ID code: '1JFI' 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' --------------------------------------------------------------------------------- 11 C1' T D 602 beta 7 12 10 31 C1' G D 603 beta 27 32 30 53 C1' G D 604 beta 49 54 52 75 C1' C D 605 beta 71 76 74 94 C1' T D 606 beta 90 95 93 114 C1' A D 607 beta 110 115 113 135 C1' T D 608 beta 131 136 134 155 C1' A D 609 beta 151 156 154 176 C1' A D 610 beta 172 177 175 197 C1' A D 611 beta 193 198 196 218 C1' A D 612 beta 214 219 217 239 C1' G D 613 beta 235 240 238 261 C1' G D 614 beta 257 262 260 283 C1' G D 615 beta 279 284 282 305 C1' C D 616 beta 301 306 304 324 C1' T D 617 beta 320 325 323 344 C1' C D 618 beta 340 345 343 361 C1' G E 702 beta 357 362 360 383 C1' A E 703 beta 379 384 382 404 C1' G E 704 beta 400 405 403 426 C1' C E 705 beta 422 427 425 445 C1' C E 706 beta 441 446 444 464 C1' C E 707 beta 460 465 463 483 C1' T E 708 beta 479 484 482 503 C1' T E 709 beta 499 504 502 523 C1' T E 710 beta 519 524 522 543 C1' T E 711 beta 539 544 542 563 C1' A E 712 beta 559 564 562 584 C1' T E 713 beta 580 585 583 604 C1' A E 714 beta 600 605 603 625 C1' G E 715 beta 621 626 624 647 C1' C E 716 beta 643 648 646 666 C1' C E 717 beta 662 667 665 685 C1' A E 718 beta 681 686 684 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T D 602 11 8 30 C2' G D 603 31 28 52 C2' G D 604 53 50 74 C2' C D 605 75 72 93 C2' T D 606 94 91 113 C2' A D 607 114 111 134 C2' T D 608 135 132 154 C2' A D 609 155 152 175 C2' A D 610 176 173 196 C2' A D 611 197 194 217 C2' A D 612 218 215 238 C2' G D 613 239 236 260 C2' G D 614 261 258 282 C2' G D 615 283 280 304 C2' C D 616 305 302 323 C2' T D 617 324 321 343 C2' C D 618 344 341 360 C2' G E 702 361 358 382 C2' A E 703 383 380 403 C2' G E 704 404 401 425 C2' C E 705 426 423 444 C2' C E 706 445 442 463 C2' C E 707 464 461 482 C2' T E 708 483 480 502 C2' T E 709 503 500 522 C2' T E 710 523 520 542 C2' T E 711 543 540 562 C2' A E 712 563 560 583 C2' T E 713 584 581 603 C2' A E 714 604 601 624 C2' G E 715 625 622 646 C2' C E 716 647 644 665 C2' C E 717 666 663 684 C2' A E 718 685 682 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T D 602 OK 6 9 10 28 C3' G D 603 OK 26 29 30 50 C3' G D 604 OK 48 51 52 72 C3' C D 605 OK 70 73 74 91 C3' T D 606 OK 89 92 93 111 C3' A D 607 OK 109 112 113 132 C3' T D 608 OK 130 133 134 152 C3' A D 609 OK 150 153 154 173 C3' A D 610 OK 171 174 175 194 C3' A D 611 OK 192 195 196 215 C3' A D 612 OK 213 216 217 236 C3' G D 613 OK 234 237 238 258 C3' G D 614 OK 256 259 260 280 C3' G D 615 OK 278 281 282 302 C3' C D 616 OK 300 303 304 321 C3' T D 617 OK 319 322 323 341 C3' C D 618 OK 339 342 343 358 C3' G E 702 OK 356 359 360 380 C3' A E 703 OK 378 381 382 401 C3' G E 704 OK 399 402 403 423 C3' C E 705 OK 421 424 425 442 C3' C E 706 OK 440 443 444 461 C3' C E 707 OK 459 462 463 480 C3' T E 708 OK 478 481 482 500 C3' T E 709 OK 498 501 502 520 C3' T E 710 OK 518 521 522 540 C3' T E 711 OK 538 541 542 560 C3' A E 712 OK 558 561 562 581 C3' T E 713 OK 579 582 583 601 C3' A E 714 OK 599 602 603 622 C3' G E 715 OK 620 623 624 644 C3' C E 716 OK 642 645 646 663 C3' C E 717 OK 661 664 665 682 C3' A E 718 OK 680 683 684 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T D 602 OK 8 5 7 26 C4' G D 603 OK 28 25 27 48 C4' G D 604 OK 50 47 49 70 C4' C D 605 OK 72 69 71 89 C4' T D 606 OK 91 88 90 109 C4' A D 607 OK 111 108 110 130 C4' T D 608 OK 132 129 