ID code: '2E9T' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 12 C1' U B 903 beta 7 13 10 32 C1' A B 904 beta 27 33 30 54 C1' G B 905 beta 49 55 52 77 C1' G B 906 beta 72 78 75 100 C1' G B 907 beta 95 101 98 123 C1' C B 908 beta 118 124 121 143 C1' C B 909 beta 138 144 141 163 C1' C B 910 beta 158 164 161 181 C1' G C 915 beta 176 182 179 204 C1' G C 916 beta 199 205 202 227 C1' G C 917 beta 222 228 225 250 C1' C C 918 beta 245 251 248 270 C1' C C 919 beta 265 271 268 290 C1' C C 920 beta 285 291 288 308 C1' 5FU C 921 beta 309 307 310 332 C1' U E 903 beta 327 333 330 352 C1' A E 904 beta 347 353 350 374 C1' G E 905 beta 369 375 372 397 C1' G E 906 beta 392 398 395 420 C1' G E 907 beta 415 421 418 443 C1' C E 908 beta 438 444 441 463 C1' C E 909 beta 458 464 461 483 C1' C E 910 beta 478 484 481 501 C1' G F 915 beta 496 502 499 524 C1' G F 916 beta 519 525 522 547 C1' G F 917 beta 542 548 545 570 C1' C F 918 beta 565 571 568 590 C1' C F 919 beta 585 591 588 610 C1' C F 920 beta 605 611 608 628 C1' 5FU F 921 beta 629 627 630 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U B 903 OK 12 8 11 30 C2' A B 904 OK 32 28 31 52 C2' G B 905 OK 54 50 53 75 C2' G B 906 OK 77 73 76 98 C2' G B 907 OK 100 96 99 121 C2' C B 908 OK 123 119 122 141 C2' C B 909 OK 143 139 142 161 C2' C B 910 OK 163 159 162 179 C2' G C 915 OK 181 177 180 202 C2' G C 916 OK 204 200 203 225 C2' G C 917 OK 227 223 226 248 C2' C C 918 OK 250 246 249 268 C2' C C 919 OK 270 266 269 288 C2' C C 920 OK 290 286 289 310 C2' 5FU C 921 OK 308 312 311 330 C2' U E 903 OK 332 328 331 350 C2' A E 904 OK 352 348 351 372 C2' G E 905 OK 374 370 373 395 C2' G E 906 OK 397 393 396 418 C2' G E 907 OK 420 416 419 441 C2' C E 908 OK 443 439 442 461 C2' C E 909 OK 463 459 462 481 C2' C E 910 OK 483 479 482 499 C2' G F 915 OK 501 497 500 522 C2' G F 916 OK 524 520 523 545 C2' G F 917 OK 547 543 546 568 C2' C F 918 OK 570 566 569 588 C2' C F 919 OK 590 586 589 608 C2' C F 920 OK 610 606 609 630 C2' 5FU F 921 OK 628 632 631 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U B 903 OK 6 9 10 28 C3' A B 904 OK 26 29 30 50 C3' G B 905 OK 48 51 52 73 C3' G B 906 OK 71 74 75 96 C3' G B 907 OK 94 97 98 119 C3' C B 908 OK 117 120 121 139 C3' C B 909 OK 137 140 141 159 C3' C B 910 OK 157 160 161 177 C3' G C 915 OK 175 178 179 200 C3' G C 916 OK 198 201 202 223 C3' G C 917 OK 221 224 225 246 C3' C C 918 OK 244 247 248 266 C3' C C 919 OK 264 267 268 286 C3' C C 920 OK 284 287 288 312 C3' 5FU C 921 OK 314 313 310 328 C3' U E 903 OK 326 329 330 348 C3' A E 904 OK 346 349 350 370 C3' G E 905 OK 368 371 372 393 C3' G E 906 OK 391 394 395 416 C3' G E 907 OK 414 417 418 439 C3' C E 908 OK 437 440 441 459 C3' C E 909 OK 457 460 461 479 C3' C E 910 OK 477 480 481 497 C3' G F 915 OK 495 498 499 520 C3' G F 916 OK 518 521 522 543 C3' G F 917 OK 541 544 545 566 C3' C F 918 OK 564 567 568 586 C3' C F 919 OK 584 587 588 606 C3' C F 920 OK 604 607 608 632 C3' 5FU F 921 OK 634 633 630 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U B 903 OK 8 5 7 26 C4' A B 904 OK 28 25 27 48 C4' G B 905 OK 50 47 