ID code: '1RAU' 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' U A 1 alpha beta 4 24 10 7 40 C1' G A 2 alpha beta 35 58 41 38 74 C1' G A 3 alpha beta 69 92 75 72 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' U A 6 alpha beta 171 192 177 174 205 C1' U B 1 alpha beta 200 220 206 203 236 C1' G B 2 alpha beta 231 254 237 234 270 C1' G B 3 alpha beta 265 288 271 268 304 C1' G B 4 alpha beta 299 322 305 302 338 C1' G B 5 alpha beta 333 356 339 336 372 C1' U B 6 alpha beta 367 388 373 370 401 C1' U C 1 alpha beta 396 416 402 399 432 C1' G C 2 alpha beta 427 450 433 430 466 C1' G C 3 alpha beta 461 484 467 464 500 C1' G C 4 alpha beta 495 518 501 498 534 C1' G C 5 alpha beta 529 552 535 532 568 C1' U C 6 alpha beta 563 584 569 566 597 C1' U D 1 alpha beta 592 612 598 595 628 C1' G D 2 alpha beta 623 646 629 626 662 C1' G D 3 alpha beta 657 680 663 660 696 C1' G D 4 alpha beta 691 714 697 694 730 C1' G D 5 alpha beta 725 748 731 728 764 C1' U D 6 alpha beta 759 780 765 762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK OK 9 5 22 8 38 C2' G A 2 OK OK 40 36 56 39 72 C2' G A 3 OK OK 74 70 90 73 106 C2' G A 4 OK OK 108 104 124 107 140 C2' G A 5 OK OK 142 138 158 141 174 C2' U A 6 OK OK 176 172 190 175 203 C2' U B 1 OK OK 205 201 218 204 234 C2' G B 2 OK OK 236 232 252 235 268 C2' G B 3 OK OK 270 266 286 269 302 C2' G B 4 OK OK 304 300 320 303 336 C2' G B 5 OK OK 338 334 354 337 370 C2' U B 6 OK OK 372 368 386 371 399 C2' U C 1 OK OK 401 397 414 400 430 C2' G C 2 OK OK 432 428 448 431 464 C2' G C 3 OK OK 466 462 482 465 498 C2' G C 4 OK OK 500 496 516 499 532 C2' G C 5 OK OK 534 530 550 533 566 C2' U C 6 OK OK 568 564 582 567 595 C2' U D 1 OK OK 597 593 610 596 626 C2' G D 2 OK OK 628 624 644 627 660 C2' G D 3 OK OK 662 658 678 661 694 C2' G D 4 OK OK 696 692 712 695 728 C2' G D 5 OK OK 730 726 746 729 762 C2' U D 6 OK OK 764 760 778 763 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK OK 3 21 6 7 36 C3' G A 2 OK OK 34 55 37 38 70 C3' G A 3 OK OK 68 89 71 72 104 C3' G A 4 OK OK 102 123 105 106 138 C3' G A 5 OK OK 136 157 139 140 172 C3' U A 6 OK OK 170 188 173 174 201 C3' U B 1 OK OK 199 217 202 203 232 C3' G B 2 OK OK 230 251 233 234 266 C3' G B 3 OK OK 264 285 267 268 300 C3' G B 4 OK OK 298 319 301 302 334 C3' G B 5 OK OK 332 353 335 336 368 C3' U B 6 OK OK 366 384 369 370 397 C3' U C 1 OK OK 395 413 398 399 428 C3' G C 2 OK OK 426 447 429 430 462 C3' G C 3 OK OK 460 481 463 464 496 C3' G C 4 OK OK 494 515 497 498 530 C3' G C 5 OK OK 528 549 531 532 564 C3' U C 6 OK OK 562 580 565 566 593 C3' U D 1 OK OK 591 609 594 595 624 C3' G D 2 OK OK 622 643 625 626 658 C3' G D 3 OK OK 656 677 659 660 692 C3' G D 4 OK OK 690 711 693 694 726 C3' G D 5 OK OK 724 745 727 728 760 C3' U D 6 OK OK 758 776 761 762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK OK 5 20 2 4 34 C4' G A 2 OK OK 36 54 33 35 68 C4' G A 3 OK OK 70 88 67 69 102 C4' G A 4 OK OK 104 122 101 103 136 C4' G A 5 OK OK 138 156 135 137 170 C4' U A 6 OK OK 172 187 169 171 199 C4' U B 1 OK OK 201 216 198 200 230 C4' G B 2 OK OK 232 250 229 231 264 C4' G B 3 OK OK 266 284 263 265 298 C4' G B 4 OK OK 300 318 297 299 332 C4' G B 5 OK OK 334 352 331 333 366 C4' U B 6 OK OK 368 383 365 367 395 C4' U C 1 OK OK 397 412 394 396 426 C4' G C 2 OK OK 428 446 425 427 460 C4' G C 3 OK OK 462 480 459 461 494 C4' G C 4 OK OK 496 514 493 495 528 C4' G C 5 OK OK 530 548 527 529 562 C4' U C 6 OK OK 564 579 561 563 591 C4' U D 1 OK OK 593 608 590 592 622 C4' G D 2 OK OK 624 642 621 623 656 C4' G D 3 OK OK 658 676 655 657 690 C4' G D 4 OK OK 692 710 689 691 724 C4' G D 5 OK OK 726 744 723 725 758 C4' U D 6 OK OK 760 775 757 759 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 OK OK 1 18 19 3 33 C5' G A 2 OK OK 32 52 53 34 67 C5' G A 3 OK OK 66 86 87 68 101 C5' G A 4 OK OK 100 120 121 102 135 C5' G A 5 OK OK 134 154 155 136 169 C5' U A 6 OK OK 168 185 186 170 198 C5' U B 1 OK OK 197 214 215 199 229 C5' G B 2 OK OK 228 248 249 230 263 C5' G B 3 OK OK 262 282 283 264 297 C5' G B 4 OK OK 296 316 317 298 331 C5' G B 5 OK OK 330 350 351 332 365 C5' U B 6 OK OK 364 381 382 366 394 C5' U C 1 OK OK 393 410 411 395 425 C5' G C 2 OK OK 424 444 445 426 459 C5' G C 3 OK OK 458 478 479 460 493 C5' G C 4 OK OK 492 512 513 494 527 C5' G C 5 OK OK 526 546 547 528 561 C5' U C 6 OK OK 560 577 578 562 590 C5' U D 1 OK OK 589 606 607 591 621 C5' G D 2 OK OK 620 640 641 622 655 C5' G D 3 OK OK 654 674 675 656 689 C5' G D 4 OK OK 688 708 709 690 723 C5' G D 5 OK OK 722 742 743 724 757 C5' U D 6 OK OK 756 773 774 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P G A 2 distorted distorted 6 30 31 32 63 P G A 3 distorted distorted 37 64 65 66 97 P G A 4 distorted distorted 71 98 99 100 131 P G A 5 distorted distorted 105 132 133 134 165 P U A 6 distorted distorted 139 166 167 168 225 P G B 2 distorted distorted 202 226 227 228 259 P G B 3 distorted distorted 233 260 261 262 293 P G B 4 distorted distorted 267 294 295 296 327 P G B 5 distorted distorted 301 328 329 330 361 P U B 6 distorted distorted 335 362 363 364 421 P G C 2 distorted distorted 398 422 423 424 455 P G C 3 distorted distorted 429 456 457 458 489 P G C 4 distorted distorted 463 490 491 492 523 P G C 5 distorted distorted 497 524 525 526 557 P U C 6 distorted distorted 531 558 559 560 617 P G D 2 distorted distorted 594 618 619 620 651 P G D 3 distorted distorted 625 652 653 654 685 P G D 4 distorted distorted 659 686 687 688 719 P G D 5 distorted distorted 693 720 721 722 753 P U D 6 distorted distorted 727 754 755 756 ---------------------------------------------------------------------------------