ID code: 1A1L, PDT061 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 C03C1' 30 C03C1' 49 G04C1' 49 G04C1' 71 T05C1' 71 T05C1' 91 G06C1' 91 G06C1' 113 G07C1' 113 G07C1' 135 G08C1' 135 G08C1' 157 C09C1' 157 C09C1' 176 A10C1' 176 A10C1' 197 C11C1' 235 T53C1' 213 G52C1' 255 G54C1' 235 T53C1' 277 C55C1' 255 G54C1' 296 C56C1' 277 C55C1' 315 C57C1' 296 C56C1' 334 A58C1' 315 C57C1' 355 C59C1' 334 A58C1' 374 G60C1' 355 C59C1' 396 C61C1' 374 G60C1' 9 G02N9 31 C03N1 31 C03N1 50 G04N9 50 G04N9 72 T05N1 72 T05N1 92 G06N9 92 G06N9 114 G07N9 114 G07N9 136 G08N9 136 G08N9 158 C09N1 158 C09N1 177 A10N9 177 A10N9 198 C11N1 236 T53N1 214 G52N9 256 G54N9 236 T53N1 278 C55N1 256 G54N9 297 C56N1 278 C55N1 316 C57N1 297 C56N1 335 A58N9 316 C57N1 356 C59N1 335 A58N9 375 G60N9 356 C59N1 397 C61N1 375 G60N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.60176*S + -4.80917 Y = 0.79847*S + 2.52521 Z = 0.01820*S + 48.21357 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.60176*S + -4.80917 Y = 0.79847*S + 2.52522 Z = 0.01820*S + 48.21357 >>>>>> HELIX ROTATION: 31.996 DISPLACEMENT: 3.2553 STATISTICS: OVERALL STANDARD DEV.: 1.1132 SIGMA(X): 1.5616, SIGMA(Y): 1.5868, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3966, SIGMA(ROTATION): 7.652 THERE ARE 11.25 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 -0.10953 0.03811 0.99325 96.29 87.82 6.66 -0.25559 -0.20621 0.94454 104.81 101.90 19.17 0.00384 -0.11369 0.99351 89.78 96.53 6.53 0.11316 -0.24732 0.96230 83.50 104.32 15.78 0.09031 -0.14960 0.98461 84.82 98.60 10.06 0.10584 -0.06896 0.99199 83.92 93.95 7.26 0.10436 0.03174 0.99403 84.01 88.18 6.26 0.13781 0.19405 0.97126 82.08 78.81 13.77 0.04827 0.03068 0.99836 87.23 88.24 3.28 -0.04563 0.22083 0.97424 92.62 77.24 13.03 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.23841 -0.12572 0.96299 103.79 97.22 15.64 -0.05946 -0.10771 0.99240 93.41 96.18 7.07 0.06107 -0.17052 0.98346 86.50 99.82 10.44 0.11704 -0.14274 0.98282 83.28 98.21 10.64 0.15183 0.04203 0.98751 81.27 87.59 9.06 0.14377 0.07961 0.98640 81.73 85.43 9.46 0.07223 0.14420 0.98691 85.86 81.71 9.28 0.04790 0.12067 0.99154 87.25 83.07 7.46 -0.10189 0.07779 0.99175 95.85 85.54 7.36 -0.07878 0.01063 0.99684 94.52 89.39 4.56 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.14740 -0.03515 0.98845 98.48 92.01 8.72 -0.12973 -0.12506 0.98363 97.45 97.18 10.38 0.03223 -0.14382 0.98908 88.15 98.27 8.48 0.09689 -0.16539 0.98146 84.44 99.52 11.05 0.13033 -0.07715 0.98846 82.51 94.42 8.71 0.10543 -0.00589 0.99441 83.95 90.34 6.06 0.08391 0.07634 0.99354 85.19 85.62 6.51 0.09109 0.14508 0.98522 84.77 81.66 9.86 -0.04815 0.11838 0.99180 92.76 83.20 7.34 -0.05447 0.11135 0.99229 93.12 83.61 7.12 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 12 15 16 14 14 17 10 9 I= 2 5 0 9 13 15 15 16 20 14 14 I= 3 12 9 0 3 6 8 12 16 15 15 I= 4 15 13 3 0 5 9 13 17 18 18 I= 5 16 15 6 5 0 4 9 12 15 15 I= 6 14 15 8 9 4 0 4 8 11 11 I= 7 14 16 12 13 9 4 0 3 7 8 I= 8 17 20 16 17 12 8 3 0 8 8 I= 9 10 14 15 18 15 11 7 8 0 0 I= 10 9 14 15 18 15 11 8 8 0 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 -3.98 5.33 8.41 14.13 0.00****** 2.75 15.38 3.94 -9.57 0.00 -0.00 -0.08 19.17 9.70-12.58 0.00 0.00 2.64 6.55 7.78 -0.69 0.00 0.00 1.48 6.36 5.98 7.92 0.00****** 5.34 8.94 3.27 -1.47****** 0.00 2.66 15.54 1.84 -5.46 0.00 0.00 4.41 9.66 7.30 -7.97 0.00 0.00 -3.42 9.45 4.63 -0.87 0.00 0.00 7.36 5.27 1.83 -1.22****** 0.00 -3.35 6.43 5.65 1.21 0.00 0.00 5.34 7.78 4.53 -3.17 0.00 0.00 -1.52 6.07 5.19 7.98****** 0.00 4.96 7.83 0.04 -1.94 0.00 0.00 -0.90 13.74 2.54-10.42 0.00 0.00 1.28 7.35 7.68 -4.59 0.00 0.00 -2.83 1.66 2.27 12.02****** 0.00 5.69 4.66 -0.25 -4.07 0.00 0.50 -4.85 12.07 0.00 0.00 0.00 0.00 3.42 3.01 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 5.26 1.58 5.02 -0.20 21.27 3.71 0.86 8.69 -0.63 1.54 5.03 -0.12 -22.64 -6.75 10.04 -2.49 0.29 9.36 -3.86 8.53 -0.52 39.02 2.87 -0.74 10.34 0.86 -4.10 8.42 -0.42 15.22 -2.73 -12.61 -1.49 0.25 3.93 1.40 3.67 -0.47 25.74 3.63 0.58 7.75 3.41 1.38 3.66 -0.42 -8.47 -3.86 2.61 -1.92 0.49 5.42 -3.22 4.37 -0.23 35.71 3.34 -0.85 10.64 2.96 -3.29 4.30 -0.18 1.73 -1.74 -5.86 -0.96 0.10 4.34 -2.88 3.24 -0.82 33.03 3.19 -0.43 8.62 1.25 -2.83 3.28 -0.78 5.50 -10.79 -4.13 -1.68 0.15 4.87 -0.16 4.87 -0.56 36.28 3.34 -0.05 6.06 0.25 -0.15 4.87 -0.48 0.41 -8.69 1.37 -2.06 -0.01 3.99 3.10 2.51 -0.56 27.17 3.40 1.04 6.39 1.27 3.09 2.48 -0.52 -8.17 -6.48 1.78 -1.94 0.37 8.14 -3.53 7.34 -0.38 33.19 3.13 -1.23 9.86 -0.09 -3.54 7.33 -0.34 9.41 -2.19 -6.39 -0.73 -0.03 0.54 0.27 0.47 -0.45 31.50 3.52 0.14 6.89 2.52 -0.29 0.46 -0.46 -12.09 -8.52 3.02 -1.99 -0.04 - - - - - - - 7.06 -0.94 - - - - -8.30 -9.07 -1.78 0.11 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.