ID code: 1QQB, PD0061 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 G06C1' 131 G06C1' 153 C07C1' 153 C07C1' 172 G08C1' 172 G08C1' 194 C09C1' 194 C09C1' 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 G06C1' 435 A05C1' 478 C07C1' 456 G06C1' 497 G08C1' 478 C07C1' 519 C09C1' 497 G08C1' 538 T10C1' 519 C09C1' 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 G06N9 132 G06N9 154 C07N1 154 C07N1 173 G08N9 173 G08N9 195 C09N1 195 C09N1 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 G06N9 436 A05N9 479 C07N1 457 G06N9 498 G08N9 479 C07N1 520 C09N1 498 G08N9 539 T10N1 520 C09N1 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 + 9.98502 Y = 0.84156*S + 0.00000 Z = 0.54016*S + -0.00000 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.00000*S + 9.98502 Y = 0.84156*S + 0.00000 Z = 0.54016*S + 0.00000 >>>>>> HELIX ROTATION: 29.146 DISPLACEMENT: 3.3053 STATISTICS: OVERALL STANDARD DEV.: 2.4200 SIGMA(X): 3.7147, SIGMA(Y): 3.2331, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.1848, SIGMA(ROTATION): 15.709 THERE ARE 12.35 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 0.09307 0.57908 0.80994 84.66 54.61 35.91 0.10127 0.55274 0.82718 84.19 56.45 34.19 0.06207 0.45891 0.88631 86.44 62.68 27.59 0.18985 0.34950 0.91750 79.06 69.54 23.44 0.05554 0.55400 0.83066 86.82 56.36 33.83 0.11762 0.56048 0.81977 83.25 55.91 34.94 -0.03105 0.38261 0.92339 91.78 67.50 22.57 -0.19489 0.46465 0.86378 101.24 62.31 30.26 0.05961 -0.37813 0.92383 86.58 112.22 22.51 0.06118 -0.26528 0.96223 86.49 105.38 15.80 -0.02205 -0.41714 0.90858 91.26 114.65 24.69 0.07941 -0.53166 0.84322 85.45 122.12 32.52 -0.01991 -0.54829 0.83605 91.14 123.25 33.27 0.01820 -0.41332 0.91041 88.96 114.41 24.44 0.12558 -0.44371 0.88733 82.79 116.34 27.46 0.19196 -0.26075 0.94613 78.93 105.11 18.89 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.19196 0.26075 0.94613 78.93 74.89 18.89 0.12558 0.44365 0.88736 82.79 63.66 27.46 0.01812 0.41330 0.91041 88.96 65.59 24.44 -0.01991 0.54832 0.83603 91.14 56.75 33.28 0.07941 0.53167 0.84322 85.45 57.88 32.52 -0.02206 0.41714 0.90857 91.26 65.35 24.69 0.06118 0.26528 0.96223 86.49 74.62 15.80 0.05961 0.37813 0.92383 86.58 67.78 22.51 -0.19489 -0.46465 0.86378 101.24 117.69 30.26 -0.03105 -0.38261 0.92339 91.78 112.50 22.57 0.11762 -0.56048 0.81977 83.25 124.09 34.94 0.05561 -0.55398 0.83067 86.81 123.64 33.83 0.18984 -0.34952 0.91749 79.06 110.46 23.44 0.06205 -0.45893 0.88630 86.44 117.32 27.59 0.10130 -0.55266 0.82723 84.19 123.55 34.18 0.09312 -0.57904 0.80996 84.66 125.38 35.91 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.14134 0.45149 0.88101 81.87 63.16 28.24 0.11059 0.50424 0.85645 83.65 59.72 31.08 0.09096 0.44511 0.89085 84.78 63.57 27.02 0.06635 0.46184 0.88448 86.20 62.49 27.81 0.05464 0.49946 0.86461 86.87 60.04 30.16 0.03883 0.47496 0.87915 87.77 61.64 28.46 -0.01208 0.35270 0.93566 90.69 69.35 20.67 -0.01836 0.42313 0.90588 91.05 64.97 25.06 -0.01836 -0.42313 0.90588 91.05 115.03 25.06 -0.01208 -0.35270 0.93566 90.69 110.65 20.67 0.03883 -0.47496 0.87915 87.77 118.36 28.46 0.05466 -0.49945 0.86462 86.87 119.96 30.16 0.06634 -0.46184 0.88448 86.20 117.51 27.81 0.09095 -0.44513 0.89084 84.78 116.43 27.02 0.11060 -0.50426 0.85644 83.65 120.28 31.08 0.14134 -0.45152 0.88099 81.87 116.84 28.24 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 3 2 4 5 6 10 9 52 48 55 57 54 53 57 53 I= 2 3 