TITL RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) CELL 1., 1., 1., 90., 90., 90. BRKH FPUN 0 PMIN 0 PMAX 0 NATM 732 BASE 18 HELX RC1' YC1' HELX RN9 YN1 BROL CYLN TRNG END 1 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) INPUT FRAC.COORDS. X,Y,Z AND ATOM NAME IN FORMAT: (T31,3F8.3,T20,A1,T25,2A1,T14,3A1) WILL READ 732 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 C02C1' 27 G03C1' 27 G03C1' 49 C04C1' 49 C04C1' 68 A05C1' 68 A05C1' 89 C06C1' 89 C06C1' 108 A07C1' 108 A07C1' 129 C08C1' 129 C08C1' 148 C09C1' 148 C09C1' 167 C10C1' 167 C10C1' 186 A11C1' 186 A11C1' 207 C12C1' 207 C12C1' 226 A13C1' 226 A13C1' 247 C14C1' 247 C14C1' 266 A15C1' 266 A15C1' 287 C16C1' 287 C16C1' 306 C17C1' 306 C17C1' 325 A18C1' 325 A18C1' 346 G19C1' 384 T22C1' 365 C21C1' 404 G23C1' 384 T22C1' 426 G24C1' 404 G23C1' 448 T25C1' 426 G24C1' 468 G26C1' 448 T25C1' 490 T27C1' 468 G26C1' 510 G28C1' 490 T27C1' 532 T29C1' 510 G28C1' 552 G30C1' 532 T29C1' 574 G31C1' 552 G30C1' 596 G32C1' 574 G31C1' 618 T33C1' 596 G32C1' 638 G34C1' 618 T33C1' 660 T35C1' 638 G34C1' 680 G36C1' 660 T35C1' 702 C37C1' 680 G36C1' 721 G38C1' 702 C37C1' 9 C02N1 28 G03N9 28 G03N9 50 C04N1 50 C04N1 69 A05N9 69 A05N9 90 C06N1 90 C06N1 109 A07N9 109 A07N9 130 C08N1 130 C08N1 149 C09N1 149 C09N1 168 C10N1 168 C10N1 187 A11N9 187 A11N9 208 C12N1 208 C12N1 227 A13N9 227 A13N9 248 C14N1 248 C14N1 267 A15N9 267 A15N9 288 C16N1 288 C16N1 307 C17N1 307 C17N1 326 A18N9 326 A18N9 347 G19N9 385 T22N1 366 C21N1 405 G23N9 385 T22N1 427 G24N9 405 G23N9 449 T25N1 427 G24N9 469 G26N9 449 T25N1 491 T27N1 469 G26N9 511 G28N9 491 T27N1 533 T29N1 511 G28N9 553 G30N9 533 T29N1 575 G31N9 553 G30N9 597 G32N9 575 G31N9 619 T33N1 597 G32N9 639 G34N9 619 T33N1 661 T35N1 639 G34N9 681 G36N9 661 T35N1 703 C37N1 681 G36N9 722 G38N9 703 C37N1 ************************************** IN ORTHONORMAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.37456*S + 19.57254 Y = 0.67842*S + 8.23198 Z = 0.63202*S + 2.76319 IN ORIGINAL CRYSTAL COORDINATES, HELIX AXIS IN PARAMETRIC FORM: X = -0.37456*S + 19.57254 Y = 0.67842*S + 8.23198 Z = 0.63202*S + 2.76319 >>>>>> HELIX ROTATION: 26.076 DISPLACEMENT: 3.4008 STATISTICS: OVERALL STANDARD DEV.: 1.9752 SIGMA(X): 3.1672, SIGMA(Y): 3.3392, SIGMA(Z)=SIGMA(DISPLACEMENT): 0.4060, SIGMA(ROTATION): 32.155 THERE ARE 13.81 RESIDUES PER TURN ***************************************************** THE FOLLOWING DIAMOND LIST HAS BEEN OUTPUT ON UNIT: 12 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) NORMAL END OF JOB: YOU HAVE GIVEN BIRTH TO A HELIX NUMBER BASE PAIRS = 18 1 ROLL+TILT OUTPUT, FREEHELIX98 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) STRAND 1 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.22344 0.08637 0.97088 102.91 85.05 13.86 -0.12646 -0.02762 0.99159 97.27 91.58 7.44 -0.07761 -0.07294 0.99431 94.45 94.18 6.11 -0.05853 -0.04508 0.99727 93.36 92.58 4.24 -0.03799 0.05621 0.99770 92.18 86.78 3.89 -0.03467 0.04765 0.99826 91.99 87.27 3.38 -0.05673 0.18395 0.98130 93.25 79.40 11.10 0.09066 0.01716 0.99573 84.80 89.02 5.29 -0.12818 -0.14042 0.98176 97.36 98.07 10.96 -0.07283 -0.06461 0.99525 94.18 93.70 5.59 -0.03046 -0.18406 0.98244 