ID code: 1YTB, PDT012 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 12 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 486 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 G01C1' 30 T02C1' 30 T02C1' 50 A03C1' 50 A03C1' 71 T04C1' 71 T04C1' 91 A05C1' 91 A05C1' 112 T06C1' 112 T06C1' 132 A07C1' 132 A07C1' 153 A08C1' 153 A08C1' 174 A09C1' 174 A09C1' 195 A10C1' 195 A10C1' 216 C11C1' 216 C11C1' 235 G12C1' 273 G19C1' 254 C18C1' 295 T20C1' 273 G19C1' 315 T21C1' 295 T20C1' 335 T22C1' 315 T21C1' 355 T23C1' 335 T22C1' 375 A24C1' 355 T23C1' 396 T25C1' 375 A24C1' 416 A26C1' 396 T25C1' 437 T27C1' 416 A26C1' 457 A28C1' 437 T27C1' 478 C29C1' 457 A28C1' 9 G01N9 31 T02N1 31 T02N1 51 A03N9 51 A03N9 72 T04N1 72 T04N1 92 A05N9 92 A05N9 113 T06N1 113 T06N1 133 A07N9 133 A07N9 154 A08N9 154 A08N9 175 A09N9 175 A09N9 196 A10N9 196 A10N9 217 C11N1 217 C11N1 236 G12N9 274 G19N9 255 C18N1 296 T20N1 274 G19N9 316 T21N1 296 T20N1 336 T22N1 316 T21N1 356 T23N1 336 T22N1 376 A24N9 356 T23N1 397 T25N1 376 A24N9 417 A26N9 397 T25N1 438 T27N1 417 A26N9 458 A28N9 438 T27N1 479 C29N1 458 A28N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.33004*S + -4.00656 Y = -0.05922*S + 37.54441 Z = 0.94211*S + 3.76344 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.33004*S + -4.00656 Y = -0.05922*S + 37.54441 Z = 0.94211*S + 3.76344 >>>>>> HELIX ROTATION: 26.103 DISPLACEMENT: 2.3001 STATISTICS: OVERALL STANDARD DEV.: 1.8788 SIGMA(X): 2.6398, SIGMA(Y): 3.2623, SIGMA(Z)=SIGMA(DISPLACEMENT): 1.3011, SIGMA(ROTATION): 8.628 THERE ARE 13.79 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 = 12 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.57050 -0.21387 0.79296 55.21 102.35 37.54 0.62597 -0.24933 0.73891 51.25 104.44 42.36 0.37229 0.58926 0.71706 68.14 53.90 44.19 0.36879 0.66736 0.64701 68.36 48.14 49.68 0.30837 0.85517 0.41665 72.04 31.22 65.38 -0.21134 0.90062 0.37975 102.20 25.76 67.68 -0.49239 0.82622 0.27371 119.50 34.29 74.11 -0.76696 0.61257 0.19114 140.08 52.22 78.98 -0.77629 -0.10265 0.62197 140.92 95.89 51.54 -0.77988 -0.08855 0.61963 141.25 95.08 51.71 -0.75598 -0.07648 0.65012 139.11 94.39 49.45 -0.62046 -0.13512 0.77251 128.35 97.77 39.42 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.80118 -0.17935 0.57092 36.76 100.33 55.19 0.74791 -0.21563 0.62780 41.59 102.45 51.11 0.81538 0.45096 0.36302 35.37 63.19 68.71 0.46138 0.85829 0.22462 62.52 30.87 77.02 0.19716 0.89817 0.39295 78.63 26.08 66.86 -0.28497 0.84464 0.45318 106.56 32.37 63.05 -0.46386 0.62746 0.62541 117.64 51.14 51.29 -0.55749 0.41915 0.71660 123.88 65.22 44.23 -0.73197 -0.10080 0.67384 137.05 95.79 47.64 -0.64824 -0.10865 0.75364 130.41 96.24 41.09 -0.62846 -0.08214 0.77349 128.94 94.71 39.33 -0.59333 -0.11071 0.79731 126.39 96.36 37.13 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.68312 -0.19201 0.70462 46.91 101.07 45.20 0.70781 -0.24032 0.66427 44.94 103.91 48.37 0.64181 0.54436 0.54014 50.07 57.02 57.31 0.40961 0.78471 0.46525 65.82 