ID code: '2HEM' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 alpha beta 7 30 13 10 47 C1' G A 2 alpha beta 42 65 48 45 81 C1' G A 3 alpha beta 76 99 82 79 115 C1' A A 4 alpha beta 110 132 116 113 148 C1' A A 5 alpha beta 143 165 149 146 181 C1' G A 6 alpha beta 176 199 182 179 215 C1' G A 7 alpha beta 210 233 216 213 249 C1' C A 8 alpha beta 244 264 250 247 280 C1' G A 9 alpha beta 275 298 281 278 314 C1' C A 10 alpha beta 309 329 315 312 345 C1' U A 11 alpha beta 340 360 346 343 375 C1' U A 12 alpha beta 370 390 376 373 405 C1' C A 13 alpha beta 400 420 406 403 436 C1' G A 14 alpha beta 431 454 437 434 470 C1' G A 15 alpha beta 465 488 471 468 504 C1' C A 16 alpha beta 499 519 505 502 535 C1' G A 17 alpha beta 530 553 536 533 569 C1' U A 18 alpha beta 564 584 570 567 599 C1' C A 19 alpha beta 594 614 600 597 630 C1' G A 20 alpha beta 625 648 631 628 664 C1' G A 21 alpha beta 659 682 665 662 698 C1' C A 22 alpha beta 693 713 699 696 729 C1' C A 23 alpha beta 724 744 730 727 760 C1' C A 24 alpha beta 755 776 761 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 45 C2' G A 2 OK OK 47 43 63 46 79 C2' G A 3 OK OK 81 77 97 80 113 C2' A A 4 OK OK 115 111 130 114 146 C2' A A 5 OK OK 148 144 163 147 179 C2' G A 6 OK OK 181 177 197 180 213 C2' G A 7 OK OK 215 211 231 214 247 C2' C A 8 OK OK 249 245 262 248 278 C2' G A 9 OK OK 280 276 296 279 312 C2' C A 10 OK OK 314 310 327 313 343 C2' U A 11 OK OK 345 341 358 344 373 C2' U A 12 OK OK 375 371 388 374 403 C2' C A 13 OK OK 405 401 418 404 434 C2' G A 14 OK OK 436 432 452 435 468 C2' G A 15 OK OK 470 466 486 469 502 C2' C A 16 OK OK 504 500 517 503 533 C2' G A 17 OK OK 535 531 551 534 567 C2' U A 18 OK OK 569 565 582 568 597 C2' C A 19 OK OK 599 595 612 598 628 C2' G A 20 OK OK 630 626 646 629 662 C2' G A 21 OK OK 664 660 680 663 696 C2' C A 22 OK OK 698 694 711 697 727 C2' C A 23 OK OK 729 725 742 728 758 C2' C A 24 OK OK 760 756 774 759 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 43 C3' G A 2 OK OK 41 62 44 45 77 C3' G A 3 OK OK 75 96 78 79 111 C3' A A 4 OK OK 109 129 112 113 144 C3' A A 5 OK OK 142 162 145 146 177 C3' G A 6 OK OK 175 196 178 179 211 C3' G A 7 OK OK 209 230 212 213 245 C3' C A 8 OK OK 243 261 246 247 276 C3' G A 9 OK OK 274 295 277 278 310 C3' C A 10 OK OK 308 326 311 312 341 C3' U A 11 OK OK 339 357 342 343 371 C3' U A 12 OK OK 369 387 372 373 401 C3' C A 13 OK OK 399 417 402 403 432 C3' G A 14 OK OK 430 451 433 434 466 C3' G A 15 OK OK 464 485 467 468 500 C3' C A 16 OK OK 498 516 501 502 531 C3' G A 17 OK OK 529 550 532 533 565 C3' U A 18 OK OK 563 581 566 567 595 C3' C A 19 OK OK 593 611 596 597 626 C3' G A 20 OK OK 624 645 627 628 660 C3' G A 21 OK OK 658 679 661 662 694 C3' C A 22 OK OK 692 710 695 696 725 C3' C A 23 OK OK 723 741 726 727 756 C3' C A 24 OK OK 754 772 757 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 41 C4' G A 2 OK OK 43 61 40 42 75 C4' G A 3 OK OK 