91.75 100.61 10.75 -0.02385 -0.25587 0.96642 91.37 104.83 14.89 0.06747 -0.20877 0.97564 86.13 102.05 12.67 -0.00687 -0.16719 0.98590 90.39 99.62 9.63 0.16625 0.08375 0.98252 80.43 85.20 10.73 0.10900 0.09973 0.98903 83.74 84.28 8.50 0.00904 0.18857 0.98202 89.48 79.13 10.88 -0.03213 0.14910 0.98830 91.84 81.43 8.77 STRAND 2 BASE NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.05194 0.02966 0.99821 92.98 88.30 3.43 -0.16578 0.07756 0.98311 99.54 85.55 10.55 -0.10862 -0.02809 0.99369 96.24 91.61 6.44 -0.21728 -0.06879 0.97368 102.55 93.94 13.17 -0.09792 -0.09500 0.99065 95.62 95.45 7.84 -0.12742 0.02062 0.99163 97.32 88.82 7.42 -0.01588 0.00480 0.99986 90.91 89.72 0.95 -0.07067 -0.04189 0.99662 94.05 92.40 4.71 0.02664 -0.11680 0.99280 88.47 96.71 6.88 0.22853 -0.22092 0.94814 76.79 102.76 18.53 -0.06490 -0.20670 0.97625 93.72 101.93 12.51 -0.04238 -0.00097 0.99910 92.43 90.06 2.43 0.02417 -0.02452 0.99941 88.61 91.41 1.97 0.11284 0.04578 0.99256 83.52 87.38 6.99 0.01744 0.04436 0.99886 89.00 87.46 2.73 -0.05114 0.06421 0.99663 92.93 86.32 4.71 -0.12399 -0.02696 0.99192 97.12 91.54 7.29 0.09001 -0.19336 0.97699 84.84 101.15 12.31 BASE PAIR NORMAL COSINES AND ANGLES COS(AX) COS(AY) COS(AZ) ANG X ANG Y ANG Z -0.10378 0.02316 0.99433 95.96 88.67 6.10 -0.10165 0.00858 0.99478 95.83 89.51 5.85 -0.07458 -0.04548 0.99618 94.28 92.61 5.01 -0.11432 -0.01839 0.99327 96.56 91.05 6.65 -0.06300 -0.03447 0.99742 93.61 91.98 4.12 -0.06592 -0.00680 0.99780 93.78 90.39 3.80 0.00740 0.06428 0.99790 89.58 86.31 3.71 0.02614 -0.03192 0.99915 88.50 91.83 2.36 0.02129 -0.10079 0.99468 88.78 95.78 5.91 0.11774 -0.15849 0.98032 83.24 99.12 11.39 -0.04875 -0.19004 0.98057 92.79 100.96 11.31 0.00719 -0.14572 0.98930 89.59 98.38 8.39 0.02384 -0.10065 0.99464 88.63 95.78 5.94 0.06483 -0.01957 0.99770 86.28 91.12 3.88 0.06011 0.03406 0.99761 86.55 88.05 3.96 0.01547 0.05546 0.99834 89.11 86.82 3.30 -0.05994 0.03864 0.99745 93.44 87.79 4.09 -0.03936 0.02002 0.99902 92.26 88.85 2.53 1 CHECK NORMALITY OF BASE STEP REFERENCE VECTORS 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 I= 12 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 13 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 14 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 15 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 16 PS= 90.0000 LS= 90.0000 PL= 90.0000 I= 17 PS= 90.0000 LS= 90.0000 PL= 90.0000 1 ANGLES BETWEEN NORMAL VECTORS TO BASE PAIRS RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) J= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 I= 1 0 0 4 2 4 2 6 8 10 16 12 11 10 9 9 7 2 3 I= 2 0 0 3 1 3 2 7 7 9 15 11 10 9 9 9 7 2 3 I= 3 4 3 0 2 0 2 7 5 6 12 8 7 6 8 8 7 4 4 I= 4 2 1 2 0 3 2 8 8 9 15 10 10 9 10 10 8 4 4 I= 5 4 3 0 3 0 1 6 5 6 12 9 7 6 7 8 6 4 3 I= 6 2 2 2 2 1 0 5 5 7 13 10 9 7 7 7 5 2 2 I= 7 6 7 7 8 6 5 0 5 9 14 14 12 9 5 3 0 4 3 I= 8 8 7 5 8 5 5 5 0 3 9 10 6 3 2 4 5 6 4 I= 9 10 9 6 9 6 7 9 3 0 6 6 2 0 5 8 8 9 7 I= 10 16 15 12 15 12 13 14 9 6 0 9 6 6 8 11 13 15 13 I= 11 12 11 8 10 9 10 14 10 6 9 0 4 6 11 14 14 13 12 I= 12 11 10 7 10 7 9 12 6 2 6 4 0 2 7 10 11 11 9 I= 13 10 9 6 9 6 7 9 3 0 6 6 2 0 5 8 8 9 7 I= 14 9 9 8 