ID code: 1NFK, PDT015 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 404 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 G02C1' 30 G03C1' 30 G03C1' 52 G04C1' 52 G04C1' 74 A05C1' 74 A05C1' 95 A06C1' 95 A06C1' 116 T07C1' 116 T07C1' 136 T08C1' 136 T08C1' 156 C09C1' 156 C09C1' 175 C10C1' 175 C10C1' 194 C11C1' 232 G03C1' 210 G02C1' 254 G04C1' 232 G03C1' 276 A05C1' 254 G04C1' 297 A06C1' 276 A05C1' 318 T07C1' 297 A06C1' 338 T08C1' 318 T07C1' 358 C09C1' 338 T08C1' 377 C10C1' 358 C09C1' 396 C11C1' 377 C10C1' 9 G02N9 31 G03N9 31 G03N9 53 G04N9 53 G04N9 75 A05N9 75 A05N9 96 A06N9 96 A06N9 117 T07N1 117 T07N1 137 T08N1 137 T08N1 157 C09N1 157 C09N1 176 C10N1 176 C10N1 195 C11N1 233 G03N9 211 G02N9 255 G04N9 233 G03N9 277 A05N9 255 G04N9 298 A06N9 277 A05N9 319 T07N1 298 A06N9 339 T08N1 319 T07N1 359 C09N1 339 T08N1 378 C10N1 359 C09N1 397 C11N1 378 C10N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.07651*S + -1.20794 Y = -0.13900*S + 17.90195 Z = 0.98733*S + 2.42676 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.07651*S + -1.20794 Y = -0.13900*S + 17.90195 Z = 0.98733*S + 2.42676 >>>>>> HELIX ROTATION: 32.190 DISPLACEMENT: 3.5027 STATISTICS: OVERALL STANDARD DEV.: 1.1998 SIGMA(X): 1.3666, SIGMA(Y): 1.3693, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.4063, SIGMA(ROTATION): 9.794 THERE ARE 11.18 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 -0.02808 0.16027 0.98667 91.61 80.78 9.36 -0.19133 0.09329 0.97708 101.03 84.65 12.29 -0.07083 -0.03496 0.99688 94.06 92.00 4.53 -0.00883 -0.08679 0.99619 90.51 94.98 5.00 0.09401 -0.22106 0.97072 84.61 102.77 13.90 0.10025 -0.23007 0.96800 84.25 103.30 14.53 0.18384 -0.09714 0.97814 79.41 95.57 12.00 0.12191 -0.09850 0.98764 83.00 95.65 9.02 0.15167 -0.09636 0.98372 81.28 95.53 10.35 -0.01584 -0.10378 0.99447 90.91 95.96 6.03 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.09903 -0.16263 0.98171 95.68 99.36 10.98 0.00561 0.04407 0.99901 89.68 87.47 2.55 0.11649 0.01904 0.99301 83.31 88.91 6.78 -0.11437 0.12029 0.98613 96.57 83.09 9.55 -0.19201 0.12922 0.97285 101.07 82.58 13.38 -0.11804 -0.01279 0.99293 96.78 90.73 6.82 -0.08091 -0.02953 0.99628 94.64 91.69 4.94 -0.02460 -0.10143 0.99454 91.41 95.82 5.99 0.10986 -0.15341 0.98204 83.69 98.82 10.88 0.16529 -0.15870 0.97339 80.49 99.13 13.25 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.03932 0.03296 0.99868 92.25 88.11 2.94 -0.10996 