38.31 62.27 0.22990 0.84758 0.47828 76.71 32.05 61.43 -0.22944 0.84903 0.47593 103.26 31.89 61.58 -0.48244 0.74067 0.46761 118.84 42.21 62.12 -0.69424 0.54349 0.47186 133.97 57.08 61.85 -0.75281 -0.09985 0.65062 138.83 95.73 49.41 -0.71088 -0.11528 0.69380 135.31 96.62 46.07 -0.68928 -0.10142 0.71736 133.57 95.82 44.16 -0.62157 -0.11290 0.77518 128.43 96.48 39.18 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 12 I= 1 0 3 44 62 70 89 98 104 92 88 86 81 I= 2 3 0 46 65 73 92 102 107 94 90 89 84 I= 3 44 46 0 19 29 55 69 83 100 98 96 92 I= 4 62 65 19 0 10 37 53 68 94 93 91 88 I= 5 70 73 29 10 0 26 42 58 86 85 84 82 I= 6 89 92 55 37 26 0 15 32 66 66 65 65 I= 7 98 102 69 53 42 15 0 16 53 54 53 54 I= 8 104 107 83 68 58 32 16 0 39 40 40 42 I= 9 92 94 100 94 86 66 53 39 0 3 5 10 I= 10 88 90 98 93 85 66 54 40 3 0 1 6 I= 11 86 89 96 91 84 65 53 40 5 1 0 5 I= 12 81 84 92 88 82 65 54 42 10 6 5 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 25.66 25.38 -0.27 3.77 0.00 -0.00 41.12 29.44 -3.28 -1.69 0.00 -0.00 -0.41 42.36 57.81-13.11 0.00 0.00 3.91 50.84 41.61 5.09 0.00 0.00 32.93 25.86 3.23 3.11 0.00****** 20.88 59.42 32.49 2.96****** 0.00 19.26 43.43 8.41 7.61 0.00 0.00 25.57 60.88 14.40 -5.61 0.00 0.00 -9.44 63.40 31.27 3.01 0.00 0.00 -2.70 66.69 28.87 -2.69****** 0.00 1.19 67.65 16.04 5.18 0.00 0.00 5.99 62.29 15.56 -4.88 0.00 0.00 -22.89 61.60 18.72 7.71****** 0.00 -14.09 47.85 13.15 -1.19 0.00 0.00 -45.26 42.65 45.64 -1.23 0.00 0.00 -29.37 29.73 31.80 8.74 0.00 0.00 -18.04 45.99 -0.80 -0.22 -0.00 0.00 -16.77 42.86 2.77 -3.94 0.00 0.50 -44.21 21.13 1.04 -1.13 0.00 0.00 -34.55 19.41 0.53 -1.82 0.00 0.00 -49.43 0.95 5.51 6.44****** 0.00 -39.27 1.85 1.09 2.36 0.00 0.00 -35.80-14.31 0.00 0.00 0.00 0.00 -33.28-14.56 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 3.87 3.75 -0.96 -0.88 36.18 3.40 0.32 27.05 33.00 2.56 -1.76 -0.89 -1.40 -15.60 10.03 -5.78 -3.34 46.98 -0.85 46.97 -0.96 17.93 3.74 -0.47 48.32 1.76 -2.34 51.85 -0.75 22.85 -4.33 8.64 -6.26 -1.42 19.72 0.86 19.70 -0.41 18.72 3.82 -1.70 44.35 27.95 0.83 19.50 -0.31 -4.92 12.85 31.48 -6.51 -1.78 10.95 -1.81 10.80 1.36 20.99 4.20 -0.20 52.07 23.69 -2.03 10.78 1.53 -24.72 -6.54 26.56 -7.34 -1.99 26.56 -0.45 26.55 0.57 9.83 4.10 0.06 60.90 -5.04 0.44 27.34 0.73 -6.63 -6.73 1.84 -7.30 0.83 15.83 1.72 15.74 1.65 19.78 4.09 -0.09 61.42 2.81 2.66 15.74 1.80 -16.82 -4.80 -4.79 -7.13 0.20 16.64 4.84 15.94 0.54 23.92 3.75 0.80 55.29 -18.97 5.03 16.01 0.70 -9.06 -8.95 -21.61 -6.71 2.67 39.16 2.36 39.10 0.55 16.20 3.85 1.32 37.93 -39.20 1.76 40.19 0.74 26.98 -16.61 -30.67 -5.16 4.37 3.56 -2.14 2.85 0.40 35.43 3.46 -1.10 44.24 -17.46 -1.65 1.96 0.41 -1.28 -1.28 -3.69 -4.20 3.63 2.00 -1.29 1.53 -0.49 33.61 3.24 -0.03 21.15 -38.55 -1.18 0.88 -0.47 5.36 -9.63 -4.98 -3.99 5.11 5.15 2.33 4.59 0.69 37.72 3.39 0.64 2.68 -44.04 2.30 3.20 0.75 -0.17 -10.18 0.38 -3.82 5.70 - - - - - - - -15.42 -34.96 - - - - -2.52 0.22 -1.73 8.41 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.