ID code: 1JGG, PDT031 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 410 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: 11 T01C1' 31 A02C1' 31 A02C1' 52 A03C1' 52 A03C1' 73 T04C1' 73 T04C1' 93 T05C1' 93 T05C1' 113 G06C1' 113 G06C1' 135 A07C1' 135 A07C1' 156 A08C1' 156 A08C1' 177 T09C1' 177 T09C1' 197 T10C1' 238 A12C1' 217 A11C1' 259 T13C1' 238 A12C1' 279 T14C1' 259 T13C1' 299 C15C1' 279 T14C1' 318 A16C1' 299 C15C1' 339 A17C1' 318 A16C1' 360 T18C1' 339 A17C1' 380 T19C1' 360 T18C1' 400 A20C1' 380 T19C1' 12 T01N1 32 A02N9 32 A02N9 53 A03N9 53 A03N9 74 T04N1 74 T04N1 94 T05N1 94 T05N1 114 G06N9 114 G06N9 136 A07N9 136 A07N9 157 A08N9 157 A08N9 178 T09N1 178 T09N1 198 T10N1 239 A12N9 218 A11N9 260 T13N1 239 A12N9 280 T14N1 260 T13N1 300 C15N1 280 T14N1 319 A16N9 300 C15N1 340 A17N9 319 A16N9 361 T18N1 340 A17N9 381 T19N1 361 T18N1 401 A20N9 381 T19N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.99938*S + -0.66494 Y = 0.03513*S + 16.88479 Z = 0.00179*S + 39.93539 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.99938*S + -0.66494 Y = 0.03513*S + 16.88480 Z = 0.00179*S + 39.93539 >>>>>> HELIX ROTATION: 35.477 DISPLACEMENT: 3.4062 STATISTICS: OVERALL STANDARD DEV.: 1.0634 SIGMA(X): 1.7594, SIGMA(Y): 1.5914, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3846, SIGMA(ROTATION): 7.587 THERE ARE 10.15 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 -0.31551 0.11613 0.94179 108.39 83.33 19.65 -0.07600 0.09930 0.99215 94.36 84.30 7.18 -0.00046 0.04269 0.99909 90.03 87.55 2.45 -0.04036 -0.04541 0.99815 92.31 92.60 3.48 -0.07958 -0.14862 0.98569 94.56 98.55 9.71 0.09638 -0.05238 0.99397 84.47 93.00 6.30 0.08852 -0.16682 0.98201 84.92 99.60 10.89 0.03344 -0.07363 0.99673 88.08 94.22 4.64 0.08086 -0.10977 0.99066 85.36 96.30 7.84 0.02149 0.04622 0.99870 88.77 87.35 2.92 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.24467 -0.09941 0.96450 104.16 95.71 15.31 -0.08433 -0.28202 0.95570 94.84 106.38 17.12 0.13743 -0.00895 0.99047 82.10 90.51 7.92 0.09006 0.01225 0.99586 84.83 89.30 5.21 0.21292 0.05083 0.97575 77.71 87.09 12.64 -0.00553 0.08268 0.99656 90.32 85.26 4.75 -0.01855 -0.00629 0.99981 91.06 90.36 1.12 -0.13986 0.07886 0.98703 98.04 85.48 9.24 -0.14740 -0.09015 0.98496 98.48 95.17 9.95 -0.21224 -0.06319 0.97517 102.25 93.62 12.79 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.12159 -0.00222 0.99258 96.98 90.13 