10 7 7 5 2 5 8 11 7 5 0 3 5 7 6 I= 15 9 9 8 10 8 7 3 4 8 11 14 10 8 3 0 2 6 5 I= 16 7 7 7 8 6 5 0 5 8 13 14 11 8 5 2 0 4 3 I= 17 2 2 4 4 4 2 4 6 9 15 13 11 9 7 6 4 0 1 I= 18 3 3 4 4 3 2 3 4 7 13 12 9 7 6 5 3 1 0 1 ROLL+TILT OUTPUT, FREEHELIX98 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) STRAND 1 ROLL AND TILT ANGLES STRAND 2 ROLL AND TILT ANGLES TIP INCL ROLL TILT RADJ TADJ TIP INCL ROLL TILT RADJ TADJ -8.12-11.16 -1.21 8.52 0.00 0.00 -1.58 -3.04 -2.27 -6.72 0.00 0.00 -4.15 -6.16 -2.65 2.75 0.00 0.00 0.63-10.53 -6.13 3.16 0.00 0.00 -2.10 -5.74 0.62 1.83 0.00 0.00 0.96 -6.37 1.88 -6.39 0.00 0.00 1.31 -4.03 0.74 5.89 0.00 0.00 8.08-10.33 -6.98 0.77 0.00 0.00 2.47 3.00 -0.06 -0.52 0.00 0.00 5.08 -5.96 -0.09 6.85 0.00 0.00 0.02 3.38 -5.47 5.73 0.00 0.00 5.25 5.22 -3.14 -5.65 0.00 0.00 -8.98 6.47 8.89 -9.22 0.00 0.00 0.03 0.95 2.92 2.92 0.00 0.00 -0.54 -5.27 5.45 14.62 0.00 0.00 2.05 4.24 5.61 -4.27 0.00 0.00 3.55 10.36 -0.60 -5.35 0.00 0.00 6.62 1.87 12.66 -3.42 0.00 0.00 -2.48 5.01 2.61 6.79 0.00 0.00 17.15 6.82-17.08 -0.37 0.00 0.00 -4.33 9.82 -1.70 3.77 0.00 0.00 -6.58 10.60 6.95 -9.66 0.00 0.00 -12.51 7.95 4.38 3.94 0.00 0.00 -1.54 -1.88 0.09 4.05 0.00 0.00 -11.34 5.59 2.99 -3.86 0.00 0.00 -1.19 1.58 3.23 5.63 0.00 0.00 -8.27 -4.90 4.76 17.06 0.00 0.00 -0.76 6.95 3.42 -4.27 0.00 0.00 -4.86 9.54 3.41 0.09 0.00 0.00 0.69 2.64 4.09 0.14 0.00 0.00 -6.09 5.90 4.37 6.31 0.00 0.00 3.04 3.59 5.30 -4.09 0.00 0.00 -6.43 8.75 3.26 0.29 0.00 0.00 6.79 2.65 -0.86-15.70 0.00 0.00 -7.28 4.86 0.00 0.00 0.00 0.00 8.43 -8.91 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 0.84 0.62 -0.57 1.14 35.47 3.73 -0.47 -4.34 -4.29 0.65 -0.54 1.10 -12.51 -6.59 8.16 2.61 -5.10 3.47 1.51 -3.12 0.91 44.49 3.23 0.66 -5.60 -1.69 1.49 -3.13 0.86 3.72 -4.78 -4.35 -1.03 -4.06 2.76 -0.79 2.65 -0.09 32.42 3.35 -0.29 -4.96 -0.72 -0.89 2.61 -0.09 -5.73 -3.06 -0.63 -2.58 -1.28 3.09 0.15 -3.09 -0.73 29.01 3.48 0.48 -4.57 4.82 0.07 -3.08 -0.76 -2.61 -6.80 -6.36 -2.96 0.57 1.59 1.57 -0.25 -1.08 41.30 3.20 0.14 -2.31 3.41 1.57 -0.25 -1.05 10.82 -2.61 -8.97 -1.74 1.23 5.85 -0.96 -5.78 -0.75 35.63 3.54 0.89 1.89 3.30 -0.89 -5.79 -0.75 -7.40 -5.23 1.86 -0.54 0.94 5.62 -1.73 5.34 -1.58 23.54 2.96 -1.29 0.78 -3.63 -1.51 5.42 -1.51 15.05 -9.04 -5.54 0.67 -0.03 3.96 1.41 3.71 0.18 24.02 3.73 -0.40 -1.34 1.95 1.30 3.74 0.27 -17.98 -2.61 9.51 -1.03 -1.53 6.50 -1.14 6.39 1.01 39.26 3.20 -0.71 1.70 5.66 -1.30 6.32 1.12 10.57 -3.05 -8.48 -1.65 -0.77 9.72 2.43 -9.42 0.09 36.30 3.46 1.36 5.89 9.71 2.06 -9.53 0.00 -1.28 -19.62 2.10 -1.73 1.32 4.12 -0.42 4.10 1.17 37.58 3.72 -1.10 9.89 -5.43 -0.63 4.04 1.21 -10.77 2.25 0.81 0.68 1.14 2.77 0.16 2.77 -0.61 29.43 3.19 0.59 5.46 -6.35 -0.02 2.75 -0.58 5.88 -10.98 -9.96 0.04 1.63 5.21 3.11 4.18 -1.15 36.72 3.05 1.00 2.20 -5.51 3.02 4.25 -1.11 15.90 -10.16 -4.07 0.86 0.55 3.09 1.81 2.50 -0.41 25.34 3.77 -0.62 2.74 -2.75 1.75 2.54 -0.39 -18.74 -7.58 11.83 1.37 -1.51 2.84 0.33 2.82 -0.31 34.44 3.25 0.14 3.61 -1.63 0.57 2.78 -0.24 4.59 -5.58 -6.91 -0.29 -2.38 4.43 0.26 4.42 0.54 35.19 3.56 -0.16 3.20 -0.79 0.09 4.43 0.65 -3.77 -9.13 -2.33 -1.67 -2.28 1.59 -1.59 0.09 0.29 34.70 3.53 0.43 3.75 1.63 -1.59 0.03 0.30 -7.67 -13.23 -6.09 -2.70 -0.52 - - - - - - - 2.52 -0.24 - - - - -15.88 -13.77 -2.05 1.06 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. 