ID code: 2DNJ, PDE006 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 14 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 562 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 G09C1' 30 C10C1' 30 C10C1' 49 G11C1' 49 G11C1' 71 A12C1' 71 A12C1' 92 T13C1' 92 T13C1' 112 C14C1' 112 C14C1' 128 G01C1' 128 G01C1' 150 C02C1' 150 C02C1' 169 G03C1' 169 G03C1' 191 A04C1' 191 A04C1' 212 T05C1' 212 T05C1' 232 C06C1' 232 C06C1' 251 G07C1' 251 G07C1' 273 C08C1' 311 C10C1' 289 G09C1' 330 G11C1' 311 C10C1' 352 A12C1' 330 G11C1' 373 T13C1' 352 A12C1' 393 C14C1' 373 T13C1' 409 G01C1' 393 C14C1' 431 C02C1' 409 G01C1' 450 G03C1' 431 C02C1' 472 A04C1' 450 G03C1' 493 T05C1' 472 A04C1' 513 C06C1' 493 T05C1' 532 G07C1' 513 C06C1' 554 C08C1' 532 G07C1' 9 G09N9 31 C10N1 31 C10N1 50 G11N9 50 G11N9 72 A12N9 72 A12N9 93 T13N1 93 T13N1 113 C14N1 113 C14N1 129 G01N9 129 G01N9 151 C02N1 151 C02N1 170 G03N9 170 G03N9 192 A04N9 192 A04N9 213 T05N1 213 T05N1 233 C06N1 233 C06N1 252 G07N9 252 G07N9 274 C08N1 312 C10N1 290 G09N9 331 G11N9 312 C10N1 353 A12N9 331 G11N9 374 T13N1 353 A12N9 394 C14N1 374 T13N1 410 G01N9 394 C14N1 432 C02N1 410 G01N9 451 G03N9 432 C02N1 473 A04N9 451 G03N9 494 T05N1 473 A04N9 514 C06N1 494 T05N1 533 G07N9 514 C06N1 555 C08N1 533 G07N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.00000*S + 51.41501 Y = -0.44477*S + 58.59300 Z = 0.89565*S + 29.09652 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.00000*S + 51.41501 Y = -0.44477*S + 58.59301 Z = 0.89565*S + 29.09653 >>>>>> HELIX ROTATION: 33.085 DISPLACEMENT: 3.3437 STATISTICS: OVERALL STANDARD DEV.: 2.0567 SIGMA(X): 2.9095, SIGMA(Y): 3.0621, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.4726, SIGMA(ROTATION): 22.039 THERE ARE 10.88 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 = 14 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.10152 -0.06683 0.99259 95.83 93.83 6.98 -0.27094 -0.11129 0.95614 105.72 96.39 17.03 -0.20005 -0.14660 0.96876 101.54 98.43 14.36 -0.13483 -0.21836 0.96651 97.75 102.61 14.87 -0.11328 -0.26838 0.95663 96.50 105.57 16.94 0.10835 -0.17722 0.97819 83.78 100.21 11.99 0.22657 -0.17428 0.95828 76.90 100.04 16.61 0.18796 -0.05236 0.98078 79.17 93.00 11.25 0.14982 0.18700 0.97087 81.38 79.22 13.86 0.08579 0.17205 0.98134 85.08 80.09 11.08 -0.09751 0.26831 0.95839 95.60 74.44 16.59 -0.16193 0.40039 0.90192 99.32 66.40 25.59 -0.28169 0.18412 0.94167 106.36 79.39 19.67 -0.35647 0.12872 0.92540 110.88 82.60 22.27 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.35647 -0.12872 0.92540 110.88 97.40 22.27 -0.28170 -0.18413 0.94167 106.36 100.61 19.67 -0.16195 -0.40041 0.90191 99.32 113.60 25.59 -0.09751 -0.26830 0.95839 95.60 105.56 16.59 0.08579 -0.17205 0.98134 85.08 99.91 11.08 0.14982 -0.18700 0.97087 81.38 100.78 13.86 0.18795 0.05237 0.98078 79.17 87.00 11.25 0.22657 0.17428 0.95828 76.90 79.96 16.61 0.10835 0.17722 0.97819 83.78 79.79 11.99 -0.11328 0.26839 0.95663 96.50 74.43 16.94 -0.13483 0.21836 0.96651 97.75 77.39 14.87 -0.20006 0.14661 0.96875 101.54 81.57 14.36 -0.27091 0.11128 0.95615 105.72 83.61 17.03 -0.10151 0.06683 0.99259 95.83 86.17 6.98 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.21974 -0.10380 0.97002 102.69 95.96 14.06 -0.25092 -0.16068 0.95458 104.53 99.25 17.34 -0.16337 -0.23932 0.95710 99.40 103.85 16.84 -0.10698 -0.23722 0.96555 96.14 103.72 15.08 -0.04037 -0.22415 0.97372 92.31 102.95 13.16 