6.98 -0.00716 -0.11676 0.99313 90.41 96.71 6.72 0.03167 -0.06308 0.99751 88.19 93.62 4.05 0.00716 0.00506 0.99996 89.59 89.71 0.50 0.00361 -0.02611 0.99965 89.79 91.50 1.51 0.09435 -0.00518 0.99553 84.59 90.30 5.42 0.06708 -0.05756 0.99609 86.15 93.30 5.07 -0.07940 0.01171 0.99677 94.55 89.33 4.60 -0.01126 -0.07150 0.99738 90.65 94.10 4.15 -0.05123 -0.03273 0.99815 92.94 91.88 3.49 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 9 9 7 7 12 11 2 7 4 I= 2 9 0 3 7 5 8 5 8 2 5 I= 3 9 3 0 4 2 4 2 7 2 5 I= 4 7 7 4 0 1 5 4 4 4 3 I= 5 7 5 2 1 0 5 4 5 2 3 I= 6 12 8 4 5 5 0 3 10 7 8 I= 7 11 5 2 4 4 3 0 9 4 6 I= 8 2 8 7 4 5 10 9 0 6 3 I= 9 7 2 2 4 2 7 4 6 0 3 I= 10 4 5 5 3 3 8 6 3 3 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 -0.97 19.62 1.56-13.80****** 0.00 9.66 11.77 10.92 -8.76 0.00 0.50 -6.89 2.01 5.24 -1.37 0.00 0.00 13.46 10.38 -4.34-20.09 0.00 0.00 -1.34 -2.05 -0.86 5.48****** 0.00 6.93 -3.81 -2.94 -0.45 0.00 0.00 -2.33 2.59 -3.80 5.07 0.00 0.00 5.17 -0.66 7.40 -0.18 0.00 0.00 -8.58 4.51 10.66 4.45****** 0.00 11.82 4.42 -6.39-10.99****** 0.00 -1.12 6.20 -6.53 -0.83 0.00 0.00 4.40 -1.79 -5.05 -1.04 0.00 0.00 -10.81 1.30 6.20 0.46****** 0.00 0.05 -1.12 8.00 -2.92 0.00 0.00 -3.96 -2.41 -3.11 -1.43 0.00 0.00 9.21 -0.78 -1.69 -9.59 0.00 0.00 -4.57 -6.35 0.51 9.59****** 0.00 8.53 -5.08 3.07 2.61****** 0.00 -2.45 1.60 0.00 0.00 0.00 0.00 12.33 3.36 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 9.29 -6.31 6.83 1.23 37.91 3.34 -0.99 6.63 2.20 -6.28 6.86 1.39 16.18 -10.66 -7.73 -0.05 -0.26 3.80 -3.68 -0.98 -0.23 35.95 3.35 0.23 2.79 6.10 -3.66 -1.02 -0.23 -10.21 -20.45 8.45 -0.62 1.03 4.15 -3.36 -2.43 -0.26 32.99 3.57 -0.40 2.07 3.48 -3.39 -2.40 -0.30 -1.49 -8.29 -1.76 0.45 0.68 1.80 1.65 -0.72 -0.56 33.62 3.24 -0.50 -0.29 0.41 1.66 -0.69 -0.53 3.19 -7.51 -3.25 0.36 0.09 5.34 3.43 4.10 0.94 37.63 3.61 0.95 1.36 -0.67 3.32 4.18 1.00 -7.91 -20.41 -0.06 -0.30 -0.56 3.38 -1.64 -2.96 1.25 39.35 3.35 -0.93 5.23 1.42 -1.73 -2.91 1.17 5.52 -5.55 -7.97 0.63 0.14 9.29 -4.13 8.33 -0.44 34.72 3.23 0.12 2.40 -4.46 -4.62 8.08 -0.39 4.06 -10.85 -2.45 -0.08 0.98 6.16 -3.43 -5.13 -0.33 34.75 3.27 -0.52 -2.01 4.14 -3.80 -4.86 -0.37 -0.37 -13.17 1.61 0.44 0.47 3.19 2.78 1.57 -0.19 31.54 3.35 0.09 -4.09 0.69 2.82 1.50 -0.14 0.56 -13.11 1.24 0.19 0.07 - - - - - - - -0.04 3.49 - - - - -14.78 1.80 0.42 -0.15 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.