1 CYLINDRICAL PARAMETERS, NEWHEL93 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) 732 ATOMS AND 18 BASE PAIRS CHECK OF O4", C1", N1/9, P ATOM NUMBERS, STR. 1 & 2 1 NO= 4 361 1 NC= 8 365 1 ND= 9 366 1 NP= 17 374 2 NO= 23 380 2 NC= 27 384 2 ND= 28 385 2 NP= 39 394 3 NO= 45 400 3 NC= 49 404 3 ND= 50 405 3 NP= 58 416 4 NO= 64 422 4 NC= 68 426 4 ND= 69 427 4 NP= 79 438 5 NO= 85 444 5 NC= 89 448 5 ND= 90 449 5 NP= 98 458 6 NO= 104 464 6 NC= 108 468 6 ND= 109 469 6 NP= 119 480 7 NO= 125 486 7 NC= 129 490 7 ND= 130 491 7 NP= 138 500 8 NO= 144 506 8 NC= 148 510 8 ND= 149 511 8 NP= 157 522 9 NO= 163 528 9 NC= 167 532 9 ND= 168 533 9 NP= 176 542 10 NO= 182 548 10 NC= 186 552 10 ND= 187 553 10 NP= 197 564 11 NO= 203 570 11 NC= 207 574 11 ND= 208 575 11 NP= 216 586 12 NO= 222 592 12 NC= 226 596 12 ND= 227 597 12 NP= 237 608 13 NO= 243 614 13 NC= 247 618 13 ND= 248 619 13 NP= 256 628 14 NO= 262 634 14 NC= 266 638 14 ND= 267 639 14 NP= 277 650 15 NO= 283 656 15 NC= 287 660 15 ND= 288 661 15 NP= 296 670 16 NO= 302 676 16 NC= 306 680 16 ND= 307 681 16 NP= 315 692 17 NO= 321 698 17 NC= 325 702 17 ND= 326 703 17 NP= 336 711 18 NO= 342 717 18 NC= 346 721 18 ND= 347 722 18 NP= 0 0 1 PHOSPHATE BACKBONE TABLE, 5" TO 3" DIRECTION IN EACH STRAND R PHI Z D Q H PI STRAND 1 4.15 170.70 1.80 7.01 5.86 3.84 33.22 7.77 218.65 5.64 6.87 5.60 3.99 35.48 10.18 251.62 9.63 6.92 5.79 3.80 33.25 11.95 280.57 13.42 6.93 4.84 4.96 45.65 10.23 304.21 18.38 6.68 6.18 2.54 22.37 10.32 339.22 20.92 6.69 5.90 3.15 28.13 8.86 14.00 24.07 6.04 5.55 2.40 23.36 9.15 49.82 26.47 6.30 4.36 4.54 46.19 9.94 75.81 31.01 7.06 6.12 3.52 29.89 10.90 109.56 34.53 6.03 5.00 3.37 33.98 10.04 136.80 37.90 7.00 6.69 2.06 17.08 10.55 174.64 39.96 6.79 4.95 4.65 43.17 8.74 202.41 44.60 6.17 5.54 2.71 26.09 7.45 241.42 47.32 6.39 4.53 4.50 44.79 7.36 277.06 51.82 6.49 5.65 3.19 29.41 8.37 318.56 55.00 6.87 6.33 2.69 23.03 11.08 353.09 57.69 - - - - STRAND 2 9.99 112.49 56.68 6.67 5.91 -3.09 -27.58 11.63 81.95 53.59 7.12 6.31 -3.31 -27.67 12.22 51.40 50.28 6.63 5.42 -3.82 -35.12 11.51 25.19 46.47 6.51 4.94 -4.24 -40.67 8.71 1.72 42.22 6.81 6.48 -2.11 -18.00 8.22 316.82 40.12 6.28 5.22 -3.49 -33.77 8.12 279.57 36.63 6.70 5.10 -4.34 -40.42 7.72 242.12 32.28 6.89 6.87 -0.49 -4.06 9.70 197.45 31.80 6.48 5.20 -3.86 -36.61 11.32 170.18 27.93 6.86 3.80 -5.72 -56.37 10.79 150.57 22.22 6.56 5.18 -4.02 -37.78 8.16 123.04 18.20 6.87 6.69 -1.56 -13.14 8.46 75.60 16.64 6.93 6.67 -1.87 -15.65 9.59 32.78 14.77 6.51 5.71 -3.13 -28.72 11.13 1.92 11.64 6.61 5.32 -3.93 -36.44 12.32 336.34 7.71 6.48 6.18 -1.95 -17.51 13.57 309.28 5.77 - - - - ______ ______ ______ ______ ______ ______ ______ 9.71 177.25 30.44 6.66 5.62 0.16 1.42 AV 1.86 111.64 16.69 0.29 0.73 3.56 33.16 SD 1 CYLINDRICAL PARAMETERS, NEWHEL93 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) ROTATION AND RISE TABLE, 5" TO 3" DIRECTION S5" S3" Dxy TwC1" TWIST Dz RISE SLIDE X DSP Y DSP Dxyz STRAND 1 - 145.46 3.98 203.61 37.06 3.511 3.665 -0.28 0.23 -5.25 5.30 58.15 -10.20 3.38 25.78 