ID code: 1NKE, PD0385 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 11 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 443 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 G19C1' 30 C20C1' 30 C20C1' 49 G21C1' 49 G21C1' 71 A22C1' 71 A22C1' 92 T23C1' 92 T23C1' 112 C24C1' 112 C24C1' 131 A25C1' 131 A25C1' 152 G26C1' 152 G26C1' 174 C27C1' 174 C27C1' 193 C28C1' 193 C28C1' 212 C29C1' 250 T07C1' 228 G06C1' 270 G08C1' 250 T07C1' 292 C09C1' 270 G08C1' 311 T10C1' 292 C09C1' 331 G11C1' 311 T10C1' 353 A12C1' 331 G11C1' 374 T13C1' 353 A12C1' 394 C14C1' 374 T13C1' 413 G15C1' 394 C14C1' 435 C16C1' 413 G15C1' 9 G19N9 31 C20N1 31 C20N1 50 G21N9 50 G21N9 72 A22N9 72 A22N9 93 T23N1 93 T23N1 113 C24N1 113 C24N1 132 A25N9 132 A25N9 153 G26N9 153 G26N9 175 C27N1 175 C27N1 194 C28N1 194 C28N1 213 C29N1 251 T07N1 229 G06N9 271 G08N9 251 T07N1 293 C09N1 271 G08N9 312 T10N1 293 C09N1 332 G11N9 312 T10N1 354 A12N9 332 G11N9 375 T13N1 354 A12N9 395 C14N1 375 T13N1 414 G15N9 395 C14N1 436 C16N1 414 G15N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.55963*S + 39.18492 Y = 0.70846*S + 15.57232 Z = 0.43000*S + 25.34145 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.55963*S + 39.18492 Y = 0.70846*S + 15.57232 Z = 0.43000*S + 25.34145 >>>>>> HELIX ROTATION: 33.409 DISPLACEMENT: 3.3550 STATISTICS: OVERALL STANDARD DEV.: 1.3790 SIGMA(X): 2.1408, SIGMA(Y): 2.1032, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.5001, SIGMA(ROTATION): 9.474 THERE ARE 10.78 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 = 11 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.01310 0.11117 0.99372 89.25 83.62 6.43 -0.06402 0.07583 0.99506 93.67 85.65 5.70 -0.13511 -0.03560 0.99019 97.77 92.04 8.03 -0.15215 -0.03399 0.98777 98.75 91.95 8.97 -0.01782 -0.06796 0.99753 91.02 93.90 4.03 0.02159 -0.00959 0.99972 88.76 90.55 1.35 0.11733 0.03402 0.99251 83.26 88.05 7.02 0.17096 0.30463 0.93700 80.16 72.26 20.45 0.15545 0.26877 0.95058 81.06 74.41 18.09 -0.04435 0.38724 0.92091 92.54 67.22 22.94 -0.37957 0.29060 0.87834 112.31 73.11 28.56 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.14813 -0.20270 0.96797 98.52 101.69 14.54 -0.19306 -0.04664 0.98008 101.13 92.67 11.46 0.07040 -0.20763 0.97567 85.96 101.98 12.66 0.10157 -0.07332 0.99212 84.17 94.20 7.20 0.13364 -0.01897 0.99085 82.32 91.09 7.76 0.19680 0.06419 0.97834 78.65 86.32 11.95 0.21749 0.24823 0.94397 77.44 75.63 19.27 0.20300 0.10886 0.97311 78.29 83.75 13.32 -0.07151 0.09710 0.99270 94.10 84.43 6.93 -0.24126 -0.10498 0.96477 103.96 96.03 15.25 -0.20064 -0.16607 0.96549 101.57 99.56 15.10 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.13621 -0.03257 0.99014 97.83 91.87 8.05 -0.13264 -0.00418 0.99116 97.62 90.24 7.63 -0.02856 -0.08274 0.99616 91.64 94.75 5.02 0.00382 -0.05056 0.99871 89.78 92.90 2.91 0.04447 -0.05014 0.99775 87.45 92.87 3.84 0.13817 0.03215 0.98989 82.06 88.16 8.16 0.18164 0.17123 0.96834 79.53 80.14 14.46 0.17220 0.19523 0.96552 80.08 78.74 15.09 0.04602 0.17224 0.98398 87.36 80.08 10.27 -0.14800 0.15719 0.97642 98.51 80.96 12.47 -0.26261 0.06357 0.96281 105.22 86.36 15.68 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 I= 1 0 1 6 8 10 16 21 22 15 10 9 I= 2 1 0 7 8 10 15 20 21 14 9 8 I= 3 6 7 0 2 4 11 19 19 15 15 15 I= 4 8 8 2 0 2 9 16 17 13 14 16 I= 5 10 10 4 2 0 7 15 16 12 16 18 I= 6 16 15 11 9 7 0 8 9 9 17 23 I= 7 21 20 19 16 15 8 0 1 7 18 26 I= 8 22 21 19 17 16 9 1 0 7 18 26 I= 9 15 14 15 13 12 9 7 7 0 11 18 I= 10 10 9 15 14 16 17 18 18 11 0 8 I= 11 9 8 15 16 18 23 26 26 18 8 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 0.84 1.86 4.50****** 0.00 13.47 5.38 -9.07 2.23****** 0.00 -5.37 1.91 3.26 6.85 0.00 0.00 -1.39 11.37 16.02 -7.95 0.00 0.00 -4.76 6.46 -0.96 0.21****** 0.00 10.66 6.75 -0.67 -7.90 NaN 0.00 -8.70 2.15 6.89 3.97 0.00 0.00 5.92 4.07 2.62 -2.50 0.00 0.00 -2.87 2.83 4.00 -0.56****** 0.00 6.04 4.85 5.97 -0.49****** 0.00 0.02 1.35 3.08 5.19 0.00 0.00 8.09 8.73 10.67 0.04 0.00 0.00 1.12 6.93 13.70 8.13****** 0.00 12.71 14.24 -7.26 -3.47************ 8.64 18.38 -0.47 -2.19 0.00 0.00 -1.61 13.22 12.52 -9.71 0.00 0.00 -4.09 17.59 12.63 4.49 0.00 0.00 5.54 4.15 7.37-13.34****** 0.00 -0.66 22.93 19.58 5.56 0.00 0.00 14.70 -3.98 -0.10 -4.21 0.00 0.00 6.34 27.72 0.00 0.00****** 0.00 15.10 -0.11 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 1.64 0.30 -1.61 -0.01 34.57 3.26 0.14 7.13 3.73 -0.27 -1.62 -0.04 4.75 -19.87 4.68 1.67 0.66 7.48 -2.21 7.15 0.34 30.40 3.52 -0.49 7.22 -2.45 -2.68 6.99 0.43 -9.06 -3.99 9.43 1.78 -0.89 2.62 -2.37 1.11 -0.01 37.39 3.29 -0.61 4.72 1.70 -2.33 1.20 0.03 1.53 -15.42 0.37 0.57 -1.51 2.33 0.57 2.26 -0.88 32.00 3.32 0.16 2.89 0.29 0.61 2.25 -0.85 0.14 -14.63 1.90 -1.09 -1.58 7.16 0.87 7.11 -0.06 34.44 3.23 0.67 3.77 0.72 0.84 7.11 0.01 5.40 -8.91 2.05 -1.86 -1.83 8.45 1.40 8.33 -0.47 31.72 3.34 0.31 6.43 4.99 1.61 8.22 -0.42 0.16 -8.08 7.44 -1.86 -0.98 1.49 0.03 1.49 -0.65 27.70 3.84 0.29 11.60 8.51 -0.05 1.48 -0.66 -12.93 -11.61 7.60 -1.65 -0.96 7.43 -5.39 5.12 -0.53 37.00 3.68 -0.30 14.67 3.45 -5.27 5.13 -0.46 -8.08 10.28 -5.33 -1.60 -1.71 11.18 -1.58 11.06 -1.78 24.50 3.74 -0.49 10.26 0.32 -2.96 10.81 -1.68 -13.14 -9.69 -13.42 -2.96 -1.52 8.52 -2.07 8.27 -1.16 30.43 3.53 -0.02 10.18 7.12 -1.04 8.45 -1.06 -0.89 -15.84 -26.56 -4.08 -2.38 - - - - - - - 12.43 9.40 - - - - -8.95 -27.45 -4.73 -1.79 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.