77 95 74 76 109 C4' A A 4 OK OK 111 128 108 110 142 C4' A A 5 OK OK 144 161 141 143 175 C4' G A 6 OK OK 177 195 174 176 209 C4' G A 7 OK OK 211 229 208 210 243 C4' C A 8 OK OK 245 260 242 244 274 C4' G A 9 OK OK 276 294 273 275 308 C4' C A 10 OK OK 310 325 307 309 339 C4' U A 11 OK OK 341 356 338 340 369 C4' U A 12 OK OK 371 386 368 370 399 C4' C A 13 OK OK 401 416 398 400 430 C4' G A 14 OK OK 432 450 429 431 464 C4' G A 15 OK OK 466 484 463 465 498 C4' C A 16 OK OK 500 515 497 499 529 C4' G A 17 OK OK 531 549 528 530 563 C4' U A 18 OK OK 565 580 562 564 593 C4' C A 19 OK OK 595 610 592 594 624 C4' G A 20 OK OK 626 644 623 625 658 C4' G A 21 OK OK 660 678 657 659 692 C4' C A 22 OK OK 694 709 691 693 723 C4' C A 23 OK OK 725 740 722 724 754 C4' C A 24 OK OK 756 771 753 755 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 40 C5' G A 2 OK OK 39 59 60 41 74 C5' G A 3 OK OK 73 93 94 75 108 C5' A A 4 OK OK 107 126 127 109 141 C5' A A 5 OK OK 140 159 160 142 174 C5' G A 6 OK OK 173 193 194 175 208 C5' G A 7 OK OK 207 227 228 209 242 C5' C A 8 OK OK 241 258 259 243 273 C5' G A 9 OK OK 272 292 293 274 307 C5' C A 10 OK OK 306 323 324 308 338 C5' U A 11 OK OK 337 354 355 339 368 C5' U A 12 OK OK 367 384 385 369 398 C5' C A 13 OK OK 397 414 415 399 429 C5' G A 14 OK OK 428 448 449 430 463 C5' G A 15 OK OK 462 482 483 464 497 C5' C A 16 OK OK 496 513 514 498 528 C5' G A 17 OK OK 527 547 548 529 562 C5' U A 18 OK OK 561 578 579 563 592 C5' C A 19 OK OK 591 608 609 593 623 C5' G A 20 OK OK 622 642 643 624 657 C5' G A 21 OK OK 656 676 677 658 691 C5' C A 22 OK OK 690 707 708 692 722 C5' C A 23 OK OK 721 738 739 723 753 C5' C A 24 OK OK 752 769 770 754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 36 P G A 2 distorted distorted 9 37 38 39 70 P G A 3 distorted distorted 44 71 72 73 104 P A A 4 distorted distorted 78 105 106 107 137 P A A 5 distorted distorted 112 138 139 140 170 P G A 6 distorted distorted 145 171 172 173 204 P G A 7 distorted distorted 178 205 206 207 238 P C A 8 distorted distorted 212 239 240 241 269 P G A 9 distorted distorted 246 270 271 272 303 P C A 10 distorted distorted 277 304 305 306 334 P U A 11 distorted distorted 311 335 336 337 364 P U A 12 distorted distorted 342 365 366 367 394 P C A 13 distorted distorted 372 395 396 397 425 P G A 14 distorted distorted 402 426 427 428 459 P G A 15 distorted distorted 433 460 461 462 493 P C A 16 distorted distorted 467 494 495 496 524 P G A 17 distorted distorted 501 525 526 527 558 P U A 18 distorted distorted 532 559 560 561 588 P C A 19 distorted distorted 566 589 590 591 619 P G A 20 distorted distorted 596 620 621 622 653 P G A 21 distorted distorted 627 654 655 656 687 P C A 22 distorted distorted 661 688 689 690 718 P C A 23 distorted distorted 695 719 720 721 749 P C A 24 distorted distorted 726 750 751 752 ---------------------------------------------------------------------------------