42.98 3.408 3.217 -1.21 -3.54 -3.92 4.80 35.98 -3.01 3.44 24.16 34.56 3.551 3.594 -1.40 -5.06 -1.38 4.95 27.18 1.77 2.53 18.28 27.42 3.795 3.477 -2.31 -5.43 0.85 4.56 16.51 7.13 4.36 34.36 41.47 3.494 3.091 -2.65 -4.19 1.13 5.59 27.23 7.77 3.22 27.10 34.44 3.132 3.274 -2.48 -3.07 1.10 4.49 19.32 15.46 4.41 48.39 24.19 2.894 3.019 -2.58 -1.80 -0.02 5.28 32.94 2.89 2.54 25.16 24.50 4.416 4.052 -1.05 -3.50 -1.46 5.10 22.27 3.72 3.85 28.32 40.39 3.289 3.372 -0.56 -4.11 -0.91 5.07 24.60 9.15 2.84 19.89 35.06 3.639 2.813 -1.69 -4.12 1.39 4.61 10.74 16.50 4.93 41.06 38.02 2.909 3.664 -0.38 -1.83 1.14 5.72 24.56 13.29 3.19 25.11 29.02 3.122 3.236 -2.11 -2.46 1.74 4.46 11.83 15.95 3.80 37.48 36.87 2.948 3.017 -2.57 -1.64 0.52 4.81 21.54 17.47 3.59 53.45 25.89 4.192 3.883 -1.94 -1.13 -1.31 5.52 35.98 -0.35 3.53 44.19 34.10 3.149 3.295 -1.58 -2.72 -2.55 4.73 44.53 -3.03 3.72 30.61 36.21 3.618 3.653 -1.09 -4.07 -2.30 5.19 33.64 0.89 2.94 21.51 35.16 3.220 3.598 -1.43 -5.25 -0.53 4.36 20.62 - - - - - - - -4.52 1.09 0.00 _____ _____ _____ _____ _____ _____ _____ _____ _____ _____ _____ 27.51 14.17 3.52 41.67 33.96 3.43 3.41 -1.61 -3.23 -0.59 4.70 AV 11.94 34.76 0.67 42.96 5.80 0.43 0.33 0.78 1.55 1.97 1.24 SD STRAND 2 0.00 -0.73 4.09 -31.61 35.16 -3.976 3.598 0.00 0.00 0.00 5.71 -30.89 0.36 3.24 -22.08 36.21 -3.687 3.653 0.00 0.00 0.00 4.91 -22.44 -8.12 3.65 -24.75 34.10 -3.441 3.295 0.00 0.00 0.00 5.02 -16.63 -9.58 2.84 -16.83 25.89 -3.573 3.883 0.00 0.00 0.00 4.56 -7.25 -16.21 4.74 -45.73 36.87 -3.086 3.017 0.00 0.00 0.00 5.66 -29.51 -15.39 3.71 -45.57 29.02 -3.350 3.236 0.00 0.00 0.00 5.00 -30.19 -7.06 2.06 -27.84 38.02 -4.420 3.664 0.00 0.00 0.00 4.88 -20.78 -16.67 4.88 -56.47 35.06 -1.988 2.813 0.00 0.00 0.00 5.27 -39.79 -4.87 3.54 -27.76 40.39 -3.454 3.372 0.00 0.00 0.00 4.94 -22.89 -4.38 2.38 -18.31 24.50 -3.688 4.052 0.00 0.00 0.00 4.39 -13.93 -5.68 2.58 -15.26 24.19 -3.145 3.019 0.00 0.00 0.00 4.07 -9.57 -17.96 4.79 -52.87 34.44 -3.416 3.274 0.00 0.00 0.00 5.88 -34.91 -12.53 4.67 -49.71 41.47 -2.688 3.091 0.00 0.00 0.00 5.39 -37.18 -5.64 3.86 -34.00 27.42 -3.158 3.477 0.00 0.00 0.00 4.99 -28.35 -2.51 2.99 -20.06 34.56 -3.637 3.594 0.00 0.00 0.00 4.71 -17.55 -8.02 4.41 -26.70 42.98 -3.027 3.217 0.00 0.00 0.00 5.35 -18.68 -8.39 2.66 -14.60 37.06 -3.818 3.665 0.00 0.00 0.00 4.66 -6.21 0.00 0.00 0.00 0.00 0.000 0.000 0.00 0.00 0.00 0.00 Twist, Rise, Dxyz and Dxy are magnitudes. All other quantities have opposite signs for ascending and descending strands. 1 CYLINDRICAL PARAMETERS, NEWHEL93 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) ANGLES BETWEEN GLYCOSIDIC BONDS AND C1' - C1' BASE - PAIR VECTORS RESIDUE LAMBDA(1) LAMBDA(2) C02 .G38 52.40 50.76 G03 .C37 52.59 55.73 C04 .G36 52.43 56.28 A05 .T35 56.03 60.96 C06 .G34 53.23 52.80 A07 .T33 53.32 61.58 C08 .G32 49.61 57.22 C09 .G31 49.47 60.73 C10 .G30 56.70 55.23 A11 .T29 55.06 53.51 C12 .G28 56.04 57.43 A13 .T27 57.56 60.24 C14 .G26 51.86 54.65 A15 .T25 55.94 62.46 C16 .G24 57.82 50.33 C17 .G23 48.37 51.36 A18 .T22 59.96 54.43 G19 .C21 55.48 50.87 1 CYLINDRICAL PARAMETERS, NEWHEL93 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) PHOSPHORUS-PHOSPHORUS DISTANCES