ID code: 2PUF, PDR044 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 16 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 650 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 A00C1' 29 C01C1' 29 C01C1' 48 G02C1' 48 G02C1' 70 C03C1' 70 C03C1' 89 A04C1' 89 A04C1' 110 A05C1' 110 A05C1' 131 A06C1' 131 A06C1' 152 C07C1' 152 C07C1' 171 G08C1' 171 G08C1' 193 T09C1' 193 T09C1' 213 T10C1' 213 T10C1' 233 T11C1' 233 T11C1' 253 G12C1' 253 G12C1' 275 C13C1' 275 C13C1' 294 G14C1' 294 G14C1' 316 T15C1' 354 C01C1' 333 A00C1' 373 G02C1' 354 C01C1' 395 C03C1' 373 G02C1' 414 A04C1' 395 C03C1' 435 A05C1' 414 A04C1' 456 A06C1' 435 A05C1' 477 C07C1' 456 A06C1' 496 G08C1' 477 C07C1' 518 T09C1' 496 G08C1' 538 T10C1' 518 T09C1' 558 T11C1' 538 T10C1' 578 G12C1' 558 T11C1' 600 C13C1' 578 G12C1' 619 G14C1' 600 C13C1' 641 T15C1' 619 G14C1' 9 A00N9 30 C01N1 30 C01N1 49 G02N9 49 G02N9 71 C03N1 71 C03N1 90 A04N9 90 A04N9 111 A05N9 111 A05N9 132 A06N9 132 A06N9 153 C07N1 153 C07N1 172 G08N9 172 G08N9 194 T09N1 194 T09N1 214 T10N1 214 T10N1 234 T11N1 234 T11N1 254 G12N9 254 G12N9 276 C13N1 276 C13N1 295 G14N9 295 G14N9 317 T15N1 355 C01N1 334 A00N9 374 G02N9 355 C01N1 396 C03N1 374 G02N9 415 A04N9 396 C03N1 436 A05N9 415 A04N9 457 A06N9 436 A05N9 478 C07N1 457 A06N9 497 G08N9 478 C07N1 519 T09N1 497 G08N9 539 T10N1 519 T09N1 559 T11N1 539 T10N1 579 G12N9 559 T11N1 601 C13N1 579 G12N9 620 G14N9 601 C13N1 642 T15N1 620 G14N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.00000*S + 9.84092 Y = 0.83597*S + 0.00000 Z = 0.54878*S + -0.00000 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.00000*S + 9.84092 Y = 0.83597*S + 0.00000 Z = 0.54878*S + 0.00000 >>>>>> HELIX ROTATION: 28.716 DISPLACEMENT: 3.3138 STATISTICS: OVERALL STANDARD DEV.: 2.3943 SIGMA(X): 3.8884, SIGMA(Y): 3.2789, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.1414, SIGMA(ROTATION): 16.323 THERE ARE 12.54 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 = 16 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.05198 0.49634 0.86657 87.02 60.24 29.94 0.04077 0.57271 0.81875 87.66 55.06 35.04 0.03739 0.44641 0.89404 87.86 63.49 26.61 0.11655 0.38260 0.91653 83.31 67.51 23.58 0.09814 0.45846 0.88328 84.37 62.71 27.96 0.09845 0.50785 0.85580 84.35 59.48 31.15 0.01641 0.66246 0.74891 89.06 48.51 41.50 -0.32789 0.60014 0.72960 109.14 53.12 43.15 0.12677 -0.35599 0.92585 82.72 110.85 22.20 0.08044 -0.11515 0.99009 85.39 96.61 8.07 -0.07824 -0.35966 0.92980 94.49 111.08 21.60 0.01449 -0.42330 0.90587 89.17 115.04 25.06 0.00555 -0.60375 0.79715 89.68 127.14 37.14 0.01493 -0.48627 