0.08667 0.99015 96.31 85.03 8.05 -0.05689 0.03785 0.99766 93.26 87.83 3.92 -0.02847 0.01774 0.99944 91.63 88.98 1.92 -0.05958 0.00171 0.99822 93.42 89.90 3.42 0.04561 -0.08279 0.99552 87.39 94.75 5.42 0.06968 -0.03386 0.99699 86.00 91.94 4.44 0.03276 -0.10415 0.99402 88.12 95.98 6.27 0.09870 -0.10704 0.98934 84.34 96.14 8.37 0.08889 -0.12473 0.98820 84.90 97.17 8.81 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 1 1 2 8 7 8 11 11 I= 2 5 0 4 6 5 13 12 13 16 16 I= 3 1 4 0 1 2 9 8 9 12 12 I= 4 1 6 1 0 2 7 6 7 10 10 I= 5 2 5 2 2 0 7 7 8 11 11 I= 6 8 13 9 7 7 0 3 1 3 3 I= 7 7 12 8 6 7 3 0 4 4 5 I= 8 8 13 9 7 8 1 4 0 3 3 I= 9 11 16 12 10 11 3 4 3 0 1 I= 10 11 16 12 10 11 3 5 3 1 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 -4.62 -8.13 -8.52 5.50 0.00 0.00 -2.19 10.75 3.71-12.85****** 0.00 -9.78 -7.37 3.45 9.52 0.00 0.00 0.80 -2.42 5.28 3.83 0.00 0.00 -4.34 -1.29 -0.70 4.58****** 0.00 5.65 3.73 -1.91-14.47 0.00 0.00 -4.92 0.93 -8.27 5.11 0.00 0.00 4.75 -8.27 0.95 -4.38 0.00 0.00 -13.90 0.05 -0.62 -0.07 0.00 0.00 11.16 -7.29 -8.95 -2.18 0.00 0.50 -11.67 -8.54 -2.72 8.61 0.00 0.00 5.49 -4.04 -2.30 -0.39 0.00 0.00 -9.70 -7.00 3.25 1.43****** 0.00 4.83 -1.03 -1.18 -5.10 0.00 0.00 -1.85 -8.82 -0.99 -1.39 0.00 0.00 4.77 -3.62 -1.47 -8.16 0.00 0.00 1.83-10.19 1.62 9.51****** 0.00 5.77 -9.19 -0.10 -3.19****** 0.00 5.79 1.66 0.00 0.00 0.00 0.00 10.29 -8.25 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 5.11 -2.78 -4.29 1.30 31.06 3.78 -0.82 -1.02 -2.76 -2.28 -4.55 1.32 -13.85 -2.44 18.88 1.61 -1.99 4.15 3.89 1.45 -0.63 31.50 3.41 1.08 -6.09 -5.24 3.77 1.69 -0.55 -0.01 -10.59 5.03 -0.31 -0.79 2.00 1.99 -0.12 -0.19 30.73 3.63 0.29 -3.81 -0.92 1.99 -0.14 -0.14 -14.21 -10.02 5.02 0.12 -1.06 2.01 -1.83 -0.82 0.14 39.26 3.28 -0.45 -1.85 0.51 -1.86 -0.74 0.15 1.87 -9.71 -9.19 -0.15 -1.05 7.74 1.32 -7.63 -0.21 37.00 3.13 0.26 -3.11 1.41 1.34 -7.64 -0.27 11.88 -25.11 -7.32 -1.08 -0.31 3.13 3.02 -0.82 -0.21 38.04 3.27 0.44 -2.79 -4.65 3.06 -0.63 -0.24 1.44 -17.21 4.56 -0.91 0.24 4.55 -2.85 3.55 -0.71 31.07 3.36 -0.39 -2.48 -3.68 -2.75 3.62 -0.67 -0.82 -14.56 6.01 -0.37 0.62 3.79 -3.14 -2.12 -0.57 28.31 3.54 -1.08 -5.82 2.31 -3.31 -1.83 -0.60 -4.23 -6.63 5.19 -0.54 0.44 1.16 0.42 1.08 -0.16 29.68 3.59 -0.10 -7.57 3.55 0.43 1.08 -0.16 -10.92 -3.94 0.96 -1.20 0.73 - - - - - - - -4.14 7.76 - - - - -4.50 -9.96 -0.36 1.37 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.