LESS 5.8 A STRAND 1 DOWN, STRAND 2 ACROSS, 5" TO 3" DIRECTION 49.74 47.43 44.86 41.36 36.61 34.32 30.51 25.60 24.85 21.30 15.80 11.73 11.96 12.54 12.33 11.61 11.56 47.19 45.45 43.07 39.30 33.99 30.74 26.22 21.03 20.63 18.05 13.93 11.44 13.12 13.79 13.14 11.67 9.91 44.91 43.24 40.45 36.09 30.30 26.31 21.64 17.04 18.15 17.28 14.71 12.84 14.11 13.54 11.82 9.56 6.64 42.65 40.62 37.11 32.10 26.08 21.85 17.72 14.54 17.58 18.19 16.61 14.51 14.40 12.17 9.36 6.91 4.25 37.46 34.90 30.88 25.65 19.76 16.13 12.98 11.04 15.09 16.23 15.02 12.59 11.34 8.51 6.54 6.72 7.29 34.52 31.11 26.46 21.15 15.88 13.84 12.49 11.94 16.02 16.85 15.29 11.99 8.89 5.09 4.43 7.57 10.86 29.80 25.94 21.45 16.84 12.45 12.21 11.90 11.43 14.30 14.32 12.56 9.26 5.78 4.01 7.01 12.23 16.45 26.01 22.03 18.21 14.81 11.56 12.79 12.88 11.95 13.08 12.06 10.17 7.45 4.81 6.23 11.26 17.07 21.44 20.62 16.87 14.16 12.22 10.10 12.32 12.75 11.78 11.37 10.12 9.57 9.01 8.65 11.96 17.36 23.07 27.08 16.37 14.02 13.58 13.41 11.86 13.61 13.26 11.44 8.78 7.21 8.67 10.90 13.11 17.72 23.18 28.45 31.73 13.45 12.85 13.79 13.99 12.06 12.59 11.47 9.46 5.89 5.97 10.10 14.11 17.49 22.03 26.94 31.57 34.04 14.00 15.27 16.75 16.46 13.56 11.98 9.45 7.14 3.33 6.28 12.49 17.53 21.68 25.77 29.84 33.56 35.01 12.14 14.09 15.29 14.53 11.53 9.15 7.41 7.76 7.07 11.95 18.23 22.73 26.12 29.18 32.53 35.89 37.07 12.54 14.01 14.02 12.28 9.13 6.20 6.06 9.24 11.13 16.68 22.56 26.26 28.71 30.70 33.40 36.52 37.67 12.06 13.12 12.41 10.57 8.70 7.07 9.41 14.25 17.08 22.50 27.98 31.06 32.66 33.95 36.36 39.57 41.00 12.16 11.93 10.07 8.30 8.44 9.09 13.38 19.01 22.25 27.25 32.12 34.48 35.16 35.88 38.23 41.76 43.74 12.42 10.62 7.79 7.05 9.92 12.97 18.31 24.02 27.11 31.44 35.65 37.39 37.27 37.71 40.28 44.31 46.98 1 CYLINDRICAL PARAMETERS, NEWHEL93 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) SUGAR O4"--O4" DISTANCES LESS 2.8 A STRAND 1 DOWN, STRAND 2 ACROSS, 5" TO 3" DIRECTION 58.18 55.03 51.67 48.20 44.28 41.09 37.58 33.36 31.39 28.66 25.04 20.28 17.92 15.81 13.28 11.14 9.97 8.93 55.06 52.31 49.20 45.78 41.66 38.07 34.17 29.65 27.54 25.02 21.76 17.27 16.10 14.68 12.45 10.47 8.82 7.72 52.16 49.61 46.53 42.95 38.59 34.67 30.59 26.03 24.21 22.36 19.72 15.61 15.04 13.54 11.13 8.95 6.89 6.25 49.44 46.83 43.57 39.62 35.06 30.93 26.94 22.73 21.64 20.83 18.96 15.31 14.49 12.18 9.18 6.57 4.47 5.38 45.58 42.81 39.37 35.23 30.62 26.52 22.75 18.91 18.38 18.23 16.88 13.66 12.45 9.73 6.96 5.51 5.39 8.30 42.16 38.85 35.05 30.75 26.33 22.77 19.70 16.60 16.62 16.65 15.32 12.31 9.55 5.77 3.54 4.83 7.67 12.03 38.41 34.84 30.95 26.80 22.62 19.54 16.87 14.14 14.17 13.99 12.68 10.15 6.78 3.59 4.29 8.06 11.82 16.33 34.73 30.98 27.21 23.55 19.84 17.44 15.13 12.59 12.08 11.01 9.42 7.61 4.07 3.75 7.51 12.40 16.47 20.86 29.83 26.12 22.71 19.83 16.71 15.05 13.11 10.92 9.77 7.95 6.81 7.18 5.91 8.67 13.22 18.26 22.22 26.42 26.47 22.98 20.11 18.14 15.69 14.67 13.02 11.14 9.38 6.93 6.43 8.60 9.14 12.97 17.73 22.77 26.60 30.62 22.46 19.58 17.31 15.80 13.36 12.11 10.24 8.63 6.80 5.42 7.16 10.87 12.98 16.87 21.31 26.03 29.50 33.36 20.21 18.68 17.49 16.56 14.00 11.96 9.23 7.25 4.90 4.95 8.66 13.26 16.90 20.92 24.96 29.19 32.09 35.57 