0.87368 89.14 119.10 29.11 0.10208 -0.58663 0.80339 84.14 125.92 36.54 0.14764 -0.23754 0.96009 81.51 103.74 16.24 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.14764 0.23754 0.96009 81.51 76.26 16.24 0.10208 0.58663 0.80339 84.14 54.08 36.54 0.01493 0.48627 0.87368 89.14 60.90 29.11 0.00555 0.60375 0.79715 89.68 52.86 37.14 0.01449 0.42330 0.90587 89.17 64.96 25.06 -0.07824 0.35966 0.92980 94.49 68.92 21.60 0.08044 0.11515 0.99009 85.39 83.39 8.07 0.12677 0.35599 0.92585 82.72 69.15 22.20 -0.32789 -0.60014 0.72960 109.14 126.88 43.15 0.01641 -0.66246 0.74892 89.06 131.49 41.50 0.09845 -0.50785 0.85580 84.35 120.52 31.15 0.09814 -0.45846 0.88328 84.37 117.29 27.96 0.11655 -0.38260 0.91653 83.31 112.49 23.58 0.03739 -0.44641 0.89404 87.86 116.51 26.61 0.04077 -0.57270 0.81875 87.66 124.94 35.04 0.05198 -0.49634 0.86657 87.02 119.76 29.94 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.06409 0.44018 0.89562 86.33 63.88 26.41 0.13022 0.53089 0.83738 82.52 57.93 33.14 0.09720 0.47356 0.87538 84.42 61.73 28.91 0.02325 0.49855 0.86655 88.67 60.10 29.94 0.07195 0.47783 0.87550 85.87 61.46 28.90 -0.01508 0.48339 0.87528 90.86 61.09 28.92 -0.02592 0.43978 0.89773 91.49 63.91 26.14 -0.01072 0.47944 0.87751 90.61 61.35 28.66 -0.01072 -0.47944 0.87751 90.61 118.65 28.66 -0.02593 -0.43978 0.89773 91.49 116.09 26.14 -0.01508 -0.48339 0.87528 90.86 118.91 28.92 0.07195 -0.47783 0.87550 85.87 118.54 28.90 0.02324 -0.49855 0.86655 88.67 119.90 29.94 0.09720 -0.47356 0.87538 84.42 118.27 28.91 0.13022 -0.53090 0.83737 82.52 122.07 33.14 0.06409 -0.44018 0.89562 86.33 116.12 26.41 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 I= 15 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 16 I= 1 0 7 2 4 2 5 5 4 54 52 55 54 56 54 58 52 I= 2 7 0 4 6 5 9 10 8 61 59 61 60 62 60 64 58 I= 3 2 4 0 4 1 6 7 6 57 54 57 56 58 56 60 54 I= 4 4 6 4 0 3 2 4 2 58 56 58 58 59 58 62 56 I= 5 2 5 1 3 0 4 6 4 57 54 57 57 58 56 60 54 I= 6 5 9 6 2 4 0 2 0 57 55 57 57 58 57 61 55 I= 7 5 10 7 4 6 2 0 2 54 52 55 54 56 54 59 52 I= 8 4 8 6 2 4 0 2 0 57 54 57 57 58 57 61 54 I= 9 54 61 57 58 57 57 54 57 0 2 0 4 2 6 8 4 I= 10 52 59 54 56 54 55 52 54 2 0 2 6 4 7 10 5 I= 11 55 61 57 58 57 57 55 57 0 2 0 4 2 6 9 5 I= 12 54 60 56 58 57 57 54 57 4 6 4 0 3 1 5 2 I= 13 56 62 58 59 58 58 56 58 2 4 2 3 0 4 6 4 I= 14 54 60 56 58 56 57 54 57 6 7 6 1 4 0 4 2 I= 15 58 64 60 62 60 61 59 61 8 10 9 5 6 4 0 7 I= 16 52 58 54 56 54 55 52 54 4 5 5 2 4 2 7 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 18.61-22.56 2.29 -3.79 0.00 0.00 14.76 -6.62 10.76-17.36 0.00 0.50 30.61-15.38 -6.87 2.32 0.00 0.00 33.59-12.73 -7.14 -2.70 0.00 0.00 26.61 0.20 -4.81 3.30 0.00 0.00 29.08 -1.26 6.62 1.42 0.00 0.00 16.00 16.84 3.48 2.81 0.00 0.00 31.52 17.58 -6.71 -7.92 0.00 0.00 5.71 27.27 0.26 2.82 0.00 0.00 9.28 23.06 4.94 -4.15 0.00 0.00 -12.69 27.93 -0.51 10.07 0.00 0.00 -0.70 21.58 -0.62-16.93 0.00 0.00 -31.58 23.95 12.85 15.67 0.00 0.00 -8.05 0.60-13.46 4.42 0.00 0.00 -33.79 23.45 72.97-27.04 0.00 0.00 -21.64 -4.75 72.97 27.04 0.00 0.00 21.64 -4.75-13.46 -4.42 0.00 0.00 33.79 23.45 12.85-15.67 0.00 0.00 8.05 0.60 -0.62 16.93 0.00 0.00 31.58 23.95 -0.51-10.07 0.00 0.00 0.70 21.58 4.94 4.15 0.00 0.00 12.69 27.93 0.26 -2.82 0.00 0.00 -9.28 23.06 -6.71 7.92 0.00 0.00 -5.71 27.27 3.48 -2.81 0.00 0.00 -31.52 17.58 6.62 -1.42 0.00 0.00 -16.00 16.84 -4.81 -3.30 0.00 0.00 -29.08 -1.26 -7.14 2.70 0.00 0.00 -26.61 0.20 -6.87 -2.32 0.00 0.00 -33.59-12.73 10.76 17.36 0.00 0.00 -30.61-15.38 2.29 3.79 0.00 0.00 -14.76 -6.62 0.00 0.00 0.00 0.00 -18.61-22.56 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 7.25 -1.76 7.04 -0.63 24.24 3.58 -0.00 -19.28 17.34 -1.60 6.24 -0.60 -14.05 3.57 16.37 -3.33 -3.46 4.37 -0.60 -4.33 -0.37 31.19 3.58 -1.44 -9.62 31.36 -0.64 -3.74 -0.49 -3.72 -2.90 2.32 -2.93 -1.74 4.50 -3.68 2.60 -0.39 36.56 3.43 -0.90 3.50 28.66 -3.65 2.59 -0.36 4.21 -2.51 -1.40 -2.86 -0.48 3.08 -0.74 -2.99 1.30 34.41 3.55 1.10 15.40 25.00 0.75 -2.94 1.29 -6.79 -15.54 2.81 -2.20 -0.02 5.00 -0.11 5.00 0.29 34.01 3.44 -0.31 27.71 7.55 -0.17 5.00 0.30 -3.09 -3.59 -3.98 0.19 0.55 2.88 -2.12 1.94 -0.13 34.93 3.87 0.35 28.19 -5.95 -1.83 1.82 -0.14 -19.04 -11.99 -7.08 -0.22 -0.93 2.70 0.33 -2.68 -0.16 33.33 3.53 -0.12 17.34 -18.93 0.35 -2.41 -0.13 -2.91 -23.58 -26.12 -1.79 -2.06 57.30 0.00 57.30 1.28 13.86 3.77 -0.00 3.93 -28.34 0.00 73.51 1.66 58.06 -13.76 -29.03 -4.36 -1.15 2.70 -0.33 -2.68 -0.16 33.33 3.53 0.12 3.93 28.34 -0.35 -2.41 -0.13 -2.91 -13.76 29.03 -4.36 1.15 2.88 2.12 1.94 -0.13 34.93 3.87 -0.35 17.34 18.93 1.83 1.82 -0.14 -19.04 -23.58 26.12 -1.79 2.06 5.00 0.11 5.00 0.29 34.01 3.44 0.31 28.19 5.95 0.17 5.00 0.30 -3.10 -11.99 7.08 -0.22 0.93 3.08 0.74 -2.99 1.30 34.41 3.55 -1.10 27.71 -7.55 -0.75 -2.94 1.29 -6.79 -3.59 3.98 0.19 -0.55 4.50 3.68 2.60 -0.39 36.56 3.43 0.90 15.40 -25.00 3.65 2.59 -0.36 4.21 -15.54 -2.81 -2.20 0.02 4.37 0.60 -4.33 -0.37 31.19 3.58 1.44 3.50 -28.66 0.64 -3.74 -0.49 -3.72 -2.51 1.40 -2.86 0.48 7.25 1.76 7.04 -0.63 24.24 3.58 0.00 -9.62 -31.36 1.60 6.24 -0.60 -14.05 -2.90 -2.32 -2.93 1.74 - - - - - - - -19.28 -17.34 - - - - 3.57 -16.37 -3.33 3.46 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.