0.13629 -0.18516 0.97321 82.17 100.67 13.29 0.16550 -0.08332 0.98268 80.47 94.78 10.68 0.16550 0.08332 0.98268 80.47 85.22 10.68 0.13630 0.18515 0.97321 82.17 79.33 13.29 -0.04037 0.22415 0.97372 92.31 77.05 13.16 -0.10696 0.23721 0.96555 96.14 76.28 15.08 -0.16337 0.23932 0.95710 99.40 76.15 16.84 -0.25092 0.16067 0.95458 104.53 80.75 17.33 -0.21973 0.10379 0.97002 102.69 84.04 14.06 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 I= 1 0 3 8 10 12 21 22 24 26 21 20 20 15 11 I= 2 3 0 6 9 12 22 24 27 30 25 24 23 18 15 I= 3 8 6 0 3 7 17 21 26 30 27 27 27 23 20 I= 4 10 9 3 0 3 14 18 24 28 26 27 27 24 20 I= 5 12 12 7 3 0 10 14 21 25 25 26 27 25 21 I= 6 21 22 17 14 10 0 6 15 21 25 28 30 30 26 I= 7 22 24 21 18 14 6 0 9 15 21 24 26 27 24 I= 8 24 27 26 24 21 15 9 0 6 14 18 21 24 22 I= 9 26 30 30 28 25 21 15 6 0 10 14 17 22 21 I= 10 21 25 27 26 25 25 21 14 10 0 3 7 12 12 I= 11 20 24 27 27 26 28 24 18 14 3 0 3 9 10 I= 12 20 23 27 27 27 30 26 21 17 7 3 0 6 8 I= 13 15 18 23 24 25 30 27 24 22 12 9 6 0 3 I= 14 11 15 20 20 21 26 24 22 21 12 10 8 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 6.37 2.85 4.47 9.02 0.00 0.00 17.46 13.39 2.24 -4.85 0.00 0.50 5.98 15.89 3.30 -3.12 0.00 0.00 10.17 16.65 14.14 -2.19 0.00 0.00 0.03 14.36 5.47 1.04****** 0.00 13.18 21.52 -1.60 -8.30 0.00 0.00 -3.45 14.45 1.44 2.77 0.00 0.00 -0.52 16.58 10.12 -6.28 0.00 0.00 -9.09 14.16 13.80 1.28****** 0.00 3.14 10.62 2.85 2.46****** 0.00 -3.29 11.52 3.64 5.73 0.00 0.00 -2.09 13.70 12.99 -5.21 0.00 0.00 -5.36 15.67 7.00 -2.21****** 0.00 6.27 9.30 7.00 2.21 0.00 0.00 -6.27 9.30 12.99 5.21 0.00 0.00 5.36 15.67 3.64 -5.73 0.00 0.00 2.09 13.70 2.85 -2.46****** 0.00 3.29 11.52 13.80 -1.28****** 0.00 -3.14 10.62 10.12 6.28 0.00 0.00 9.09 14.16 1.44 -2.77 0.00 0.00 0.52 16.58 -1.60 8.30****** 0.00 3.45 14.45 5.47 -1.04****** 0.00 -13.18 21.52 14.14 2.19 0.00 0.00 -0.03 14.36 3.30 3.12 0.00 0.00 -10.17 16.65 2.24 4.85 0.00 0.00 -5.97 15.89 4.47 -9.02****** 0.00 -17.46 13.39 0.00 0.00 0.00 0.00 -6.37 2.85 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 3.82 1.01 3.69 -0.00 34.05 3.56 -0.46 7.45 11.86 1.09 3.56 0.07 -9.95 -11.16 10.87 2.33 -2.28 6.75 -3.21 5.94 1.05 33.11 3.32 -1.08 14.78 8.86 -3.17 5.96 1.15 6.71 -4.20 0.92 0.67 -3.92 3.27 -2.05 2.55 0.49 34.23 3.49 0.00 15.84 5.57 -2.04 2.51 0.56 -5.53 -13.20 7.64 -2.28 -3.31 3.92 -1.10 3.76 -0.06 27.36 3.65 0.96 15.00 -1.59 -1.03 3.75 -0.01 -5.79 -2.93 2.10 -3.83 -1.84 10.38 2.84 9.99 -0.21 36.45 3.41 0.11 12.34 -4.51 2.73 10.05 -0.10 5.86 -12.23 -3.69 -3.74 -0.90 6.10 -1.60 5.88 -1.21 23.51 3.49 1.28 13.04 -2.54 -1.58 5.87 -1.13 -8.52 -1.20 2.17 -3.89 0.74 9.56 0.00 9.56 -1.44 36.23 3.12 0.00 10.57 -1.52 -0.00 9.59 -1.28 12.71 -11.65 -6.35 -2.53 0.18 6.10 1.60 5.88 -1.21 23.51 3.49 -1.28 10.57 1.52 1.58 5.87 -1.13 -8.52 -11.65 6.35 -2.53 -0.18 10.38 -2.84 9.99 -0.21 36.45 3.41 -0.11 13.04 2.54 -2.73 10.05 -0.10 5.86 -1.20 -2.17 -3.89 -0.74 3.92 1.10 3.76 -0.06 27.36 3.65 -0.96 12.34 4.51 1.03 3.75 -0.01 -5.79 -12.23 3.69 -3.74 0.90 3.27 2.05 2.55 0.49 34.23 3.49 -0.00 14.99 1.59 2.04 2.51 0.56 -5.53 -2.93 -2.10 -3.83 1.84 6.75 3.21 5.94 1.05 33.11 3.32 1.08 15.84 -5.57 3.16 5.97 1.15 6.71 -13.20 -7.64 -2.28 3.31 3.82 -1.01 3.69 -0.00 34.05 3.56 0.46 14.78 -8.86 -1.09 3.56 0.07 -9.95 -4.20 -0.92 0.67 3.92 - - - - - - - 7.45 -11.86 - - - - -11.16 -10.87 2.33 2.28 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.