17.56 16.75 15.98 15.03 12.32 9.85 7.17 6.40 5.66 8.17 12.53 17.01 20.59 24.08 27.70 31.59 34.26 37.68 15.46 14.80 13.87 12.41 9.44 6.65 4.89 6.60 8.11 12.11 16.56 20.67 23.63 26.36 29.56 33.19 35.81 39.35 13.60 12.83 11.62 9.59 6.85 4.78 5.85 9.98 12.90 17.40 21.69 25.45 27.63 29.60 32.43 35.88 38.54 42.25 12.42 11.15 9.58 7.30 5.69 5.76 8.99 13.91 17.22 21.62 25.68 29.23 30.76 32.30 35.00 38.46 41.31 45.21 11.58 9.28 7.26 5.37 6.36 9.10 13.54 18.73 22.04 26.04 29.75 33.13 34.00 35.26 38.02 41.66 44.81 48.95 10.11 7.32 5.84 5.94 9.03 12.90 17.51 22.58 25.57 29.11 32.60 36.04 36.72 38.11 41.11 44.99 48.37 52.64 1 TORSION ANGLE CALCULATION, NEWHEL93 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) 732 ATOMS AND 18 BASE PAIRS STRAND 1 ALPHA BETA GAMMA DELTA EPSILON ZETA CHI DIF EP-ZE - - 62.1 137.5 259.9 173.7 258.0 44.1 86.2 298.8 124.7 49.8 139.9 196.6 232.1 268.4 -6.5 -35.5 306.0 155.7 54.2 131.5 189.0 244.8 246.2 -20.7 -55.8 289.0 177.0 55.4 139.9 189.6 265.9 246.5 10.5 -76.3 286.3 164.4 58.5 88.1 142.7 290.2 226.1 -63.9 -147.5 297.3 197.9 54.3 138.7 177.4 279.0 240.1 -1.1 -101.6 293.4 181.9 53.8 119.6 187.9 252.8 238.7 45.6 -64.9 297.8 184.0 43.2 117.0 195.1 270.9 223.2 7.5 -75.8 286.4 187.6 37.6 145.9 242.3 174.1 292.5 1.4 68.2 292.1 145.1 43.2 154.5 182.8 264.3 260.6 13.2 -81.5 275.1 187.2 52.6 130.0 270.4 154.4 254.0 -27.0 116.1 279.5 148.6 49.3 147.6 177.0 272.4 265.2 29.7 -95.4 274.5 188.2 51.8 114.1 154.7 275.1 244.5 -29.5 -120.4 300.4 177.6 52.4 117.5 202.3 258.5 222.2 -24.1 -56.2 286.2 174.0 55.7 114.9 189.9 237.7 254.7 -28.6 -47.8 330.5 152.4 39.3 135.0 206.6 216.6 242.3 -2.6 -9.9 323.0 161.5 43.4 137.1 181.5 262.0 263.9 -0.2 -80.5 292.1 170.7 58.3 147.3 - - 267.9 59.7 0.0 STRAND 2 ALPHA BETA GAMMA DELTA EPSILON ZETA CHI MEAN EP-ZE - - 64.0 87.6 197.4 292.2 196.2 117.5 -94.8 270.8 198.3 67.6 137.3 216.3 217.2 239.9 137.2 -0.9 338.9 142.3 33.9 137.7 200.2 253.9 251.8 136.4 -53.7 269.6 189.2 43.7 143.5 187.5 267.2 254.1 129.2 -79.8 278.6 182.6 43.5 141.6 201.7 198.6 261.0 129.5 3.1 310.8 166.4 49.3 143.5 185.7 268.5 237.2 128.8 -82.8 283.5 181.3 57.3 117.9 197.4 270.2 227.4 132.8 -72.8 297.3 178.7 44.9 157.1 258.8 143.7 268.4 143.5 115.2 308.1 142.9 47.1 141.3 188.3 256.1 245.1 147.9 -67.8 317.3 172.3 24.7 144.5 195.6 247.3 280.8 145.2 -51.7 293.4 147.3 54.6 109.5 181.0 299.7 262.3 113.2 -118.7 245.2 100.3 160.5 74.0 231.4 260.5 174.1 96.8 -29.0 309.6 165.1 50.3 139.8 189.5 265.7 237.0 139.2 -76.1 294.5 207.6 32.0 152.0 156.8 276.6 252.3 120.0 -119.8 276.4 187.1 59.9 129.4 206.7 238.8 242.7 134.6 -32.1 287.7 170.8 47.6 152.2 258.2 152.8 273.0 141.9 105.3 303.1 148.9 37.6 146.4 202.5 194.2 256.3 143.2 8.3 47.2 63.3 53.7 93.4 - - 263.1 115.5 0.0 ______ ______ ______ ______ ______ ______ ______ ______ 286.48 165.37 52.43 130.69 200.03 241.99 248.27 AV 46.11 28.70 20.71 20.28 29.61 42.28 22.29 SD 1 SUGAR PSEUDOROTATION PARAMS, NEWHEL93 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) STRAND 1 V0 V1 V2 V3 V4 Pseud. Delta -40.9 48.9 -34.2 12.7 16.8 138.3 137.5 -28.3 41.6 -42.0 24.1 2.1 159.6 139.9 -35.4 42.2 -31.7 9.6 16.2 139.2 131.5 -29.9 40.3 -35.8 16.5 9.2 150.2 139.9 -51.7 30.8 -0.7 -30.7 50.2 