ID code: '1JUR' 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' C A 3 alpha beta 73 93 79 76 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' U A 5 alpha beta 135 155 141 138 170 C1' G A 6 alpha beta 165 188 171 168 204 C1' A A 7 alpha beta 199 221 205 202 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' A A 10 alpha beta 300 322 306 303 338 C1' G A 11 alpha beta 333 356 339 336 372 C1' A A 12 alpha beta 367 389 373 370 405 C1' C A 13 alpha beta 400 420 406 403 436 C1' U A 14 alpha beta 431 451 437 434 466 C1' C A 15 alpha beta 461 481 467 464 497 C1' A A 16 alpha beta 492 514 498 495 530 C1' G A 17 alpha beta 525 548 531 528 564 C1' A A 18 alpha beta 559 581 565 562 597 C1' A A 19 alpha beta 592 614 598 595 630 C1' G A 20 alpha beta 625 648 631 628 664 C1' C A 21 alpha beta 659 679 665 662 695 C1' C A 22 alpha beta 690 711 696 693 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' C A 4 OK OK 109 105 122 108 138 C2' U A 5 OK OK 140 136 153 139 168 C2' G A 6 OK OK 170 166 186 169 202 C2' A A 7 OK OK 204 200 219 203 235 C2' G A 8 OK OK 237 233 253 236 269 C2' G A 9 OK OK 271 267 287 270 303 C2' A A 10 OK OK 305 301 320 304 336 C2' G A 11 OK OK 338 334 354 337 370 C2' A A 12 OK OK 372 368 387 371 403 C2' C A 13 OK OK 405 401 418 404 434 C2' U A 14 OK OK 436 432 449 435 464 C2' C A 15 OK OK 466 462 479 465 495 C2' A A 16 OK OK 497 493 512 496 528 C2' G A 17 OK OK 530 526 546 529 562 C2' A A 18 OK OK 564 560 579 563 595 C2' A A 19 OK OK 597 593 612 596 628 C2' G A 20 OK OK 630 626 646 629 662 C2' C A 21 OK OK 664 660 677 663 693 C2' C A 22 OK OK 695 691 709 694 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' C A 4 OK OK 103 121 106 107 136 C3' U A 5 OK OK 134 152 137 138 166 C3' G A 6 OK OK 164 185 167 168 200 C3' A A 7 OK OK 198 218 201 202 233 C3' G A 8 OK OK 231 252 234 235 267 C3' G A 9 OK OK 265 286 268 269 301 C3' A A 10 OK OK 299 319 302 303 334 C3' G A 11 OK OK 332 353 335 336 368 C3' A A 12 OK OK 366 386 369 370 401 C3' C A 13 OK OK 399 417 402 403 432 C3' U A 14 OK OK 430 448 433 434 462 C3' C A 15 OK OK 460 478 463 464 493 C3' A A 16 OK OK 491 511 494 495 526 C3' G A 17 OK OK 524 545 527 528 560 C3' A A 18 OK OK 558 578 561 562 593 C3' A A 19 OK OK 591 611 594 595 626 C3' G A 20 OK OK 624 645 627 628 660 C3' C A 21 OK OK 658 676 661 662 691 C3' C A 22 OK OK 689 707 692 693 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' C A 4 OK OK 105 120 102 104 134 C4' U A 5 OK OK 136 151 133 135 164 C4' G A 6 OK OK 166 184 163 165 198 C4' A A 7 OK OK 200 217 197 199 231 C4' G A 8 OK OK 233 251 230 232 265 C4' G A 9 OK OK 267 285 264 266 299 C4' A A 10 OK OK 301 318 298 300 332 C4' G A 11 OK OK 334 352 331 333 366 C4' A A 12 OK OK 368 385 365 367 399 C4' C A 13 OK OK 401 416 398 400 430 C4' U A 14 OK OK 432 447 429 431 460 C4' C A 15 OK OK 462 477 459 461 491 C4' A A 16 OK OK 493 510 490 492 524 C4' G A 17 OK OK 526 544 523 525 558 C4' A A 18 OK OK 560 577 557 559 591 C4' A A 19 OK OK 593 610 590 592 624 C4' G A 20 OK OK 626 644 623 625 658 C4' C A 21 OK OK 660 675 657 659 689 C4' C A 22 OK OK 691 706 688 690 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' C A 4 OK OK 101 118 119 103 133 C5' U A 5 OK OK 132 149 150 134 163 C5' G A 6 OK OK 162 182 183 164 197 C5' A A 7 OK OK 196 215 216 198 230 C5' G A 8 OK OK 229 249 250 231 264 C5' G A 9 OK OK 263 283 284 265 298 C5' A A 10 OK OK 297 316 317 299 331 C5' G A 11 OK OK 330 350 351 332 365 C5' A A 12 OK OK 364 383 384 366 398 C5' C A 13 OK OK 397 414 415 399 429 C5' U A 14 OK OK 428 445 446 430 459 C5' C A 15 OK OK 458 475 476 460 490 C5' A A 16 OK OK 489 508 509 491 523 C5' G A 17 OK OK 522 542 543 524 557 C5' A A 18 OK OK 556 575 576 558 590 C5' A A 19 OK OK 589 608 609 591 623 C5' G A 20 OK OK 622 642 643 624 657 C5' C A 21 OK OK 656 673 674 658 688 C5' C A 22 OK OK 687 704 705 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P C A 4 distorted distorted 75 99 100 101 129 P U A 5 distorted distorted 106 130 131 132 159 P G A 6 distorted distorted 137 160 161 162 193 P A A 7 distorted distorted 167 194 195 196 226 P G A 8 distorted distorted 201 227 228 229 260 P G A 9 distorted distorted 234 261 262 263 294 P A A 10 distorted distorted 268 295 296 297 327 P G A 11 distorted distorted 302 328 329 330 361 P A A 12 distorted distorted 335 362 363 364 394 P C A 13 distorted distorted 369 395 396 397 425 P U A 14 distorted distorted 402 426 427 428 455 P C A 15 distorted distorted 433 456 457 458 486 P A A 16 distorted distorted 463 487 488 489 519 P G A 17 distorted distorted 494 520 521 522 553 P A A 18 distorted distorted 527 554 555 556 586 P A A 19 distorted distorted 561 587 588 589 619 P G A 20 distorted distorted 594 620 621 622 653 P C A 21 distorted distorted 627 654 655 656 684 P C A 22 distorted distorted 661 685 686 687 ---------------------------------------------------------------------------------