ID code: '4PCJ' 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' C A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' G A 3 beta 44 50 47 72 C1' C A 4 beta 67 73 70 89 C1' PSU A 5 beta 95 85 90 112 C1' G A 6 beta 107 113 110 135 C1' G A 7 beta 130 136 133 158 C1' C A 8 beta 153 159 156 178 C1' U A 9 beta 173 179 176 198 C1' A A 10 beta 193 199 196 220 C1' A A 11 beta 215 221 218 242 C1' G A 12 beta 237 243 240 265 C1' G A 13 beta 260 266 263 288 C1' C A 14 beta 283 289 286 308 C1' A A 15 beta 303 309 306 330 C1' U A 16 beta 325 331 328 350 C1' G A 17 beta 345 351 348 373 C1' A A 18 beta 368 374 371 395 C1' A A 19 beta 390 396 393 417 C1' A A 20 beta 412 418 415 439 C1' G A 21 beta 434 440 437 462 C1' U A 22 beta 457 463 460 482 C1' G A 23 beta 477 483 480 505 C1' C A 24 beta 500 506 503 525 C1' U A 25 beta 520 526 523 545 C1' A A 26 beta 540 546 543 567 C1' U A 27 beta 562 568 565 587 C1' G A 28 beta 582 588 585 610 C1' C A 29 beta 605 611 608 630 C1' C A 30 beta 625 631 628 650 C1' U A 31 beta 645 651 648 670 C1' G A 32 beta 665 671 668 693 C1' C A 33 beta 688 694 691 713 C1' U A 34 beta 708 714 711 733 C1' G A 35 beta 728 734 731 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' G A 3 OK 49 45 48 70 C2' C A 4 OK 72 68 71 90 C2' PSU A 5 OK 89 92 91 110 C2' G A 6 OK 112 108 111 133 C2' G A 7 OK 135 131 134 156 C2' C A 8 OK 158 154 157 176 C2' U A 9 OK 178 174 177 196 C2' A A 10 OK 198 194 197 218 C2' A A 11 OK 220 216 219 240 C2' G A 12 OK 242 238 241 263 C2' G A 13 OK 265 261 264 286 C2' C A 14 OK 288 284 287 306 C2' A A 15 OK 308 304 307 328 C2' U A 16 OK 330 326 329 348 C2' G A 17 OK 350 346 349 371 C2' A A 18 OK 373 369 372 393 C2' A A 19 OK 395 391 394 415 C2' A A 20 OK 417 413 416 437 C2' G A 21 OK 439 435 438 460 C2' U A 22 OK 462 458 461 480 C2' G A 23 OK 482 478 481 503 C2' C A 24 OK 505 501 504 523 C2' U A 25 OK 525 521 524 543 C2' A A 26 OK 545 541 544 565 C2' U A 27 OK 567 563 566 585 C2' G A 28 OK 587 583 586 608 C2' C A 29 OK 610 606 609 628 C2' C A 30 OK 630 626 629 648 C2' U A 31 OK 650 646 649 668 C2' G A 32 OK 670 666 669 691 C2' C A 33 OK 693 689 692 711 C2' U A 34 OK 713 709 712 731 C2' G A 35 OK 733 729 732 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' G A 3 OK 43 46 47 68 C3' C A 4 OK 66 69 70 92 C3' PSU A 5 OK 93 94 90 108 C3' G A 6 OK 106 109 110 131 C3' G A 7 OK 129 132 133 154 C3' C A 8 OK 152 155 156 174 C3' U A 9 OK 172 175 176 194 C3' A A 10 OK 192 195 196 216 C3' A A 11 OK 214 217 218 238 C3' G A 12 OK 236 239 240 261 C3' G A 13 OK 259 262 263 284 C3' C A 14 OK 282 285 286 304 C3' A A 15 OK 302 305 306 326 C3' U A 16 OK 324 327 328 346 C3' G A 17 OK 344 347 348 369 C3' A A 18 OK 367 370 371 391 C3' A A 19 OK 389 392 393 413 C3' A A 20 OK 411 414 415 435 C3' G A 21 OK 433 436 437 458 C3' U A 22 OK 456 459 460 478 C3' G A 23 OK 476 479 480 501 C3' C A 24 OK 499 502 503 521 C3' U A 25 OK 519 522 523 541 C3' A A 26 OK 539 542 543 563 C3' U A 27 OK 561 564 565 583 C3' G A 28 OK 581 584 585 606 C3' C A 29 OK 604 607 608 626 C3' C A 30 OK 624 627 628 646 C3' U A 31 OK 644 647 648 666 C3' G A 32 OK 664 667 668 689 C3' C A 33 OK 687 690 691 709 C3' U A 34 OK 707 710 711 729 C3' G A 35 OK 727 730 731 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' G A 3 OK 45 42 44 66 C4' C A 4 OK 68 65 67 93 C4' PSU A 5 OK 92 96 95 106 C4' G A 6 OK 108 105 107 129 C4' G A 7 OK 