ID code: 1GU5 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 15 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 615 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 T02C1' 31 G03C1' 31 G03C1' 53 T04C1' 53 T04C1' 73 G05C1' 73 G05C1' 95 T06C1' 95 T06C1' 115 T07C1' 115 T07C1' 135 G08C1' 135 G08C1' 157 G09C1' 157 G09C1' 179 C10C1' 179 C10C1' 198 C11C1' 198 C11C1' 217 A12C1' 217 A12C1' 238 A13C1' 238 A13C1' 259 T14C1' 259 T14C1' 279 C15C1' 279 C15C1' 298 A16C1' 339 G03C1' 319 T02C1' 361 A04C1' 339 G03C1' 382 T05C1' 361 A04C1' 402 T06C1' 382 T05C1' 422 G07C1' 402 T06C1' 444 G08C1' 422 G07C1' 466 C09C1' 444 G08C1' 485 C10C1' 466 C09C1' 504 A11C1' 485 C10C1' 525 A12C1' 504 A11C1' 546 C13C1' 525 A12C1' 565 A14C1' 546 C13C1' 586 C15C1' 565 A14C1' 605 A16C1' 586 C15C1' 12 T02N1 32 G03N9 32 G03N9 54 T04N1 54 T04N1 74 G05N9 74 G05N9 96 T06N1 96 T06N1 116 T07N1 116 T07N1 136 G08N9 136 G08N9 158 G09N9 158 G09N9 180 C10N1 180 C10N1 199 C11N1 199 C11N1 218 A12N9 218 A12N9 239 A13N9 239 A13N9 260 T14N1 260 T14N1 280 C15N1 280 C15N1 299 A16N9 340 G03N9 320 T02N1 362 A04N9 340 G03N9 383 T05N1 362 A04N9 403 T06N1 383 T05N1 423 G07N9 403 T06N1 445 G08N9 423 G07N9 467 C09N1 445 G08N9 486 C10N1 467 C09N1 505 A11N9 486 C10N1 526 A12N9 505 A11N9 547 C13N1 526 A12N9 566 A14N9 547 C13N1 587 C15N1 566 A14N9 606 A16N9 587 C15N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.99013*S + -5.36053 Y = -0.07461*S + 33.55250 Z = 0.11867*S + 65.81875 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.99013*S + -5.36053 Y = -0.07461*S + 33.55251 Z = 0.11867*S + 65.81875 >>>>>> HELIX ROTATION: 33.836 DISPLACEMENT: 3.2096 STATISTICS: OVERALL STANDARD DEV.: 0.8455 SIGMA(X): 1.2549, SIGMA(Y): 1.1870, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3737, SIGMA(ROTATION): 5.548 THERE ARE 10.64 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 = 15 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.18664 -0.04160 0.98155 100.76 92.38 11.02 0.00381 0.04351 0.99905 89.78 87.51 2.50 0.01649 -0.02124 0.99964 89.06 91.22 1.54 -0.05804 0.07024 0.99584 93.33 85.97 5.23 -0.01597 0.02881 0.99946 90.92 88.35 1.89 0.09152 0.14315 0.98546 84.75 81.77 9.78 -0.04616 0.23076 0.97192 92.65 76.66 13.61 -0.05134 0.09484 0.99417 92.94 84.56 6.19 -0.11413 -0.02728 0.99309 96.55 91.56 6.74 -0.06024 -0.08269 0.99475 93.45 94.74 5.87 -0.24086 -0.21397 0.94668 103.94 102.36 18.79 -0.09448 -0.20548 0.97409 95.42 101.86 13.07 -0.00177 -0.24518 0.96948 90.10 