ID code: 1EHV, BD0032 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 10 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 410 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: 11 G14C1' 33 C15C1' 33 C15C1' 52 G16C1' 52 G16C1' 74 A17C1' 74 A17C1' 95 A18C1' 95 A18C1' 116 T19C1' 116 T19C1' 136 T20C1' 136 T20C1' 156 C21C1' 156 C21C1' 175 G22C1' 175 G22C1' 197 C23C1' 238 C15C1' 216 G14C1' 257 G16C1' 238 C15C1' 279 A17C1' 257 G16C1' 300 A18C1' 279 A17C1' 321 T19C1' 300 A18C1' 341 T20C1' 321 T19C1' 361 C21C1' 341 T20C1' 380 G22C1' 361 C21C1' 402 C23C1' 380 G22C1' 12 G14N9 34 C15N1 34 C15N1 53 G16N9 53 G16N9 75 A17N9 75 A17N9 96 A18N9 96 A18N9 117 T19N1 117 T19N1 137 T20N1 137 T20N1 157 C21N1 157 C21N1 176 G22N9 176 G22N9 198 C23N1 239 C15N1 217 G14N9 258 G16N9 239 C15N1 280 A17N9 258 G16N9 301 A18N9 280 A17N9 322 T19N1 301 A18N9 342 T20N1 322 T19N1 362 C21N1 342 T20N1 381 G22N9 362 C21N1 403 C23N1 381 G22N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.02802*S + 14.10697 Y = 0.00004*S + 25.29195 Z = 0.99961*S + 0.39432 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.02802*S + 14.10697 Y = 0.00004*S + 25.29195 Z = 0.99961*S + 0.39433 >>>>>> HELIX ROTATION: 33.451 DISPLACEMENT: 3.3650 STATISTICS: OVERALL STANDARD DEV.: 0.9312 SIGMA(X): 1.0349, SIGMA(Y): 1.1411, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.3939, SIGMA(ROTATION): 6.286 THERE ARE 10.76 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 = 10 1 ROLL+TILT OUTPUT, FREEHELIX98 STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.11305 -0.07940 0.99041 96.49 94.55 7.94 0.08294 -0.06932 0.99414 85.24 93.97 6.21 0.10260 0.14464 0.98415 84.11 81.68 10.21 0.09374 0.04679 0.99450 84.62 87.32 6.01 0.04059 0.14489 0.98861 87.67 81.67 8.65 -0.05695 0.14775 0.98738 93.26 81.50 9.11 -0.20960 0.09620 0.97304 102.10 84.48 13.33 -0.12298 0.12775 0.98415 97.06 82.66 10.21 0.09420 0.12451 0.98774 84.59 82.85 8.98 0.13375 -0.01268 0.99093 82.31 90.73 7.72 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.13371 0.01317 0.99093 82.32 89.25 7.72 0.09459 -0.12415 0.98775 84.57 97.13 8.98 -0.12260 -0.12803 0.98416 97.04 97.36 10.21 -0.20949 -0.09696 0.97299 102.09 95.56 13.35 -0.05650 -0.14785 0.98739 93.24 98.50 9.11 0.04103 -0.14470 0.98862 87.65 98.32 8.65 0.09388 -0.04642 0.99450 84.61 92.66 6.01 0.10304 -0.14426 0.98416 84.09 98.29 10.21 0.08274 0.06965 0.99413 85.25 86.01 6.21 -0.11330 0.07915 0.99040 96.51 85.46 7.94 