ID code: 1KML 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 G03C1' 50 G03C1' 72 G04C1' 72 G04C1' 94 C05C1' 94 C05C1' 113 G06C1' 113 G06C1' 135 G07C1' 135 G07C1' 157 C08C1' 157 C08C1' 176 G09C1' 176 G09C1' 198 G10C1' 198 G10C1' 220 C11C1' 220 C11C1' 239 C12C1' 277 G02C1' 255 G01C1' 299 C03C1' 277 G02C1' 318 C04C1' 299 C03C1' 337 G05C1' 318 C04C1' 359 C06C1' 337 G05C1' 378 C07C1' 359 C06C1' 397 G08C1' 378 C07C1' 419 C09C1' 397 G08C1' 438 C10C1' 419 C09C1' 457 A11C1' 438 C10C1' 478 C12C1' 457 A11C1' 9 G01N9 31 T02N1 31 T02N1 51 G03N9 51 G03N9 73 G04N9 73 G04N9 95 C05N1 95 C05N1 114 G06N9 114 G06N9 136 G07N9 136 G07N9 158 C08N1 158 C08N1 177 G09N9 177 G09N9 199 G10N9 199 G10N9 221 C11N1 221 C11N1 240 C12N1 278 G02N9 256 G01N9 300 C03N1 278 G02N9 319 C04N1 300 C03N1 338 G05N9 319 C04N1 360 C06N1 338 G05N9 379 C07N1 360 C06N1 398 G08N9 379 C07N1 420 C09N1 398 G08N9 439 C10N1 420 C09N1 458 A11N9 439 C10N1 479 C12N1 458 A11N9 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.95378*S + 6.93740 Y = -0.29291*S + 27.40329 Z = 0.06709*S + 21.01260 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = 0.95378*S + 6.93740 Y = -0.29291*S + 27.40329 Z = 0.06709*S + 21.01260 >>>>>> HELIX ROTATION: 33.467 DISPLACEMENT: 3.2594 STATISTICS: OVERALL STANDARD DEV.: 1.2102 SIGMA(X): 1.7776, SIGMA(Y): 1.9552, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.4902, SIGMA(ROTATION): 6.934 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 = 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 -0.03604 -0.14184 0.98923 92.07 98.15 8.42 0.08650 -0.17514 0.98074 85.04 100.09 11.26 0.16527 0.05449 0.98474 80.49 86.88 10.02 0.17370 0.12927 0.97628 80.00 82.57 12.50 0.15200 0.12498 0.98045 81.26 82.82 11.35 -0.09425 0.15920 0.98274 95.41 80.84 10.66 -0.16666 0.14859 0.97475 99.59 81.46 12.90 -0.16778 0.07429 0.98302 99.66 85.74 10.57 -0.18674 -0.14466 0.97170 100.76 98.32 13.66 -0.10791 -0.18929 0.97597 96.19 100.91 12.58 -0.02870 -0.25617 0.96620 91.64 104.84 14.94 0.15654 -0.37075 0.91544 80.99 111.76 23.73 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.14724 -0.17970 0.97264 81.53 100.35 13.43 0.25772 -0.06592 0.96397 75.07 93.78 15.43 0.03383 0.09538 0.99487 88.06 84.53 5.81 0.08845 0.22164 0.97111 84.93 77.19 13.81 0.00747 0.19746 0.98028 89.57 78.61 11.40 -0.11069 0.06289 0.99186 96.35 86.39 7.31 -0.36126 0.08187 0.92886 111.18 85.30 21.74 -0.27137 -0.03900 0.96168 105.75 92.24 15.91 -0.01402 -0.16882 0.98555 90.80 99.72 9.75 -0.09119 -0.27376 0.95747 95.23 105.89 16.77 -0.01772 -0.16292 0.98648 91.02 99.38 9.43 0.04290 -0.20486 0.97785 87.54 101.82 12.08 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z 0.06211 -0.15775 0.98552 86.44 99.08 9.76 0.15318 -0.12307 0.98051 81.19 97.07 11.33 0.13784 0.07465 0.98764 82.08 85.72 9.02 0.12453 0.14797 0.98112 82.85 81.49 11.15 0.06849 0.16875 