90.7 88.1 -26.0 39.0 -38.6 20.3 3.6 157.9 138.7 -46.6 50.3 -34.7 7.0 26.1 132.6 119.6 -47.6 42.0 -23.9 -5.0 33.4 119.9 117.0 -21.6 36.6 -37.4 28.0 -4.4 167.4 145.9 -19.2 38.9 -41.8 31.5 -7.4 171.5 154.5 -55.0 55.6 -34.9 3.9 32.4 127.7 130.0 -19.9 35.9 -39.7 26.7 -4.6 168.6 147.6 -61.0 47.2 -20.2 -14.8 47.7 110.0 114.1 -45.5 35.9 -14.4 -12.6 35.5 108.9 117.5 -37.3 30.7 -14.2 -7.0 26.0 113.3 114.9 -40.3 45.6 -35.1 11.5 18.1 139.4 135.0 -5.0 24.0 -31.2 29.0 -15.9 189.4 137.1 -23.8 40.6 -42.4 28.8 -4.2 166.4 147.3 STRAND 2 V0 V1 V2 V3 V4 Pseud. Delta -5.1 -14.5 27.6 -30.4 22.8 27.3 87.6 -30.0 36.5 -32.4 13.2 11.0 147.2 137.3 -25.7 39.8 -37.6 22.5 2.0 158.8 137.7 -23.5 38.1 -37.2 24.3 -0.4 162.1 143.5 -26.2 36.8 -34.6 19.3 4.5 155.6 141.6 -26.8 38.9 -38.6 21.2 3.5 158.0 143.5 -50.3 45.7 -28.4 -1.8 34.4 123.5 117.9 -37.7 48.7 -46.6 23.1 9.9 153.0 157.1 -31.2 44.4 -37.7 17.6 8.8 150.1 141.3 -22.5 39.7 -42.2 28.5 -4.0 167.1 144.5 -23.9 24.1 -12.6 -1.3 15.3 120.9 109.5 -12.8 -16.6 37.1 -46.5 37.7 35.2 74.0 -10.4 24.0 -29.6 22.3 -7.8 177.3 139.8 -10.2 30.5 -38.5 32.6 -14.3 183.0 152.0 -39.6 40.8 -29.0 5.5 21.8 132.6 129.4 -24.5 41.8 -41.3 28.0 -2.9 164.4 152.2 -21.8 36.4 -40.7 27.8 -4.0 168.1 146.4 -39.4 35.0 -18.7 -5.0 28.9 118.0 93.4 ______ ______ ______ ______ ______ ______ -30.48 36.01 -28.72 10.56 12.45 140.37 AV 13.91 14.54 18.10 19.46 17.44 35.49 SD 1 RAP1 C-G-C-A-C-A-C-C-C-A-C-A-C-A-C-C-A-G B10A_PDT035 (Test Run 1 June 98) STRAND 1 SUGAR ANGLES C4-O4-C1 O4-C1-C2 C1-C2-C3 C2-C3-C4 C3-C4-O4 AVERAGE THAU(M) 101.7 107.1 98.2 102.3 108.3 103.5 49.0884 113.2 99.4 102.3 102.1 103.4 104.1 45.9315 108.2 100.8 106.5 99.8 107.5 104.6 42.9322 113.9 96.7 107.5 99.0 106.5 104.7 41.9856 99.9 104.4 101.2 103.1 103.3 102.4 54.9860 115.3 95.4 108.6 99.1 105.4 104.8 41.7801 107.7 96.7 103.0 98.8 107.1 102.7 53.6136 107.0 97.8 103.4 104.6 104.4 103.4 49.5236 107.8 111.0 95.6 105.8 104.0 104.8 41.2951 108.0 104.6 101.4 100.9 106.3 104.3 44.8759 104.9 97.4 99.4 101.1 103.0 101.2 60.6780 114.0 100.8 103.8 102.2 103.3 104.8 41.3600 103.1 96.7 100.1 101.6 102.6 100.8 62.1339 104.5 102.8 103.2 106.5 103.4 104.1 45.8199 105.7 108.3 100.1 108.6 105.0 105.5 36.4779 107.6 100.8 100.8 104.6 104.7 103.7 48.0951 110.3 106.3 105.7 99.2 108.1 105.9 33.6030 110.6 104.7 100.1 101.5 103.6 104.1 45.8523 STRAND 2 SUGAR ANGLES C4-O4-C1 O4-C1-C2 C1-C2-C3 C2-C3-C4 C3-C4-O4 AVERAGE THAU(M) 110.5 106.3 105.9 103.0 104.9 106.1 31.8917 114.4 98.8 105.8 105.9 101.3 105.2 38.6041 110.9 101.5 103.9 99.4 107.7 104.7 42.3202 110.6 102.1 102.6 100.2 108.5 104.8 41.4624 111.3 103.1 102.3 104.7 104.4 105.1 39.1784 115.0 98.7 104.8 102.4 102.6 104.7 42.2041 109.9 93.9 104.3 102.9 102.6 102.7 53.2038 113.9 94.5 100.2 102.4 101.8 102.6 53.9841 108.4 98.7 107.5 95.4 111.1 104.2 45.0553 112.5 100.7 102.6 100.6 104.8 104.2 45.0996 102.7 111.6 105.3 102.0 112.7 106.9 24.8600 105.3 107.6 103.1 98.2 104.1 103.7 48.2742 114.4 104.3 105.2 105.8 102.1 106.4 29.7241 111.4 103.2 103.7 101.0 105.7 105.0 40.2589 109.4 100.0 102.7 105.0 104.9 104.4 44.0299 107.2 105.7 100.6 100.5 106.6 104.1 45.6734 114.1 102.5 99.7 105.2 101.5 104.6 42.7785 108.1 100.7 105.6 102.1 108.2 104.9 40.6831