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.00900 -0.01721 0.99981 90.52 90.99 1.11 0.10183 -0.09313 0.99043 84.16 95.34 7.93 0.03810 -0.03217 0.99876 87.82 91.84 2.86 -0.06534 -0.08530 0.99421 93.75 94.89 6.17 0.02457 -0.04915 0.99849 88.59 92.82 3.15 0.02443 0.04930 0.99849 88.60 87.17 3.15 -0.06550 0.08501 0.99422 93.76 85.12 6.16 0.03800 0.03237 0.99875 87.82 88.14 2.86 0.10155 0.09352 0.99043 84.17 84.63 7.93 -0.00905 0.01727 0.99981 90.52 89.01 1.12 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 I= 1 0 7 2 5 2 4 6 3 8 1 I= 2 7 0 5 9 5 9 14 8 10 8 I= 3 2 5 0 6 1 4 8 3 8 3 I= 4 5 9 6 0 5 9 9 8 14 6 I= 5 2 5 1 5 0 5 9 4 9 4 I= 6 4 9 4 9 5 0 5 1 5 2 I= 7 6 14 8 9 9 5 0 6 9 5 I= 8 3 8 3 8 4 1 6 0 5 2 I= 9 8 10 8 14 9 5 9 5 0 7 I= 10 1 8 3 6 4 2 5 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 -1.47 -7.80 -6.81 9.00 0.00 0.00 -2.47 7.31 -4.58 -6.80 0.00 0.00 -6.13 -0.98 2.67 12.11 0.00 0.00 -8.33 -3.33 11.87 -4.01 0.00 0.00 -5.44 8.62 2.23 -5.18 0.00 0.00 6.64 -7.72 4.18 3.24 NaN 0.00 -5.93 -1.01 -2.77 5.77 0.00 0.00 13.08 2.61 -2.77 -8.85 0.00 0.00 -8.65 0.35 -0.17 5.60 0.00 0.00 9.10 0.46 -0.17 -5.60 0.00 0.00 -9.10 0.46 -2.76 8.85 0.00 0.00 8.64 0.35 -2.77 -5.77 0.00 0.00 -13.07 2.61 4.17 -3.25 0.00 0.00 5.92 -1.02 2.23 5.18 0.00 0.00 -6.64 -7.72 11.87 4.01 0.00 0.00 5.44 8.61 2.67-12.11 0.00 0.00 8.33 -3.34 -4.58 6.80 0.00 0.00 6.13 -0.98 -6.81 -9.00 0.00 0.00 2.48 7.31 0.00 0.00 0.00 0.00 1.48 -7.80 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 7.72 1.83 -7.50 0.63 34.81 3.80 0.93 -0.88 -0.69 2.06 -7.44 0.55 -17.48 1.01 15.11 0.62 -1.65 5.08 2.29 4.53 0.52 27.59 3.62 -0.13 -1.59 -7.77 2.21 4.55 0.59 -13.97 2.20 -2.37 0.39 -1.29 6.67 -1.23 6.56 -0.38 39.24 2.81 -0.21 -1.73 -2.28 -1.05 6.59 -0.26 19.94 -12.21 -16.34 -0.52 -0.58 5.56 -2.96 -4.71 -0.43 35.66 3.23 -0.30 -1.73 5.92 -2.96 -4.70 -0.41 -3.50 -19.03 3.61 -0.96 -0.29 5.64 0.00 -5.64 -0.81 36.18 3.10 0.00 -2.21 2.24 0.00 -5.65 -0.81 -0.21 -17.75 0.10 -1.14 0.02 5.55 2.96 -4.70 -0.43 35.66 3.23 0.30 -2.21 -2.25 2.97 -4.69 -0.41 -3.51 -17.75 -0.10 -1.14 -0.02 6.66 1.22 6.55 -0.38 39.24 2.81 0.21 -1.73 -5.91 1.04 6.59 -0.26 19.95 -19.01 -3.61 -0.96 0.29 5.08 -2.29 4.53 0.52 27.59 3.62 0.13 -1.73 2.28 -2.21 4.55 0.59 -13.97 -12.21 16.34 -0.52 0.58 7.72 -1.83 -7.50 0.63 34.81 3.80 -0.93 -1.60 7.77 -2.06 -7.44 0.55 -17.48 2.20 2.37 0.39 1.29 - - - - - - - -0.88 0.69 - - - - 1.01 -15.11 0.63 1.65 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.