49 71 C4' G B 906 OK 73 70 72 94 C4' G B 907 OK 96 93 95 117 C4' C B 908 OK 119 116 118 137 C4' C B 909 OK 139 136 138 157 C4' C B 910 OK 159 156 158 175 C4' G C 915 OK 177 174 176 198 C4' G C 916 OK 200 197 199 221 C4' G C 917 OK 223 220 222 244 C4' C C 918 OK 246 243 245 264 C4' C C 919 OK 266 263 265 284 C4' C C 920 OK 286 283 285 314 C4' 5FU C 921 OK 312 315 309 326 C4' U E 903 OK 328 325 327 346 C4' A E 904 OK 348 345 347 368 C4' G E 905 OK 370 367 369 391 C4' G E 906 OK 393 390 392 414 C4' G E 907 OK 416 413 415 437 C4' C E 908 OK 439 436 438 457 C4' C E 909 OK 459 456 458 477 C4' C E 910 OK 479 476 478 495 C4' G F 915 OK 497 494 496 518 C4' G F 916 OK 520 517 519 541 C4' G F 917 OK 543 540 542 564 C4' C F 918 OK 566 563 565 584 C4' C F 919 OK 586 583 585 604 C4' C F 920 OK 606 603 605 634 C4' 5FU F 921 OK 632 635 629 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U B 903 4 6 25 C5' A B 904 24 26 47 C5' G B 905 46 48 70 C5' G B 906 69 71 93 C5' G B 907 92 94 116 C5' C B 908 115 117 136 C5' C B 909 135 137 156 C5' C B 910 155 157 174 C5' G C 915 173 175 197 C5' G C 916 196 198 220 C5' G C 917 219 221 243 C5' C C 918 242 244 263 C5' C C 919 262 264 283 C5' C C 920 282 284 315 C5' 5FU C 921 316 314 325 C5' U E 903 324 326 345 C5' A E 904 344 346 367 C5' G E 905 366 368 390 C5' G E 906 389 391 413 C5' G E 907 412 414 436 C5' C E 908 435 437 456 C5' C E 909 455 457 476 C5' C E 910 475 477 494 C5' G F 915 493 495 517 C5' G F 916 516 518 540 C5' G F 917 539 541 563 C5' C F 918 562 564 583 C5' C F 919 582 584 603 C5' C F 920 602 604 635 C5' 5FU F 921 636 634 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U B 903 distorted distorted 2 3 4 21 P A B 904 distorted distorted 9 22 23 24 43 P G B 905 distorted distorted 29 44 45 46 66 P G B 906 distorted distorted 51 67 68 69 89 P G B 907 distorted distorted 74 90 91 92 112 P C B 908 distorted distorted 97 113 114 115 132 P C B 909 distorted distorted 120 133 134 135 152 P C B 910 distorted distorted 140 153 154 155 193 P G C 916 distorted distorted 178 194 195 196 216 P G C 917 distorted distorted 201 217 218 219 239 P C C 918 distorted distorted 224 240 241 242 259 P C C 919 distorted distorted 247 260 261 262 279 P C C 920 distorted distorted 267 280 281 282 317 P 5FU C 921 distorted distorted 287 318 319 316 321 P U E 903 distorted distorted 322 323 324 341 P A E 904 distorted distorted 329 342 343 344 363 P G E 905 distorted distorted 349 364 365 366 386 P G E 906 distorted distorted 371 387 388 389 409 P G E 907 distorted distorted 394 410 411 412 432 P C E 908 distorted distorted 417 433 434 435 452 P C E 909 distorted distorted 440 453 454 455 472 P C E 910 distorted distorted 460 473 474 475 513 P G F 916 distorted distorted 498 514 515 516 536 P G F 917 distorted distorted 521 537 538 539 559 P C F 918 distorted distorted 544 560 561 562 579 P C F 919 distorted distorted 567 580 581 582 599 P C F 920 distorted distorted 587 600 601 602 637 P 5FU F 921 distorted distorted 607 638 639 636 ---------------------------------------------------------------------------------