104.19 14.19 0.02183 -0.13590 0.99048 88.75 97.81 7.91 -0.02061 -0.06773 0.99749 91.18 93.88 4.06 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.02625 0.04101 0.99881 91.50 87.65 2.79 0.01746 0.12979 0.99139 89.00 82.54 7.53 0.03507 0.16357 0.98591 87.99 80.59 9.63 0.13851 0.19535 0.97090 82.04 78.73 13.86 0.02200 0.21572 0.97621 88.74 77.54 12.52 -0.04108 0.21001 0.97684 92.35 77.88 12.36 0.01753 0.03274 0.99931 89.00 88.12 2.13 -0.18062 0.06406 0.98147 100.41 86.33 11.05 -0.15267 -0.05981 0.98647 98.78 93.43 9.44 -0.14356 -0.10131 0.98444 98.25 95.81 10.12 -0.01812 -0.16398 0.98630 91.04 99.44 9.50 0.00884 -0.06354 0.99794 89.49 93.64 3.68 -0.02452 -0.06976 0.99726 91.40 94.00 4.24 0.08231 -0.07927 0.99345 85.28 94.55 6.56 0.02547 0.08317 0.99621 88.54 85.23 4.99 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.12001 0.05907 0.99101 96.89 86.61 7.69 0.01443 0.06933 0.99749 89.17 86.02 4.06 0.00935 0.05614 0.99838 89.46 86.78 3.26 0.02156 0.14041 0.98986 88.76 81.93 8.17 0.02699 0.13862 0.98998 88.45 82.03 8.12 0.03624 0.15969 0.98650 87.92 80.81 9.42 -0.00690 0.15170 0.98840 90.40 81.27 8.73 -0.06580 0.05861 0.99611 93.77 86.64 5.06 -0.10621 -0.06080 0.99248 96.10 93.49 7.03 -0.12517 -0.10355 0.98672 97.19 95.94 9.35 -0.11082 -0.17648 0.97805 96.36 100.16 12.03 -0.03496 -0.17646 0.98369 92.00 100.16 10.36 -0.01304 -0.18676 0.98232 90.75 100.76 10.79 0.03656 -0.09134 0.99515 87.90 95.24 5.65 0.01764 0.02675 0.99949 88.99 88.47 1.84 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 I= 10 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 11 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 12 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 13 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 14 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 11 12 13 14 15 I= 1 0 7 7 9 9 10 8 3 6 9 13 14 15 12 8 I= 2 7 0 0 4 4 5 4 4 10 12 15 14 14 9 2 I= 3 7 0 0 4 4 6 5 4 9 12 15 13 14 8 1 I= 4 9 4 4 0 0 1 1 6 13 16 19 18 18 13 6 I= 5 9 4 4 0 0 1 2 7 13 16 19 18 18 13 6 I= 6 10 5 6 1 1 0 2 8 15 17 21 19 20 14 7 I= 7 8 4 5 1 2 2 0 6 13 16 19 18 19 14 7 I= 8 3 4 4 6 7 8 6 0 7 9 13 13 14 10 5 I= 9 6 10 9 13 13 15 13 7 0 2 6 7 9 8 8 I= 10 9 12 12 16 16 17 16 9 2 0 4 6 8 9 11 I= 11 13 15 15 19 19 21 19 13 6 4 0 4 5 9 13 I= 12 14 14 13 18 18 19 18 13 7 6 4 0 1 6 12 I= 13 15 14 14 18 18 20 19 14 9 8 5 1 0 6 12 I= 14 12 9 8 13 13 14 14 10 8 9 9 6 6 0 6 I= 15 8 2 1 6 6 7 7 5 8 11 13 12 12 6 