ID code: '2H1M' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' A A 3 beta 47 53 50 74 C1' XUG A 4 beta 75 73 76 98 C1' A A 5 beta 93 99 96 120 C1' G A 6 beta 115 121 118 143 C1' U A 7 beta 138 144 141 163 C1' U A 8 beta 158 164 161 183 C1' A A 9 beta 178 184 181 205 C1' A A 10 beta 200 206 203 227 C1' A A 11 beta 222 228 225 249 C1' U A 12 beta 244 250 247 269 C1' C A 13 beta 264 270 267 289 C1' U A 14 beta 284 290 287 309 C1' G A 15 beta 304 310 307 332 C1' C A 16 beta 327 333 330 350 C1' G B 17 beta 345 351 348 373 C1' C B 18 beta 368 374 371 393 C1' A B 19 beta 388 394 391 415 C1' XUG B 20 beta 416 414 417 439 C1' A B 21 beta 434 440 437 461 C1' G B 22 beta 456 462 459 484 C1' U B 23 beta 479 485 482 504 C1' U B 24 beta 499 505 502 524 C1' A B 25 beta 519 525 522 546 C1' A B 26 beta 541 547 544 568 C1' A B 27 beta 563 569 566 590 C1' U B 28 beta 585 591 588 610 C1' C B 29 beta 605 611 608 630 C1' U B 30 beta 625 631 628 650 C1' G B 31 beta 645 651 648 673 C1' C B 32 beta 668 674 671 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' A A 3 OK 52 48 51 76 C2' XUG A 4 74 79 96 C2' A A 5 OK 98 94 97 118 C2' G A 6 OK 120 116 119 141 C2' U A 7 OK 143 139 142 161 C2' U A 8 OK 163 159 162 181 C2' A A 9 OK 183 179 182 203 C2' A A 10 OK 205 201 204 225 C2' A A 11 OK 227 223 226 247 C2' U A 12 OK 249 245 248 267 C2' C A 13 OK 269 265 268 287 C2' U A 14 OK 289 285 288 307 C2' G A 15 OK 309 305 308 330 C2' C A 16 OK 332 328 331 348 C2' G B 17 OK 350 346 349 371 C2' C B 18 OK 373 369 372 391 C2' A B 19 OK 393 389 392 417 C2' XUG B 20 415 420 437 C2' A B 21 OK 439 435 438 459 C2' G B 22 OK 461 457 460 482 C2' U B 23 OK 484 480 483 502 C2' U B 24 OK 504 500 503 522 C2' A B 25 OK 524 520 523 544 C2' A B 26 OK 546 542 545 566 C2' A B 27 OK 568 564 567 588 C2' U B 28 OK 590 586 589 608 C2' C B 29 OK 610 606 609 628 C2' U B 30 OK 630 626 629 648 C2' G B 31 OK 650 646 649 671 C2' C B 32 OK 673 669 672 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' A A 3 OK 46 49 50 79 C3' XUG A 4 OK 81 80 76 94 C3' A A 5 OK 92 95 96 116 C3' G A 6 OK 114 117 118 139 C3' U A 7 OK 137 140 141 159 C3' U A 8 OK 157 160 161 179 C3' A A 9 OK 177 180 181 201 C3' A A 10 OK 199 202 203 223 C3' A A 11 OK 221 224 225 245 C3' U A 12 OK 243 246 247 265 C3' C A 13 OK 263 266 267 285 C3' U A 14 OK 283 286 287 305 C3' G A 15 OK 303 306 307 328 C3' C A 16 OK 326 329 330 346 C3' G B 17 OK 344 347 348 369 C3' C B 18 OK 367 370 371 389 C3' A B 19 OK 387 390 391 420 C3' XUG B 20 OK 422 421 417 435 C3' A B 21 OK 433 436 437 457 C3' G B 22 OK 455 458 459 480 C3' U B 23 OK 478 481 482 500 C3' U B 24 OK 498 501 502 520 C3' A B 25 OK 518 521 522 542 C3' A B 26 OK 540 543 544 564 C3' A B 27 OK 562 565 566 586 C3' U B 28 OK 584 587 588 606 C3' C B 29 OK 604 607 608 626 C3' U B 30 OK 624 627 628 646 C3' G B 31 OK 644 647 648 669 C3' C B 32 OK 667 670 671 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' A A 3 OK 48 45 47 81 C4' XUG A 4 OK 79 82 75 92 C4' A A 5 OK 94 91 93 114 C4' G A 6 OK 116 113 