 21 24 28 I= 2 5 0 4 13 16 19 17 16 19 23 I= 3 9 4 0 9 13 15 13 12 16 20 I= 4 18 13 9 0 3 6 5 12 16 21 I= 5 21 16 13 3 0 5 6 15 19 24 I= 6 24 19 15 6 5 0 3 13 16 21 I= 7 22 17 13 5 6 3 0 10 13 18 I= 8 21 16 12 12 15 13 10 0 4 9 I= 9 24 19 16 16 19 16 13 4 0 5 I= 10 28 23 20 21 24 21 18 9 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 -26.38 9.03 -0.37 1.59****** 0.00 -20.91 16.42 12.87 3.69 0.00 0.50 -28.50 -3.73 2.36 4.48 0.00 0.00 -14.92 10.99 0.62 -5.05 0.00 0.00 -21.79-10.73 7.05 4.17****** 0.00 -16.84 -1.63 8.57 4.16 0.00 0.00 -8.66-13.98 -6.92 7.93 0.00 0.00 -6.17 -3.77 4.19 0.55 0.00 0.00 -0.86 -9.40 -4.87 5.20****** 0.00 4.29 -5.01 -5.19 -6.39****** 0.00 -3.75 -4.71 3.24 -0.39 0.00 0.00 1.18-10.68 -8.41 -7.89 0.00 0.00 5.31 -3.63 9.42 -4.06****** 0.00 8.78-15.19 6.90 -3.12 0.00 0.00 16.73 -1.22 0.88 3.04 0.00 0.00 21.82-10.71 2.17 -4.20 0.00 0.00 15.52 9.34 11.37 -2.60****** 0.00 28.22 -3.63 -0.21 -2.02****** 0.00 20.56 16.03 0.00 0.00 0.00 0.00 26.39 8.57 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 5.59 1.63 5.35 -2.17 31.85 3.05 -0.14 11.65 -23.78 1.73 4.96 -2.09 7.58 -5.45 6.91 -0.05 4.92 4.29 2.80 3.25 -1.26 27.52 3.34 0.28 1.40 -22.11 2.95 2.86 -1.21 -5.23 -13.59 14.49 0.48 2.24 9.90 4.86 8.64 -0.33 21.36 3.36 0.79 -4.94 -17.92 6.35 7.24 -0.31 0.98 -5.02 9.26 0.30 0.90 3.61 2.71 2.38 -1.86 63.54 3.31 -1.62 -5.00 -7.15 2.99 1.97 -1.90 -5.87 -2.57 10.24 0.67 0.75 5.05 0.01 -5.05 0.56 15.98 3.58 -0.02 -5.08 1.95 -0.07 -5.05 0.64 -10.34 -5.16 4.38 -1.29 -0.60 3.14 -2.62 1.73 -1.86 63.66 3.33 1.62 -5.06 -1.72 -2.82 1.34 -1.91 -5.64 -4.94 -5.96 -1.30 0.63 10.09 -4.91 8.82 -0.32 21.56 3.38 -0.75 -5.06 6.65 -6.55 7.33 -0.30 1.94 -3.58 -11.60 0.69 -0.73 4.30 -2.56 3.46 -1.25 27.10 3.31 -0.27 -5.15 17.67 -2.72 3.07 -1.21 -3.12 -5.15 -9.66 0.35 -0.87 5.13 -1.36 4.94 -2.16 31.89 3.09 0.05 1.28 22.15 -1.45 4.58 -2.09 5.84 -12.72 -12.79 0.55 -2.22 - - - - - - - 11.73 23.43 - - - - -5.82 -6.95 -0.05 -4.92 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.