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 -10.36 3.73 11.31 -4.06 0.00 0.00 -1.79 -2.14 2.87 -4.89****** 0.00 1.21 -2.19 -1.82 3.31 0.00 0.00 3.93 -6.41 2.02 -0.84 0.00 0.00 -0.54 1.44 4.31 -5.22****** 0.00 9.06 -3.24 2.94 5.47 0.00 0.00 4.51 -2.63 -3.20 1.10 0.00 0.00 9.81 9.69 4.03 -5.46 0.00 0.00 1.85 0.36 -1.77 8.85 0.00 0.00 8.68 8.96 2.90 -2.19 0.00 0.50 -3.06 9.28 7.99 4.91 0.00 0.00 5.26 11.15 -3.51-10.16 0.00 0.00 -0.17 13.61 4.28 -6.53****** 0.00 -1.37 1.63 8.83 7.42 0.00 0.00 -2.43 5.69 7.85 0.81 0.00 0.00 3.57 10.44 6.04 -4.08 0.00 0.00 2.25 6.35 3.72 -2.41****** 0.00 4.35 8.36 2.43 -0.05****** 0.00 2.32 5.39 -2.80 12.58 0.00 0.00 0.80 10.09 7.79 -2.05 0.00 0.00 -6.18 17.68 8.09 -2.34****** 0.00 3.63 8.76 0.22 -5.97 0.00 0.00 -6.62 11.22 4.21 3.96 0.00 0.00 0.13 3.68 -1.92 -0.32 0.00 0.00 -8.59 11.21 6.01 -2.25****** 0.00 -3.53 2.34 2.86 5.45****** 0.00 -7.29 3.05 4.07 -2.15 0.00 0.00 -3.31 5.66 9.56 -2.60 0.00 0.00 -3.23 -2.46 0.00 0.00****** 0.00 3.96 3.03 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 7.74 -0.55 7.72 -0.30 31.25 3.29 -0.23 -2.48 -7.27 -0.02 7.75 -0.21 1.62 -8.61 -5.84 -0.07 -0.84 0.81 0.38 -0.72 -0.82 34.27 3.33 -0.30 -3.30 2.37 0.39 -0.71 -0.83 -0.48 -2.73 -4.22 -0.87 -0.64 4.91 0.25 4.90 -0.46 41.36 2.81 0.20 -1.24 3.02 -0.26 4.88 -0.40 17.05 -9.60 -4.70 -1.41 -0.65 0.33 -0.24 -0.22 -0.71 30.82 3.28 -0.53 2.52 7.76 0.23 -0.23 -0.71 -3.69 -5.34 12.35 -1.20 -0.15 1.33 1.32 0.20 -0.02 35.42 3.30 0.38 6.31 5.09 1.30 0.19 -0.02 -6.77 -6.83 8.66 -1.50 -0.42 2.52 -0.52 2.46 -0.18 26.02 3.73 0.21 9.42 0.25 -0.49 2.47 -0.16 -13.87 -8.32 1.89 -1.09 -0.10 6.33 -2.79 5.68 -0.53 39.22 2.91 0.30 8.62 -1.43 -2.83 5.65 -0.46 16.74 1.21 -11.98 -1.03 -0.38 7.23 -0.43 7.22 -0.70 32.14 3.40 -0.72 5.05 -0.28 -0.33 7.23 -0.59 -2.73 -6.00 4.76 -1.11 -0.52 2.70 1.61 2.17 -0.15 36.52 3.32 -0.08 5.69 4.12 1.54 2.19 -0.12 2.66 -2.10 2.03 -2.06 -0.61 4.29 2.47 3.51 -0.03 30.00 3.63 0.43 9.23 1.45 2.59 3.38 0.00 -13.66 1.52 4.69 -2.10 0.16 4.36 -0.91 4.26 -0.17 34.27 3.12 -0.16 12.01 -0.68 -0.97 4.24 -0.13 1.36 -9.84 -8.97 -1.45 0.41 1.39 1.01 0.95 -0.92 30.84 3.31 0.45 9.90 -3.05 0.99 0.98 -0.94 -1.34 -6.75 -7.61 -1.44 0.54 6.21 0.69 6.17 -1.11 39.27 2.92 0.05 8.11 -7.07 -0.57 6.15 -1.06 11.53 -5.06 -8.94 -1.20 -0.22 6.86 -0.69 6.83 0.01 34.05 3.22 0.22 3.27 -4.60 -0.61 6.84 0.07 2.90 -3.99 2.59 -1.78 -0.61 - - - - - - - 1.48 1.08 - - - - -7.20 5.49 -1.73 0.39 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.