ID code: '2L7D' 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 71 103 C1' G A 4 alpha beta 98 121 104 101 136 C1' DA A 5 alpha beta 132 153 137 135 168 C1' DA A 6 alpha beta 164 185 169 167 200 C1' DT A 7 alpha beta 196 216 201 199 232 C1' DT A 8 alpha beta 228 248 233 231 264 C1' DC A 9 alpha beta 260 279 265 263 294 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 449 468 454 452 484 C1' G B 16 alpha beta 479 502 485 482 517 C1' DA B 17 alpha beta 513 534 518 516 549 C1' DA B 18 alpha beta 545 566 550 548 581 C1' DT B 19 alpha beta 577 597 582 580 613 C1' DT B 20 alpha beta 609 629 614 612 645 C1' DC B 21 alpha beta 641 660 646 644 675 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' G A 4 OK OK 103 99 119 102 135 C2' DA A 5 OK OK 136 133 151 152 167 C2' DA A 6 OK OK 168 165 183 184 199 C2' DT A 7 OK OK 200 197 214 215 231 C2' DT A 8 OK OK 232 229 246 247 263 C2' DC A 9 OK OK 264 261 277 278 293 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' G B 16 OK OK 484 480 500 483 516 C2' DA B 17 OK OK 517 514 532 533 548 C2' DA B 18 OK OK 549 546 564 565 580 C2' DT B 19 OK OK 581 578 595 596 612 C2' DT B 20 OK OK 613 610 627 628 644 C2' DC B 21 OK OK 645 642 658 659 674 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' G A 4 OK OK 97 118 100 101 133 C3' DA A 5 OK OK 131 150 134 135 165 C3' DA A 6 OK OK 163 182 166 167 197 C3' DT A 7 OK OK 195 213 198 199 229 C3' DT A 8 OK OK 227 245 230 231 261 C3' DC A 9 OK OK 259 276 262 263 291 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' G B 16 OK OK 478 499 481 482 514 C3' DA B 17 OK OK 512 531 515 516 546 C3' DA B 18 OK OK 544 563 547 548 578 C3' DT B 19 OK OK 576 594 579 580 610 C3' DT B 20 OK OK 608 626 611 612 642 C3' DC B 21 OK OK 640 657 643 644 672 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' G A 4 OK OK 99 117 96 98 131 C4' DA A 5 OK OK 133 149 130 132 163 C4' DA A 6 OK OK 165 181 162 164 195 C4' DT A 7 OK OK 197 212 194 196 227 C4' DT A 8 OK OK 229 244 226 228 259 C4' DC A 9 OK OK 261 275 258 260 289 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' G B 16 OK OK 480 498 477 479 512 C4' DA B 17 OK OK 514 530 511 513 544 C4' DA B 18 OK OK 546 562 543 545 576 C4' DT B 19 OK OK 578 593 575 577 608 C4' DT B 20 OK OK 610 625 607 609 640 C4' DC B 21 OK OK 642 656 639 641 670 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' G A 4 OK OK 95 115 116 97 130 C5' DA A 5 OK OK 129 147 148 131 162 C5' DA A 6 OK OK 161 179 180 163 194 C5' DT A 7 OK OK 193 210 211 195 226 C5' DT A 8 OK OK 225 242 243 227 258 C5' DC A 9 OK OK 257 273 274 259 288 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' G B 16 OK OK 476 496 497 478 511 C5' DA B 17 OK OK 510 528 529 512 543 C5' DA B 18 OK OK 542 560 561 544 575 C5' DT B 19 OK OK 574 591 592 576 607 C5' DT B 20 OK OK 606 623 624 608 639 C5' DC B 21 OK OK 638 654 655 640 669 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 G A 4 distorted distorted 70 93 94 95 126 P DA A 5 distorted distorted 100 127 128 129 158 P DA A 6 distorted distorted 134 159 160 161 190 P DT A 7 distorted distorted 166 191 192 193 222 P DT A 8 distorted distorted 198 223 224 225 254 P DC A 9 distorted distorted 230 255 256 257 284 P DG A 10 distorted distorted 262 285 286 287 317 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 G B 16 distorted distorted 451 474 475 476 507 P DA B 17 distorted distorted 481 508 509 510 539 P DA B 18 distorted distorted 515 540 541 542 571 P DT B 19 distorted distorted 547 572 573 574 603 P DT B 20 distorted distorted 579 604 605 606 635 P DC B 21 distorted distorted 611 636 637 638 665 P DG B 22 distorted distorted 643 666 667 668 698 P DC B 23 distorted distorted 673 699 700 701 728 P DG B 24 distorted distorted 706 729 730 731 ---------------------------------------------------------------------------------