ID code: '170D' 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' --------------------------------------------------------------------------------- 8 C1' DC A 1 alpha beta 4 23 9 7 39 C1' DG A 2 alpha beta 35 57 40 38 72 C1' DC A 3 alpha beta 68 87 73 71 102 C1' DG A 4 alpha beta 98 120 103 101 135 C1' DA A 5 alpha beta 131 152 136 134 167 C1' DA A 6 alpha beta 163 184 168 166 199 C1' DT A 7 alpha beta 195 215 200 198 231 C1' DT A 8 alpha beta 227 247 232 230 264 C1' CAR A 9 alpha beta 259 279 265 262 294 C1' DG A 10 alpha beta 290 312 295 293 327 C1' DC A 11 alpha beta 323 342 328 326 357 C1' DG A 12 alpha beta 353 376 358 356 389 C1' DC B 13 alpha beta 385 404 390 388 420 C1' DG B 14 alpha beta 416 438 421 419 453 C1' DC B 15 alpha beta 449 468 454 452 483 C1' DG B 16 alpha beta 479 501 484 482 516 C1' DA B 17 alpha beta 512 533 517 515 548 C1' DA B 18 alpha beta 544 565 549 547 580 C1' DT B 19 alpha beta 576 596 581 579 612 C1' DT B 20 alpha beta 608 628 613 611 645 C1' CAR B 21 alpha beta 640 660 646 643 675 C1' DG B 22 alpha beta 671 693 676 674 708 C1' DC B 23 alpha beta 704 723 709 707 738 C1' DG B 24 alpha beta 734 757 739 737 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC A 1 OK OK 8 5 21 22 38 C2' DG A 2 OK OK 39 36 55 56 71 C2' DC A 3 OK OK 72 69 85 86 101 C2' DG A 4 OK OK 102 99 118 119 134 C2' DA A 5 OK OK 135 132 150 151 166 C2' DA A 6 OK OK 167 164 182 183 198 C2' DT A 7 OK OK 199 196 213 214 230 C2' DT A 8 OK OK 231 228 245 246 262 C2' CAR A 9 distorted distorted 264 260 277 263 293 C2' DG A 10 OK OK 294 291 310 311 326 C2' DC A 11 OK OK 327 324 340 341 356 C2' DG A 12 OK OK 357 354 374 375 388 C2' DC B 13 OK OK 389 386 402 403 419 C2' DG B 14 OK OK 420 417 436 437 452 C2' DC B 15 OK OK 453 450 466 467 482 C2' DG B 16 OK OK 483 480 499 500 515 C2' DA B 17 OK OK 516 513 531 532 547 C2' DA B 18 OK OK 548 545 563 564 579 C2' DT B 19 OK OK 580 577 594 595 611 C2' DT B 20 OK OK 612 609 626 627 643 C2' CAR B 21 distorted distorted 645 641 658 644 674 C2' DG B 22 OK OK 675 672 691 692 707 C2' DC B 23 OK OK 708 705 721 722 737 C2' DG B 24 OK OK 738 735 755 756 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC A 1 OK OK 3 20 6 7 36 C3' DG A 2 OK OK 34 54 37 38 69 C3' DC A 3 OK OK 67 84 70 71 99 C3' DG A 4 OK OK 97 117 100 101 132 C3' DA A 5 OK OK 130 149 133 134 164 C3' DA A 6 OK OK 162 181 165 166 196 C3' DT A 7 OK OK 194 212 197 198 228 C3' DT A 8 OK OK 226 244 229 230 260 C3' CAR A 9 OK OK 258 276 261 262 291 C3' DG A 10 OK OK 289 309 292 293 324 C3' DC A 11 OK OK 322 339 325 326 354 C3' DG A 12 OK OK 352 372 355 356 386 C3' DC B 13 OK OK 384 401 387 388 417 C3' DG B 14 OK OK 415 435 418 419 450 C3' DC B 15 OK OK 448 465 451 452 480 C3' DG B 16 OK OK 478 498 481 482 513 C3' DA B 17 OK OK 511 530 514 515 545 C3' DA B 18 OK OK 543 562 546 547 577 C3' DT B 19 OK OK 575 593 578 579 609 C3' DT B 20 OK OK 607 625 610 611 641 C3' CAR B 21 OK OK 639 657 642 643 672 C3' DG B 22 OK OK 670 690 673 674 705 C3' DC B 23 OK OK 703 720 706 707 735 C3' DG B 24 OK OK 733 753 736 737 