ID code: '1N53' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' U A 6 alpha beta 174 194 180 177 209 C1' G A 7 alpha beta 204 227 210 207 243 C1' G A 8 alpha beta 238 261 244 241 277 C1' A A 9 alpha beta 272 294 278 275 310 C1' A A 10 alpha beta 305 327 311 308 343 C1' C A 11 alpha beta 338 358 344 341 374 C1' C A 12 alpha beta 369 389 375 372 405 C1' G A 13 alpha beta 400 423 406 403 439 C1' C A 14 alpha beta 434 454 440 437 470 C1' G A 15 alpha beta 465 488 471 468 504 C1' C A 16 alpha beta 499 520 505 502 534 C1' G B 17 alpha beta 529 552 535 532 569 C1' C B 18 alpha beta 564 584 570 567 600 C1' G B 19 alpha beta 595 618 601 598 634 C1' U B 20 alpha beta 629 649 635 632 664 C1' C B 21 alpha beta 659 679 665 662 695 C1' C B 22 alpha beta 690 710 696 693 726 C1' C B 23 alpha beta 721 741 727 724 757 C1' U B 24 alpha beta 752 772 758 755 787 C1' C B 25 alpha beta 782 803 788 785 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' G A 4 OK OK 111 107 127 110 143 C2' G A 5 OK OK 145 141 161 144 177 C2' U A 6 OK OK 179 175 192 178 207 C2' G A 7 OK OK 209 205 225 208 241 C2' G A 8 OK OK 243 239 259 242 275 C2' A A 9 OK OK 277 273 292 276 308 C2' A A 10 OK OK 310 306 325 309 341 C2' C A 11 OK OK 343 339 356 342 372 C2' C A 12 OK OK 374 370 387 373 403 C2' G A 13 OK OK 405 401 421 404 437 C2' C A 14 OK OK 439 435 452 438 468 C2' G A 15 OK OK 470 466 486 469 502 C2' C A 16 OK OK 504 500 518 503 532 C2' G B 17 OK OK 534 530 550 533 567 C2' C B 18 OK OK 569 565 582 568 598 C2' G B 19 OK OK 600 596 616 599 632 C2' U B 20 OK OK 634 630 647 633 662 C2' C B 21 OK OK 664 660 677 663 693 C2' C B 22 OK OK 695 691 708 694 724 C2' C B 23 OK OK 726 722 739 725 755 C2' U B 24 OK OK 757 753 770 756 785 C2' C B 25 OK OK 787 783 801 786 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' G A 4 OK OK 105 126 108 109 141 C3' G A 5 OK OK 139 160 142 143 175 C3' U A 6 OK OK 173 191 176 177 205 C3' G A 7 OK OK 203 224 206 207 239 C3' G A 8 OK OK 237 258 240 241 273 C3' A A 9 OK OK 271 291 274 275 306 C3' A A 10 OK OK 304 324 307 308 339 C3' C A 11 OK OK 337 355 340 341 370 C3' C A 12 OK OK 368 386 371 372 401 C3' G A 13 OK OK 399 420 402 403 435 C3' C A 14 OK OK 433 451 436 437 466 C3' G A 15 OK OK 464 485 467 468 500 C3' C A 16 OK OK 498 516 501 502 530 C3' G B 17 OK OK 528 549 531 532 565 C3' C B 18 OK OK 563 581 566 567 596 C3' G B 19 OK OK 594 615 597 598 630 C3' U B 20 OK OK 628 646 631 632 660 C3' C B 21 OK OK 658 676 661 662 691 C3' C B 22 OK OK 689 707 692 693 722 C3' C B 23 OK OK 720 738 723 724 753 C3' U B 24 OK OK 751 769 754 755 783 C3' C B 25 OK OK 781 799 784 785 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' G A 4 OK OK 107 125 104 106 139 C4' G A 5 OK OK 141 159 138 140 173 C4' U A 6 OK OK 175 190 172 174 203 C4' G A 7 OK OK 205 223 202 204 237 C4' G A 8 OK OK 239 257 236 238 271 C4' A A 9 OK OK 273 290 270 272 304 C4' A A 10 OK OK 306 323 303 305 337 C4' C A 11 OK OK 339 354 336 338 368 C4' C A 12 OK OK 370 385 367 369 399 C4' G A 13 OK OK 401 419 398 400 433 C4' C A 14 OK OK 435 450 432 434 464 C4' G A 15 OK OK 466 484 463 465 498 C4' C A 16 OK OK 500 515 497 499 528 C4' G B 17 OK OK 530 548 527 529 563 C4' C B 18 OK OK 565 580 562 564 594 C4' G B 19 OK OK 596 614 593 595 628 C4' U B 20 OK OK 630 645 627 629 658 C4' C B 21 OK OK 660 675 657 659 689 C4' C B 22 OK OK 691 706 688 690 720 C4' C B 23 OK OK 722 737 719 721 751 C4' U B 24 OK OK 753 768 750 752 781 C4' C B 25 OK OK 783 798 780 782 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' G A 4 OK OK 103 123 124 105 138 C5' G A 5 OK OK 137 157 158 139 172 C5' U A 6 OK OK 171 188 189 173 202 C5' G A 7 OK OK 201 221 222 203 236 C5' G A 8 OK OK 235 255 256 237 270 C5' A A 9 OK OK 269 288 289 271 303 C5' A A 10 OK OK 302 321 322 304 336 C5' C A 11 OK OK 335 352 353 337 367 C5' C A 12 OK OK 366 383 384 368 398 C5' G A 13 OK OK 397 417 418 399 432 C5' C A 14 OK OK 431 448 449 433 463 C5' G A 15 OK OK 462 482 483 464 497 C5' C A 16 OK OK 496 513 514 498 527 C5' G B 17 OK OK 526 546 547 528 562 C5' C B 18 OK OK 561 578 579 563 593 C5' G B 19 OK OK 592 612 613 594 627 C5' U B 20 OK OK 626 643 644 628 657 C5' C B 21 OK OK 656 673 674 658 688 C5' C B 22 OK OK 687 704 705 689 719 C5' C B 23 OK OK 718 735 736 720 750 C5' U B 24 OK OK 749 766 767 751 780 C5' C B 25 OK OK 779 796 797 781 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P G A 4 distorted distorted 74 101 102 103 134 P G A 5 distorted distorted 108 135 136 137 168 P U A 6 distorted distorted 142 169 170 171 198 P G A 7 distorted distorted 176 199 200 201 232 P G A 8 distorted distorted 206 233 234 235 266 P A A 9 distorted distorted 240 267 268 269 299 P A A 10 distorted distorted 274 300 301 302 332 P C A 11 distorted distorted 307 333 334 335 363 P C A 12 distorted distorted 340 364 365 366 394 P G A 13 distorted distorted 371 395 396 397 428 P C A 14 distorted distorted 402 429 430 431 459 P G A 15 distorted distorted 436 460 461 462 493 P C A 16 distorted distorted 467 494 495 496 558 P C B 18 distorted distorted 531 559 560 561 589 P G B 19 distorted distorted 566 590 591 592 623 P U B 20 distorted distorted 597 624 625 626 653 P C B 21 distorted distorted 631 654 655 656 684 P C B 22 distorted distorted 661 685 686 687 715 P C B 23 distorted distorted 692 716 717 718 746 P U B 24 distorted distorted 723 747 748 749 776 P C B 25 distorted distorted 754 777 778 779 ---------------------------------------------------------------------------------