115 137 C4' U A 7 OK 139 136 138 157 C4' U A 8 OK 159 156 158 177 C4' A A 9 OK 179 176 178 199 C4' A A 10 OK 201 198 200 221 C4' A A 11 OK 223 220 222 243 C4' U A 12 OK 245 242 244 263 C4' C A 13 OK 265 262 264 283 C4' U A 14 OK 285 282 284 303 C4' G A 15 OK 305 302 304 326 C4' C A 16 OK 328 325 327 344 C4' G B 17 OK 346 343 345 367 C4' C B 18 OK 369 366 368 387 C4' A B 19 OK 389 386 388 422 C4' XUG B 20 OK 420 423 416 433 C4' A B 21 OK 435 432 434 455 C4' G B 22 OK 457 454 456 478 C4' U B 23 OK 480 477 479 498 C4' U B 24 OK 500 497 499 518 C4' A B 25 OK 520 517 519 540 C4' A B 26 OK 542 539 541 562 C4' A B 27 OK 564 561 563 584 C4' U B 28 OK 586 583 585 604 C4' C B 29 OK 606 603 605 624 C4' U B 30 OK 626 623 625 644 C4' G B 31 OK 646 643 645 667 C4' C B 32 OK 669 666 668 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' A A 3 44 46 82 C5' XUG A 4 83 81 91 C5' A A 5 90 92 113 C5' G A 6 112 114 136 C5' U A 7 135 137 156 C5' U A 8 155 157 176 C5' A A 9 175 177 198 C5' A A 10 197 199 220 C5' A A 11 219 221 242 C5' U A 12 241 243 262 C5' C A 13 261 263 282 C5' U A 14 281 283 302 C5' G A 15 301 303 325 C5' C A 16 324 326 343 C5' G B 17 342 344 366 C5' C B 18 365 367 386 C5' A B 19 385 387 423 C5' XUG B 20 424 422 432 C5' A B 21 431 433 454 C5' G B 22 453 455 477 C5' U B 23 476 478 497 C5' U B 24 496 498 517 C5' A B 25 516 518 539 C5' A B 26 538 540 561 C5' A B 27 560 562 583 C5' U B 28 582 584 603 C5' C B 29 602 604 623 C5' U B 30 622 624 643 C5' G B 31 642 644 666 C5' C B 32 665 667 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P A A 3 distorted distorted 29 42 43 44 84 P XUG A 4 distorted distorted 49 85 86 83 87 P A A 5 distorted distorted 80 88 89 90 109 P G A 6 distorted distorted 95 110 111 112 132 P U A 7 distorted distorted 117 133 134 135 152 P U A 8 distorted distorted 140 153 154 155 172 P A A 9 distorted distorted 160 173 174 175 194 P A A 10 distorted distorted 180 195 196 197 216 P A A 11 distorted distorted 202 217 218 219 238 P U A 12 distorted distorted 224 239 240 241 258 P C A 13 distorted distorted 246 259 260 261 278 P U A 14 distorted distorted 266 279 280 281 298 P G A 15 distorted distorted 286 299 300 301 321 P C A 16 distorted distorted 306 322 323 324 362 P C B 18 distorted distorted 347 363 364 365 382 P A B 19 distorted distorted 370 383 384 385 425 P XUG B 20 distorted distorted 390 426 427 424 428 P A B 21 distorted distorted 421 429 430 431 450 P G B 22 distorted distorted 436 451 452 453 473 P U B 23 distorted distorted 458 474 475 476 493 P U B 24 distorted distorted 481 494 495 496 513 P A B 25 distorted distorted 501 514 515 516 535 P A B 26 distorted distorted 521 536 537 538 557 P A B 27 distorted distorted 543 558 559 560 579 P U B 28 distorted distorted 565 580 581 582 599 P C B 29 distorted distorted 587 600 601 602 619 P U B 30 distorted distorted 607 620 621 622 639 P G B 31 distorted distorted 627 640 641 642 662 P C B 32 distorted distorted 647 663 664 665 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