ID code: '4GHL' 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' A E 1 beta 4 10 7 31 C1' G E 2 beta 26 32 29 54 C1' A E 3 beta 49 55 52 76 C1' C E 4 beta 71 77 74 96 C1' A E 5 beta 91 97 94 118 C1' G E 6 beta 113 119 116 141 C1' C E 7 beta 136 142 139 161 C1' A E 8 beta 156 162 159 183 C1' U E 9 beta 178 184 181 203 C1' A E 10 beta 198 204 201 225 C1' U E 11 beta 220 226 223 245 C1' G E 12 beta 240 246 243 268 C1' C E 13 beta 263 269 266 288 C1' U E 14 beta 283 289 286 308 C1' G E 15 beta 303 309 306 331 C1' U E 16 beta 326 332 329 351 C1' C E 17 beta 346 352 349 371 C1' U E 18 beta 366 372 369 389 C1' A F 1 beta 384 390 387 411 C1' G F 2 beta 406 412 409 434 C1' A F 3 beta 429 435 432 456 C1' C F 4 beta 451 457 454 476 C1' A F 5 beta 471 477 474 498 C1' G F 6 beta 493 499 496 521 C1' C F 7 beta 516 522 519 541 C1' A F 8 beta 536 542 539 563 C1' U F 9 beta 558 564 561 583 C1' A F 10 beta 578 584 581 605 C1' U F 11 beta 600 606 603 625 C1' G F 12 beta 620 626 623 648 C1' C F 13 beta 643 649 646 668 C1' U F 14 beta 663 669 666 688 C1' G F 15 beta 683 689 686 711 C1' U F 16 beta 706 712 709 731 C1' C F 17 beta 726 732 729 751 C1' U F 18 beta 746 752 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A E 1 OK 9 5 8 29 C2' G E 2 OK 31 27 30 52 C2' A E 3 OK 54 50 53 74 C2' C E 4 OK 76 72 75 94 C2' A E 5 OK 96 92 95 116 C2' G E 6 OK 118 114 117 139 C2' C E 7 OK 141 137 140 159 C2' A E 8 OK 161 157 160 181 C2' U E 9 OK 183 179 182 201 C2' A E 10 OK 203 199 202 223 C2' U E 11 OK 225 221 224 243 C2' G E 12 OK 245 241 244 266 C2' C E 13 OK 268 264 267 286 C2' U E 14 OK 288 284 287 306 C2' G E 15 OK 308 304 307 329 C2' U E 16 OK 331 327 330 349 C2' C E 17 OK 351 347 350 369 C2' U E 18 OK 371 367 370 387 C2' A F 1 OK 389 385 388 409 C2' G F 2 OK 411 407 410 432 C2' A F 3 OK 434 430 433 454 C2' C F 4 OK 456 452 455 474 C2' A F 5 OK 476 472 475 496 C2' G F 6 OK 498 494 497 519 C2' C F 7 OK 521 517 520 539 C2' A F 8 OK 541 537 540 561 C2' U F 9 OK 563 559 562 581 C2' A F 10 OK 583 579 582 603 C2' U F 11 OK 605 601 604 623 C2' G F 12 OK 625 621 624 646 C2' C F 13 OK 648 644 647 666 C2' U F 14 OK 668 664 667 686 C2' G F 15 OK 688 684 687 709 C2' U F 16 OK 711 707 710 729 C2' C F 17 OK 731 727 730 749 C2' U F 18 OK 751 747 750 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A E 1 OK 3 6 7 27 C3' G E 2 OK 25 28 29 50 C3' A E 3 OK 48 51 52 72 C3' C E 4 OK 70 73 74 92 C3' A E 5 OK 90 93 94 114 C3' G E 6 OK 112 115 116 137 C3' C E 7 OK 135 138 139 157 C3' A E 8 OK 155 158 159 179 C3' U E 9 OK 177 180 181 199 C3' A E 10 OK 197 200 201 221 C3' U E 11 OK 219 222 223 241 C3' G E 12 OK 239 242 243 264 C3' C E 13 OK 262 265 266 284 C3' U E 14 OK 282 285 286 304 C3' G E 15 OK 302 305 306 327 C3' U E 16 OK 325 328 329 347 C3' C E 17 OK 345 348 349 367 C3' U E 18 OK 365 368 369 385 C3' A F 1 OK 383 386 387 407 C3' G F 2 OK 405 408 409 430 C3' A F 3 OK 428 431 432 452 C3' C F 4 OK 450 453 454 472 C3' A F 5 OK 470 473 474 494 C3' G F 6 OK 492 495 496 517 C3' C F 7 OK 515 518 519 537 C3' A F 8 OK 535 538 539 559 C3' U F 9 OK 557 560 561 579 C3' A F 10 OK 577 580 581 601 C3' U F 11 OK 599 602 603 621 C3' G F 12 OK 619 622 623 644 C3' C F 13 OK 642 645 646 664 C3' U F 14 OK 662 665 666 684 C3' G F 15 OK 682 685 686 707 C3' U F 16 OK 705 708 709 727 C3' C F 17 OK 725 728 729 747 C3' U F 18 OK 745 748 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A E 1 OK 5 2 4 25 C4' G E 2 OK 27 24 26 48 C4' A E 3 OK 50 47 49 70 C4' C E 4 OK 72 69 71 90 C4' A E 5 OK 92 89 91 