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC A 1 OK OK 5 19 2 4 34 C4' DG A 2 OK OK 36 53 33 35 67 C4' DC A 3 OK OK 69 83 66 68 97 C4' DG A 4 OK OK 99 116 96 98 130 C4' DA A 5 OK OK 132 148 129 131 162 C4' DA A 6 OK OK 164 180 161 163 194 C4' DT A 7 OK OK 196 211 193 195 226 C4' DT A 8 OK OK 228 243 225 227 258 C4' CAR A 9 OK OK 260 275 257 259 289 C4' DG A 10 OK OK 291 308 288 290 322 C4' DC A 11 OK OK 324 338 321 323 352 C4' DG A 12 OK OK 354 371 351 353 384 C4' DC B 13 OK OK 386 400 383 385 415 C4' DG B 14 OK OK 417 434 414 416 448 C4' DC B 15 OK OK 450 464 447 449 478 C4' DG B 16 OK OK 480 497 477 479 511 C4' DA B 17 OK OK 513 529 510 512 543 C4' DA B 18 OK OK 545 561 542 544 575 C4' DT B 19 OK OK 577 592 574 576 607 C4' DT B 20 OK OK 609 624 606 608 639 C4' CAR B 21 OK OK 641 656 638 640 670 C4' DG B 22 OK OK 672 689 669 671 703 C4' DC B 23 OK OK 705 719 702 704 733 C4' DG B 24 OK OK 735 752 732 734 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC A 1 OK OK 1 17 18 3 33 C5' DG A 2 OK OK 32 51 52 34 66 C5' DC A 3 OK OK 65 81 82 67 96 C5' DG A 4 OK OK 95 114 115 97 129 C5' DA A 5 OK OK 128 146 147 130 161 C5' DA A 6 OK OK 160 178 179 162 193 C5' DT A 7 OK OK 192 209 210 194 225 C5' DT A 8 OK OK 224 241 242 226 257 C5' CAR A 9 OK OK 256 273 274 258 288 C5' DG A 10 OK OK 287 306 307 289 321 C5' DC A 11 OK OK 320 336 337 322 351 C5' DG A 12 OK OK 350 369 370 352 383 C5' DC B 13 OK OK 382 398 399 384 414 C5' DG B 14 OK OK 413 432 433 415 447 C5' DC B 15 OK OK 446 462 463 448 477 C5' DG B 16 OK OK 476 495 496 478 510 C5' DA B 17 OK OK 509 527 528 511 542 C5' DA B 18 OK OK 541 559 560 543 574 C5' DT B 19 OK OK 573 590 591 575 606 C5' DT B 20 OK OK 605 622 623 607 638 C5' CAR B 21 OK OK 637 654 655 639 669 C5' DG B 22 OK OK 668 687 688 670 702 C5' DC B 23 OK OK 701 717 718 703 732 C5' DG B 24 OK OK 731 750 751 733 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P DG A 2 distorted distorted 6 30 31 32 62 P DC A 3 distorted distorted 37 63 64 65 92 P DG A 4 distorted distorted 70 93 94 95 125 P DA A 5 distorted distorted 100 126 127 128 157 P DA A 6 distorted distorted 133 158 159 160 189 P DT A 7 distorted distorted 165 190 191 192 221 P DT A 8 distorted distorted 197 222 223 224 253 P CAR A 9 distorted distorted 229 254 255 256 284 P DG A 10 distorted distorted 261 285 286 287 317 P DC A 11 distorted distorted 292 318 319 320 347 P DG A 12 distorted distorted 325 348 349 350 410 P DG B 14 distorted distorted 387 411 412 413 443 P DC B 15 distorted distorted 418 444 445 446 473 P DG B 16 distorted distorted 451 474 475 476 506 P DA B 17 distorted distorted 481 507 508 509 538 P DA B 18 distorted distorted 514 539 540 541 570 P DT B 19 distorted distorted 546 571 572 573 602 P DT B 20 distorted distorted 578 603 604 605 634 P CAR B 21 distorted distorted 610 635 636 637 665 P DG B 22 distorted distorted 642 666 667 668 698 P DC B 23 distorted distorted 673 699 700 701 728 P DG B 24 distorted distorted 706 729 730 731 ---------------------------------------------------------------------------------