0 4 3 3 4 12 9 55 51 58 60 57 56 60 57 I= 3 2 4 0 1 4 3 8 6 51 47 54 56 53 52 56 53 I= 4 4 3 1 0 2 1 8 5 52 48 55 57 55 53 57 54 I= 5 5 3 4 2 0 1 10 6 55 50 58 59 57 56 60 57 I= 6 6 4 3 1 1 0 8 4 53 49 56 58 55 54 58 55 I= 7 10 12 8 8 10 8 0 4 45 41 49 50 48 47 51 48 I= 8 9 9 6 5 6 4 4 0 50 45 53 55 52 51 55 52 I= 9 52 55 51 52 55 53 45 50 0 4 4 6 5 6 9 9 I= 10 48 51 47 48 50 49 41 45 4 0 8 10 8 8 12 10 I= 11 55 58 54 55 58 56 49 53 4 8 0 1 1 3 4 6 I= 12 57 60 56 57 59 58 50 55 6 10 1 0 2 4 3 5 I= 13 54 57 53 55 57 55 48 52 5 8 1 2 0 1 3 4 I= 14 53 56 52 53 56 54 47 51 6 8 3 4 1 0 4 2 I= 15 57 60 56 57 60 58 51 55 9 12 4 3 3 4 0 3 I= 16 53 57 53 54 57 55 48 52 9 10 6 5 4 2 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 21.60-27.16 -0.55 1.48 0.00 0.00 17.22 -7.53 3.39-10.68 0.00 -0.00 31.04-12.91 -5.83 -0.23 0.00 0.00 26.01 -8.19 -3.78 -5.17 0.00 0.00 27.52 1.79 -8.27 5.00 0.00****** 24.43 -0.54 8.06 0.35 -0.00 0.00 11.61 20.06 12.96 5.61 0.00 0.00 28.67 15.43 -5.29 2.31 0.00 0.00 9.06 32.28 -3.51 0.70 0.00 0.00 7.29 31.49 5.19 -7.09 -0.00 0.00 -15.87 30.21 12.21 -5.44 0.00 0.00 -5.65 23.95 -0.48 -9.96 0.00 0.00 -15.80 15.70 -0.29 10.55****** 0.00 -14.01 7.15 -5.83 2.81 0.00 0.00 -26.40 13.72 57.43-14.74 0.00 0.00 -22.46 -1.39 57.43 14.74 0.00 0.00 22.46 -1.39 -5.83 -2.81 0.00 0.00 26.40 13.72 -0.29-10.55 0.00 0.50 14.01 7.15 -0.48 9.96 0.00 0.00 15.80 15.70 12.21 5.44 0.00 0.00 5.65 23.95 5.19 7.09 -0.00 0.00 15.87 30.21 -3.51 -0.70 0.00 0.00 -7.29 31.49 -5.29 -2.31 0.00 0.00 -9.05 32.28 12.95 -5.61 0.00 0.00 -28.67 15.43 8.06 -0.34 -0.00 0.00 -11.61 20.06 -8.27 -5.00 -0.00 0.00 -24.43 -0.54 -3.78 5.17 0.00 0.00 -27.52 1.79 -5.83 0.24 0.00 0.00 -26.01 -8.20 3.39 10.69 -0.00 0.00 -31.04-12.91 -0.55 -1.48 0.00 0.00 -17.22 -7.53 0.00 0.00 0.00 0.00 -21.61-27.16 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 3.77 -3.67 0.87 -0.85 26.25 3.78 0.14 -18.77 20.29 -3.47 0.45 -0.85 -15.04 4.26 20.31 -3.41 -3.63 4.08 -0.19 -4.07 -0.51 33.48 3.69 -1.05 -10.88 28.72 0.13 -3.57 -0.59 -7.68 5.02 5.27 -2.96 -1.95 1.74 1.06 1.39 -0.17 37.89 3.42 -0.62 3.50 26.76 -1.04 1.35 -0.17 -0.21 3.05 -2.41 -2.78 -0.68 2.53 1.55 1.99 1.28 34.86 3.47 1.14 17.18 21.17 1.44 1.74 1.35 1.67 -17.07 -2.61 -2.08 -0.04 1.87 -1.67 0.84 0.52 33.96 3.66 -0.27 28.90 7.91 -1.48 0.77 0.57 -6.35 1.77 -0.94 0.19 0.46 8.26 -5.08 6.52 -0.50 33.28 3.43 0.32 26.35 -9.99 -5.03 5.70 -0.44 -1.38 -10.25 -7.29 -0.35 -0.90 4.40 2.14 -3.84 -0.31 35.37 3.58 -0.43 13.70 -15.17 2.03 -3.51 -0.34 -6.59 -1.72 -8.68 -1.74 -2.01 50.07 -0.00 50.07 1.24 10.63 3.99 -0.00 3.30 -24.81 -0.00 57.81 1.48 30.52 -4.23 -15.26 -4.42 -0.99 4.40 -2.14 -3.84 -0.31 35.37 3.58 0.43 3.30 24.81 -2.03 -3.51 -0.34 -6.59 -4.23 15.26 -4.42 0.99 8.26 5.08 6.52 -0.50 33.28 3.43 -0.32 13.70 15.17 5.03 5.70 -0.44 -1.38 -1.72 8.68 -1.74 2.01 1.87 1.66 0.85 0.52 33.96 3.66 0.27 26.35 9.99 1.48 0.77 0.57 -6.35 -10.25 7.29 -0.35 0.90 2.53 -1.56 1.99 1.28 34.86 3.47 -1.14 28.89 -7.91 -1.44 1.74 1.35 1.68 1.77 0.94 0.19 -0.46 1.74 -1.06 1.38 -0.18 37.89 3.42 0.62 17.18 -21.18 1.04 1.35 -0.17 -0.22 -17.07 2.62 -2.08 0.04 4.08 0.19 -4.07 -0.52 33.48 3.68 1.05 3.50 -26.76 -0.13 -3.57 -0.59 -7.66 3.05 2.40 -2.78 0.68 3.77 3.67 0.87 -0.85 26.25 3.78 -0.14 -10.88 -28.72 3.47 0.45 -0.85 -15.04 5.01 -5.27 -2.96 1.95 - - - - - - - -18.77 -20.29 - - - - 4.26 -20.30 -3.41 3.63 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.