112 C4' G E 6 OK 114 111 113 135 C4' C E 7 OK 137 134 136 155 C4' A E 8 OK 157 154 156 177 C4' U E 9 OK 179 176 178 197 C4' A E 10 OK 199 196 198 219 C4' U E 11 OK 221 218 220 239 C4' G E 12 OK 241 238 240 262 C4' C E 13 OK 264 261 263 282 C4' U E 14 OK 284 281 283 302 C4' G E 15 OK 304 301 303 325 C4' U E 16 OK 327 324 326 345 C4' C E 17 OK 347 344 346 365 C4' U E 18 OK 367 364 366 383 C4' A F 1 OK 385 382 384 405 C4' G F 2 OK 407 404 406 428 C4' A F 3 OK 430 427 429 450 C4' C F 4 OK 452 449 451 470 C4' A F 5 OK 472 469 471 492 C4' G F 6 OK 494 491 493 515 C4' C F 7 OK 517 514 516 535 C4' A F 8 OK 537 534 536 557 C4' U F 9 OK 559 556 558 577 C4' A F 10 OK 579 576 578 599 C4' U F 11 OK 601 598 600 619 C4' G F 12 OK 621 618 620 642 C4' C F 13 OK 644 641 643 662 C4' U F 14 OK 664 661 663 682 C4' G F 15 OK 684 681 683 705 C4' U F 16 OK 707 704 706 725 C4' C F 17 OK 727 724 726 745 C4' U F 18 OK 747 744 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A E 1 1 3 24 C5' G E 2 23 25 47 C5' A E 3 46 48 69 C5' C E 4 68 70 89 C5' A E 5 88 90 111 C5' G E 6 110 112 134 C5' C E 7 133 135 154 C5' A E 8 153 155 176 C5' U E 9 175 177 196 C5' A E 10 195 197 218 C5' U E 11 217 219 238 C5' G E 12 237 239 261 C5' C E 13 260 262 281 C5' U E 14 280 282 301 C5' G E 15 300 302 324 C5' U E 16 323 325 344 C5' C E 17 343 345 364 C5' U E 18 363 365 382 C5' A F 1 381 383 404 C5' G F 2 403 405 427 C5' A F 3 426 428 449 C5' C F 4 448 450 469 C5' A F 5 468 470 491 C5' G F 6 490 492 514 C5' C F 7 513 515 534 C5' A F 8 533 535 556 C5' U F 9 555 557 576 C5' A F 10 575 577 598 C5' U F 11 597 599 618 C5' G F 12 617 619 641 C5' C F 13 640 642 661 C5' U F 14 660 662 681 C5' G F 15 680 682 704 C5' U F 16 703 705 724 C5' C F 17 723 725 744 C5' U F 18 743 745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G E 2 distorted distorted 6 21 22 23 43 P A E 3 distorted distorted 28 44 45 46 65 P C E 4 distorted distorted 51 66 67 68 85 P A E 5 distorted distorted 73 86 87 88 107 P G E 6 distorted distorted 93 108 109 110 130 P C E 7 distorted distorted 115 131 132 133 150 P A E 8 distorted distorted 138 151 152 153 172 P U E 9 distorted distorted 158 173 174 175 192 P A E 10 distorted distorted 180 193 194 195 214 P U E 11 distorted distorted 200 215 216 217 234 P G E 12 distorted distorted 222 235 236 237 257 P C E 13 distorted distorted 242 258 259 260 277 P U E 14 distorted distorted 265 278 279 280 297 P G E 15 distorted distorted 285 298 299 300 320 P U E 16 distorted distorted 305 321 322 323 340 P C E 17 distorted distorted 328 341 342 343 360 P U E 18 distorted distorted 348 361 362 363 400 P G F 2 distorted distorted 386 401 402 403 423 P A F 3 distorted distorted 408 424 425 426 445 P C F 4 distorted distorted 431 446 447 448 465 P A F 5 distorted distorted 453 466 467 468 487 P G F 6 distorted distorted 473 488 489 490 510 P C F 7 distorted distorted 495 511 512 513 530 P A F 8 distorted distorted 518 531 532 533 552 P U F 9 distorted distorted 538 553 554 555 572 P A F 10 distorted distorted 560 573 574 575 594 P U F 11 distorted distorted 580 595 596 597 614 P G F 12 distorted distorted 602 615 616 617 637 P C F 13 distorted distorted 622 638 639 640 657 P U F 14 distorted distorted 645 658 659 660 677 P G F 15 distorted distorted 665 678 679 680 700 P U F 16 distorted distorted 685 701 702 703 720 P C F 17 distorted distorted 708 721 722 723 740 P U F 18 distorted distorted 728 741 742 743 ---------------------------------------------------------------------------------