ID code: '2RO2' 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 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' A A 4 alpha beta 107 129 113 110 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' A A 6 alpha beta 174 196 180 177 212 C1' C A 7 alpha beta 207 227 213 210 243 C1' C A 8 alpha beta 238 258 244 241 274 C1' U A 9 alpha beta 269 289 275 272 304 C1' G A 10 alpha beta 299 322 305 302 338 C1' A A 11 alpha beta 333 355 339 336 371 C1' A A 12 alpha beta 366 388 372 369 404 C1' G A 13 alpha beta 399 422 405 402 438 C1' U A 14 alpha beta 433 453 439 436 468 C1' G A 15 alpha beta 463 486 469 466 502 C1' G A 16 alpha beta 497 520 503 500 536 C1' G A 17 alpha beta 531 554 537 534 570 C1' U A 18 alpha beta 565 585 571 568 600 C1' U A 19 alpha beta 595 615 601 598 630 C1' U A 20 alpha beta 625 645 631 628 660 C1' C A 21 alpha beta 655 675 661 658 691 C1' C A 22 alpha beta 686 706 692 689 722 C1' C A 23 alpha beta 717 738 723 720 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' A A 4 OK OK 112 108 127 111 143 C2' G A 5 OK OK 145 141 161 144 177 C2' A A 6 OK OK 179 175 194 178 210 C2' C A 7 OK OK 212 208 225 211 241 C2' C A 8 OK OK 243 239 256 242 272 C2' U A 9 OK OK 274 270 287 273 302 C2' G A 10 OK OK 304 300 320 303 336 C2' A A 11 OK OK 338 334 353 337 369 C2' A A 12 OK OK 371 367 386 370 402 C2' G A 13 OK OK 404 400 420 403 436 C2' U A 14 OK OK 438 434 451 437 466 C2' G A 15 OK OK 468 464 484 467 500 C2' G A 16 OK OK 502 498 518 501 534 C2' G A 17 OK OK 536 532 552 535 568 C2' U A 18 OK OK 570 566 583 569 598 C2' U A 19 OK OK 600 596 613 599 628 C2' U A 20 OK OK 630 626 643 629 658 C2' C A 21 OK OK 660 656 673 659 689 C2' C A 22 OK OK 691 687 704 690 720 C2' C A 23 OK OK 722 718 736 721 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' A A 4 OK OK 106 126 109 110 141 C3' G A 5 OK OK 139 160 142 143 175 C3' A A 6 OK OK 173 193 176 177 208 C3' C A 7 OK OK 206 224 209 210 239 C3' C A 8 OK OK 237 255 240 241 270 C3' U A 9 OK OK 268 286 271 272 300 C3' G A 10 OK OK 298 319 301 302 334 C3' A A 11 OK OK 332 352 335 336 367 C3' A A 12 OK OK 365 385 368 369 400 C3' G A 13 OK OK 398 419 401 402 434 C3' U A 14 OK OK 432 450 435 436 464 C3' G A 15 OK OK 462 483 465 466 498 C3' G A 16 OK OK 496 517 499 500 532 C3' G A 17 OK OK 530 551 533 534 566 C3' U A 18 OK OK 564 582 567 568 596 C3' U A 19 OK OK 594 612 597 598 626 C3' U A 20 OK OK 624 642 627 628 656 C3' C A 21 OK OK 654 672 657 658 687 C3' C A 22 OK OK 685 703 688 689 718 C3' C A 23 OK OK 716 734 719 720 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' A A 4 OK OK 108 125 105 107 139 C4' G A 5 OK OK 141 159 138 140 173 C4' A A 6 OK OK 175 192 172 174 206 C4' C A 7 OK OK 208 223 205 207 237 C4' C A 8 OK OK 239 254 236 238 268 C4' U A 9 OK OK 270 285 267 269 298 C4' G A 10 OK OK 300 318 297 299 332 C4' A A 11 OK OK 334 351 331 333 365 C4' A A 12 OK OK 367 384 364 366 398 C4' G A 13 OK OK 400 418 397 399 432 C4' U A 14 OK OK 434 449 431 433 462 C4' G A 15 OK OK 464 482 461 463 496 C4' G A 16 OK OK 498 516 495 497 530 C4' G A 17 OK OK 532 550 529 531 564 C4' U A 18 OK OK 566 581 563 565 594 C4' U A 19 OK OK 596 611 593 595 624 C4' U A 20 OK OK 626 641 623 625 654 C4' C A 21 OK OK 656 671 653 655 685 C4' C A 22 OK OK 687 702 684 686 716 C4' C A 23 OK OK 718 733 715 717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' A A 4 OK OK 104 123 124 106 138 C5' G A 5 OK OK 137 157 158 139 172 C5' A A 6 OK OK 171 190 191 173 205 C5' C A 7 OK OK 204 221 222 206 236 C5' C A 8 OK OK 235 252 253 237 267 C5' U A 9 OK OK 266 283 284 268 297 C5' G A 10 OK OK 296 316 317 298 331 C5' A A 11 OK OK 330 349 350 332 364 C5' A A 12 OK OK 363 382 383 365 397 C5' G A 13 OK OK 396 416 417 398 431 C5' U A 14 OK OK 430 447 448 432 461 C5' G A 15 OK OK 460 480 481 462 495 C5' G A 16 OK OK 494 514 515 496 529 C5' G A 17 OK OK 528 548 549 530 563 C5' U A 18 OK OK 562 579 580 564 593 C5' U A 19 OK OK 592 609 610 594 623 C5' U A 20 OK OK 622 639 640 624 653 C5' C A 21 OK OK 652 669 670 654 684 C5' C A 22 OK OK 683 700 701 685 715 C5' C A 23 OK OK 714 731 732 716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P A A 4 distorted distorted 75 102 103 104 134 P G A 5 distorted distorted 109 135 136 137 168 P A A 6 distorted distorted 142 169 170 171 201 P C A 7 distorted distorted 176 202 203 204 232 P C A 8 distorted distorted 209 233 234 235 263 P U A 9 distorted distorted 240 264 265 266 293 P G A 10 distorted distorted 271 294 295 296 327 P A A 11 distorted distorted 301 328 329 330 360 P A A 12 distorted distorted 335 361 362 363 393 P G A 13 distorted distorted 368 394 395 396 427 P U A 14 distorted distorted 401 428 429 430 457 P G A 15 distorted distorted 435 458 459 460 491 P G A 16 distorted distorted 465 492 493 494 525 P G A 17 distorted distorted 499 526 527 528 559 P U A 18 distorted distorted 533 560 561 562 589 P U A 19 distorted distorted 567 590 591 592 619 P U A 20 distorted distorted 597 620 621 622 649 P C A 21 distorted distorted 627 650 651 652 680 P C A 22 distorted distorted 657 681 682 683 711 P C A 23 distorted distorted 688 712 713 714 ---------------------------------------------------------------------------------