ID code: 1DNE, GDL004 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 C01C1' 27 G02C1' 27 G02C1' 49 C03C1' 49 C03C1' 68 G04C1' 68 G04C1' 90 A05C1' 90 A05C1' 111 T06C1' 111 T06C1' 131 A07C1' 131 A07C1' 152 T08C1' 152 T08C1' 172 C09C1' 172 C09C1' 191 G10C1' 191 G10C1' 213 C11C1' 213 C11C1' 232 G12C1' 270 G14C1' 251 C13C1' 292 C15C1' 270 G14C1' 311 G16C1' 292 C15C1' 333 A17C1' 311 G16C1' 354 T18C1' 333 A17C1' 374 A19C1' 354 T18C1' 395 T20C1' 374 A19C1' 415 C21C1' 395 T20C1' 434 G22C1' 415 C21C1' 456 C23C1' 434 G22C1' 475 G24C1' 456 C23C1' 9 C01N1 28 G02N9 28 G02N9 50 C03N1 50 C03N1 69 G04N9 69 G04N9 91 A05N9 91 A05N9 112 T06N1 112 T06N1 132 A07N9 132 A07N9 153 T08N1 153 T08N1 173 C09N1 173 C09N1 192 G10N9 192 G10N9 214 C11N1 214 C11N1 233 G12N9 271 G14N9 252 C13N1 293 C15N1 271 G14N9 312 G16N9 293 C15N1 334 A17N9 312 G16N9 355 T18N1 334 A17N9 375 A19N9 355 T18N1 396 T20N1 375 A19N9 416 C21N1 396 T20N1 435 G22N9 416 C21N1 457 C23N1 435 G22N9 476 G24N9 457 C23N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.06922*S + 10.18345 Y = 0.24009*S + 2.04529 Z = 0.96828*S + -1.23508 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.06922*S + 10.18345 Y = 0.24009*S + 2.04529 Z = 0.96828*S + -1.23508 >>>>>> HELIX ROTATION: 36.388 DISPLACEMENT: 3.3549 STATISTICS: OVERALL STANDARD DEV.: 1.2655 SIGMA(X): 1.5623, SIGMA(Y): 1.4078, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.5514, SIGMA(ROTATION): 11.655 THERE ARE 9.89 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 -0.15000 0.11960 0.98143 98.63 83.13 11.06 -0.15819 -0.07087 0.98486 99.10 94.06 9.98 -0.09672 0.17090 0.98053 95.55 80.16 11.33 -0.05854 -0.17317 0.98315 93.36 99.97 10.53 0.04665 -0.04623 0.99784 87.33 92.65 3.77 0.05929 -0.19323 0.97936 86.60 101.14 11.66 0.10561 -0.24747 0.96312 83.94 104.33 15.61 0.02905 -0.07674 0.99663 88.34 94.40 4.71 0.12475 -0.13383 0.98312 82.83 97.69 10.54 0.02314 0.05645 0.99814 88.67 86.76 3.50 0.35103 0.07755 0.93315 69.45 85.55 21.07 0.16750 0.04580 0.98481 80.36 87.38 10.00 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.08125 0.01476 0.99658 94.66 89.15 4.74 -0.02436 -0.25810 0.96581 91.40 104.96 15.03 -0.08465 -0.06062 0.99457 94.86 93.48 5.98 0.07725 0.09584 0.99239 85.57 84.50 7.07 0.05483 -0.00300 0.99849 86.86 90.17 3.15 -0.01016 0.08386 0.99643 90.58 85.19 4.85 0.05707 0.02324 0.99810 86.73 88.67 3.53 -0.09423 -0.02719 0.99518 95.41 91.56 5.63 -0.08124 -0.00500 0.99668 94.66 90.29 4.67 -0.04575 -0.16379 0.98543 92.62 99.43 9.79 0.07189 -0.09645 0.99274 85.88 95.54 6.91 0.11918 -0.01567 0.99275 83.16 90.90 6.90 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.14426 0.08354 0.98601 98.29 85.21 9.60 -0.08606 -0.13619 0.98694 94.94 97.83 9.27 -0.14169 -0.02815 0.98951 98.15 91.61 8.31 -0.00849 -0.06100 0.99810 90.49 93.50 3.53 0.03387 0.00058 0.99943 88.06 89.97 1.94 -0.02343 -0.07223 0.99711 91.34 94.14 4.36 0.05250 -0.09314 0.99427 86.99 95.34 6.14 0.00251 -0.03456 0.99940 89.86 91.98 1.99 0.01131 -0.01422 0.99983 89.35 90.81 1.04 -0.01075 -0.03243 0.99942 90.62 91.86 1.96 0.06609 0.06482 0.99571 86.21 86.28 5.31 0.12276 -0.00522 0.99242 82.95 90.30 7.06 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 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS J= 1 2 3 4 5 6 7 8 9 10 11 12 I= 1 0 13 6 11 11 11 15 10 10 10 12 16 I= 2 13 0 6 6 10 5 8 7 8 7 14 14 I= 3 6 6 0 7 10 7 11 8 8 7 13 15 I= 4 11 6 7 0 4 1 3 1 2 1 8 8 I= 5 11 10 10 4 0 5 5 2 1 3 4 5 I= 6 11 5 7 1 5 0 4 2 3 2 9 9 I= 7 15 8 11 3 5 4 0 4 5 5 9 6 I= 8 10 7 8 1 2 2 4 0 1 0 6 7 I= 9 10 8 8 2 1 3 5 1 0 1 5 6 I= 10 10 7 7 1 3 2 5 0 1 0 7 7 I= 11 12 14 13 8 4 9 9 6 5 7 0 5 I= 12 16 14 15 8 5 9 6 7 6 7 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 -5.10 9.79 10.61 2.83****** 0.00 0.06 4.74 16.18 0.21 0.00 0.50 -1.03 9.93 -7.99-11.95 0.00 0.00 12.19 8.65-10.80 -4.98 0.00 0.00 -9.58 -5.98 5.75 19.35****** 0.00 -2.61 5.37 7.51-10.56 0.00 0.00 -3.87 9.78 7.94 -5.17 0.00 0.00 4.71 -5.26 -2.90 5.04 0.00 0.00 0.45 3.74 -6.80 5.05****** 0.00 2.36 2.09 2.28 -5.79****** 0.00 -9.53 6.66 -3.19 2.56 0.00 0.00 4.40 -2.03 -3.59 3.75 0.00 0.00 -15.61 0.06 10.59 2.02****** 0.00 -0.04 3.53 2.61 -8.79 0.00 0.00 -4.11 -2.29 -6.24 -1.40 0.00 0.00 3.13 -4.68 -0.31 1.44 0.00 0.00 -6.98 -7.86 2.15 12.26****** 0.00 4.67 -0.18 0.89 -9.32****** 0.00 -3.05 1.71-11.14-15.41 0.00 0.00 7.91 -5.73 -6.88 -3.63 0.00 0.00 -11.83-17.17 1.98 10.55****** 0.00 3.55 -5.92 -4.67 -2.64************ 1.87 -9.82 0.00 0.00 0.00 0.00 3.82 -5.75 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 13.05 1.21 13.00 0.90 40.58 3.27 -1.02 9.06 -3.13 -0.52 13.13 1.05 4.02 -5.15 -5.09 0.90 0.21 6.97 -2.23 -6.60 -0.73 31.36 3.25 0.09 8.21 4.29 -1.76 -6.75 -0.78 12.36 -13.22 -1.06 0.06 0.39 7.88 0.12 7.88 0.86 31.32 3.97 -0.76 5.29 -6.38 0.46 7.87 0.90 -26.34 -7.12 11.30 -0.05 -0.83 4.28 -2.44 3.52 -0.67 35.42 3.18 0.54 3.47 -0.67 -2.65 3.36 -0.62 13.39 -8.65 -15.04 -1.28 0.19 5.31 -0.32 -5.30 0.53 33.65 3.45 -0.22 1.18 1.54 -0.60 -5.28 0.52 -7.05 -1.91 -1.65 -0.65 -0.00 4.52 4.30 -1.39 -0.36 40.61 2.97 0.34 -0.00 -4.35 4.32 -1.33 -0.34 12.11 -13.99 -8.70 -0.71 0.87 4.42 -0.32 4.41 -0.41 27.15 3.44 -0.12 0.70 -6.10 -0.42 4.40 -0.37 -5.80 -15.57 3.42 -0.02 0.72 1.27 1.27 -0.09 0.14 41.44 3.10 -0.12 -1.42 -1.39 1.26 -0.12 0.12 10.07 -7.24 -2.38 -0.12 0.39 1.64 0.55 1.54 1.26 37.07 3.73 0.18 -0.83 -0.63 -0.60 1.53 1.27 -15.14 -11.70 7.69 0.08 0.62 7.11 -0.18 -7.11 0.32 29.32 3.14 -0.94 -1.07 1.64 -0.74 -7.08 0.21 18.79 -10.99 -7.45 1.06 1.65 5.17 -3.12 4.12 1.05 48.27 3.49 0.14 -2.09 -4.88 -3.31 3.97 1.02 -7.27 -15.71 11.34 0.83 1.52 - - - - - - - -6.20 3.37 - - - - -1.94 4.06 2.30 1.63 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.