0.98328 86.07 80.29 10.49 -0.11125 0.14033 0.98384 96.39 81.93 10.32 -0.21089 0.09826 0.97256 102.17 84.36 13.45 -0.21984 0.00054 0.97554 102.70 89.97 12.70 -0.13239 -0.15987 0.97822 97.61 99.20 11.98 -0.09485 -0.20858 0.97339 95.44 102.04 13.25 -0.02891 -0.21729 0.97568 91.66 102.55 12.66 0.06708 -0.26569 0.96172 86.15 105.41 15.90 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 5 14 17 18 19 21 18 11 9 6 6 I= 2 5 0 11 15 17 21 24 22 16 15 11 9 I= 3 14 11 0 4 6 14 20 21 20 21 19 20 I= 4 17 15 4 0 3 13 19 21 23 24 22 24 I= 5 18 17 6 3 0 10 16 19 22 23 22 25 I= 6 19 21 14 13 10 0 6 10 17 20 21 25 I= 7 21 24 20 19 16 6 0 5 15 18 20 26 I= 8 18 22 21 21 19 10 5 0 10 13 16 22 I= 9 11 16 20 23 22 17 15 10 0 3 6 12 I= 10 9 15 21 24 23 20 18 13 3 0 3 9 I= 11 6 11 19 22 22 21 20 16 6 3 0 6 I= 12 6 9 20 24 25 25 26 22 12 9 6 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 -6.89 4.81 2.23 6.94 0.00 0.00 -0.33 13.43 8.95 1.75****** 0.00 -8.15 7.72 13.51 3.79 0.00 0.00 0.75 15.41 8.56-13.44 0.00 0.00 1.13 9.96 3.56 2.44****** 0.00 4.96 3.01 4.92 6.17 0.00 0.00 -1.39 12.43 0.97 -0.81 0.00 0.00 5.82 12.47 3.41 -3.44 0.00 0.00 -7.29 8.65 13.93 3.55 -0.00 0.00 1.63 11.28 7.62 -6.91 0.00 0.50 1.33 10.58 3.55 2.23 0.00 0.00 4.39 5.84 10.27 10.20 0.00 0.00 -1.78 12.77 4.10 -1.14****** 0.00 7.62 20.24 5.19 -6.92 0.00 0.00 -4.42 9.59 11.68 4.91 0.00 0.00 1.97 15.78 11.70-11.82 0.00 0.00 0.92 13.63 5.14 -0.77****** 0.00 7.61 6.07 0.23 7.48****** 0.00 -2.19 12.39 4.78 3.53 0.00 0.00 0.34 16.77 3.80 -6.62 0.00 0.00 -5.07 14.01 5.30 11.38****** 0.00 -3.19 8.87 1.59 3.91 0.00 0.00 -10.06 21.25 0.00 0.00 0.00 0.00 -7.20 9.65 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 5.59 3.27 4.54 -1.22 31.39 3.39 -0.12 9.21 -3.21 3.29 4.52 -1.15 -0.97 -6.58 8.55 -1.64 0.99 11.39 -1.46 11.30 -0.63 28.52 3.59 0.11 10.53 -4.15 -1.50 11.34 -0.52 -14.49 -8.92 7.58 -1.66 0.10 4.29 1.30 4.09 -0.98 30.96 3.32 0.36 8.64 2.58 1.30 4.07 -0.93 7.02 -3.85 -6.92 -1.65 -0.23 3.43 -0.51 3.39 -0.42 35.76 3.25 -0.43 11.07 1.32 -0.49 3.39 -0.35 2.43 -7.21 0.11 -1.47 -0.94 10.44 -0.45 10.43 0.15 33.32 3.52 0.04 10.27 -2.11 -0.45 10.47 0.25 -7.25 -8.92 2.54 -2.49 -0.70 6.23 1.89 5.94 -0.56 32.27 3.25 0.94 9.96 2.65 1.87 5.92 -0.48 12.30 -3.07 -4.71 -2.53 0.41 5.63 -1.09 5.52 -0.68 33.67 3.36 -0.14 13.29 2.03 -1.09 5.52 -0.58 -1.42 -9.43 7.59 -1.19 0.28 10.48 -2.02 10.29 -0.45 32.10 3.62 -0.29 12.70 -0.24 -1.93 10.34 -0.34 -13.63 -6.41 6.17 -1.33 -0.40 3.53 0.92 3.41 -0.40 35.65 3.16 0.86 11.48 3.38 0.87 3.42 -0.35 11.83 -6.72 -7.46 -1.85 -0.65 3.81 -0.27 3.80 0.11 32.42 3.54 -0.88 13.20 -1.11 0.25 3.81 0.17 -9.55 -2.53 4.37 -1.32 -0.73 6.21 5.26 3.31 0.73 33.65 3.52 1.38 11.79 -4.55 5.34 3.09 0.80 -6.55 -1.88 -5.18 -2.70 -0.21 - - - - - - - 13.06 -8.92 - - - - -2.93 -11.73 -1.42 1.00 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.