131 128 130 152 C4' C A 8 OK 154 151 153 172 C4' U A 9 OK 174 171 173 192 C4' A A 10 OK 194 191 193 214 C4' A A 11 OK 216 213 215 236 C4' G A 12 OK 238 235 237 259 C4' G A 13 OK 261 258 260 282 C4' C A 14 OK 284 281 283 302 C4' A A 15 OK 304 301 303 324 C4' U A 16 OK 326 323 325 344 C4' G A 17 OK 346 343 345 367 C4' A A 18 OK 369 366 368 389 C4' A A 19 OK 391 388 390 411 C4' A A 20 OK 413 410 412 433 C4' G A 21 OK 435 432 434 456 C4' U A 22 OK 458 455 457 476 C4' G A 23 OK 478 475 477 499 C4' C A 24 OK 501 498 500 519 C4' U A 25 OK 521 518 520 539 C4' A A 26 OK 541 538 540 561 C4' U A 27 OK 563 560 562 581 C4' G A 28 OK 583 580 582 604 C4' C A 29 OK 606 603 605 624 C4' C A 30 OK 626 623 625 644 C4' U A 31 OK 646 643 645 664 C4' G A 32 OK 666 663 665 687 C4' C A 33 OK 689 686 688 707 C4' U A 34 OK 709 706 708 727 C4' G A 35 OK 729 726 728 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' U A 2 21 23 42 C5' G A 3 41 43 65 C5' C A 4 64 66 96 C5' PSU A 5 97 93 105 C5' G A 6 104 106 128 C5' G A 7 127 129 151 C5' C A 8 150 152 171 C5' U A 9 170 172 191 C5' A A 10 190 192 213 C5' A A 11 212 214 235 C5' G A 12 234 236 258 C5' G A 13 257 259 281 C5' C A 14 280 282 301 C5' A A 15 300 302 323 C5' U A 16 322 324 343 C5' G A 17 342 344 366 C5' A A 18 365 367 388 C5' A A 19 387 389 410 C5' A A 20 409 411 432 C5' G A 21 431 433 455 C5' U A 22 454 456 475 C5' G A 23 474 476 498 C5' C A 24 497 499 518 C5' U A 25 517 519 538 C5' A A 26 537 539 560 C5' U A 27 559 561 580 C5' G A 28 579 581 603 C5' C A 29 602 604 623 C5' C A 30 622 624 643 C5' U A 31 642 644 663 C5' G A 32 662 664 686 C5' C A 33 685 687 706 C5' U A 34 705 707 726 C5' G A 35 725 727 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P G A 3 distorted distorted 26 39 40 41 61 P C A 4 distorted distorted 46 62 63 64 98 P PSU A 5 OK OK 69 99 100 97 101 P G A 6 distorted distorted 94 102 103 104 124 P G A 7 distorted distorted 109 125 126 127 147 P C A 8 distorted distorted 132 148 149 150 167 P U A 9 distorted distorted 155 168 169 170 187 P A A 10 distorted distorted 175 188 189 190 209 P A A 11 distorted distorted 195 210 211 212 231 P G A 12 distorted distorted 217 232 233 234 254 P G A 13 distorted distorted 239 255 256 257 277 P C A 14 distorted distorted 262 278 279 280 297 P A A 15 distorted distorted 285 298 299 300 319 P U A 16 distorted distorted 305 320 321 322 339 P G A 17 distorted distorted 327 340 341 342 362 P A A 18 distorted distorted 347 363 364 365 384 P A A 19 distorted distorted 370 385 386 387 406 P A A 20 distorted distorted 392 407 408 409 428 P G A 21 distorted distorted 414 429 430 431 451 P U A 22 distorted distorted 436 452 453 454 471 P G A 23 distorted distorted 459 472 473 474 494 P C A 24 distorted distorted 479 495 496 497 514 P U A 25 distorted distorted 502 515 516 517 534 P A A 26 distorted distorted 522 535 536 537 556 P U A 27 distorted distorted 542 557 558 559 576 P G A 28 distorted distorted 564 577 578 579 599 P C A 29 distorted distorted 584 600 601 602 619 P C A 30 distorted distorted 607 620 621 622 639 P U A 31 distorted distorted 627 640 641 642 659 P G A 32 distorted distorted 647 660 661 662 682 P C A 33 distorted distorted 667 683 684 685 702 P U A 34 distorted distorted 690 703 704 705 722 P G A 35 distorted distorted 710 723 724 725 ---------------------------------------------------------------------------------