131 150 C4' A D 609 OK 152 149 151 171 C4' A D 610 OK 173 170 172 192 C4' A D 611 OK 194 191 193 213 C4' A D 612 OK 215 212 214 234 C4' G D 613 OK 236 233 235 256 C4' G D 614 OK 258 255 257 278 C4' G D 615 OK 280 277 279 300 C4' C D 616 OK 302 299 301 319 C4' T D 617 OK 321 318 320 339 C4' C D 618 OK 341 338 340 356 C4' G E 702 OK 358 355 357 378 C4' A E 703 OK 380 377 379 399 C4' G E 704 OK 401 398 400 421 C4' C E 705 OK 423 420 422 440 C4' C E 706 OK 442 439 441 459 C4' C E 707 OK 461 458 460 478 C4' T E 708 OK 480 477 479 498 C4' T E 709 OK 500 497 499 518 C4' T E 710 OK 520 517 519 538 C4' T E 711 OK 540 537 539 558 C4' A E 712 OK 560 557 559 579 C4' T E 713 OK 581 578 580 599 C4' A E 714 OK 601 598 600 620 C4' G E 715 OK 622 619 621 642 C4' C E 716 OK 644 641 643 661 C4' C E 717 OK 663 660 662 680 C4' A E 718 OK 682 679 681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T D 602 4 6 25 C5' G D 603 24 26 47 C5' G D 604 46 48 69 C5' C D 605 68 70 88 C5' T D 606 87 89 108 C5' A D 607 107 109 129 C5' T D 608 128 130 149 C5' A D 609 148 150 170 C5' A D 610 169 171 191 C5' A D 611 190 192 212 C5' A D 612 211 213 233 C5' G D 613 232 234 255 C5' G D 614 254 256 277 C5' G D 615 276 278 299 C5' C D 616 298 300 318 C5' T D 617 317 319 338 C5' C D 618 337 339 355 C5' G E 702 354 356 377 C5' A E 703 376 378 398 C5' G E 704 397 399 420 C5' C E 705 419 421 439 C5' C E 706 438 440 458 C5' C E 707 457 459 477 C5' T E 708 476 478 497 C5' T E 709 496 498 517 C5' T E 710 516 518 537 C5' T E 711 536 538 557 C5' A E 712 556 558 578 C5' T E 713 577 579 598 C5' A E 714 597 599 619 C5' G E 715 618 620 641 C5' C E 716 640 642 660 C5' C E 717 659 661 679 C5' A E 718 678 680 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T D 602 distorted distorted 2 3 4 21 P G D 603 distorted distorted 9 22 23 24 43 P G D 604 distorted distorted 29 44 45 46 65 P C D 605 distorted distorted 51 66 67 68 84 P T D 606 distorted distorted 73 85 86 87 104 P A D 607 distorted distorted 92 105 106 107 125 P T D 608 distorted distorted 112 126 127 128 145 P A D 609 distorted distorted 133 146 147 148 166 P A D 610 distorted distorted 153 167 168 169 187 P A D 611 distorted distorted 174 188 189 190 208 P A D 612 distorted distorted 195 209 210 211 229 P G D 613 distorted distorted 216 230 231 232 251 P G D 614 distorted distorted 237 252 253 254 273 P G D 615 distorted distorted 259 274 275 276 295 P C D 616 distorted distorted 281 296 297 298 314 P T D 617 distorted distorted 303 315 316 317 334 P C D 618 distorted distorted 322 335 336 337 373 P A E 703 distorted distorted 359 374 375 376 394 P G E 704 distorted distorted 381 395 396 397 416 P C E 705 distorted distorted 402 417 418 419 435 P C E 706 distorted distorted 424 436 437 438 454 P C E 707 distorted distorted 443 455 456 457 473 P T E 708 distorted distorted 462 474 475 476 493 P T E 709 distorted distorted 481 494 495 496 513 P T E 710 distorted distorted 501 514 515 516 533 P T E 711 distorted distorted 521 534 535 536 553 P A E 712 distorted distorted 541 554 555 556 574 P T E 713 distorted distorted 561 575 576 577 594 P A E 714 distorted distorted 582 595 596 597 615 P G E 715 distorted distorted 602 616 617 618 637 P C E 716 distorted distorted 623 638 639 640 656 P C E 717 distorted distorted 645 657 658 659 675 P A E 718 distorted distorted 664 676 677 678 ---------------------------------------------------------------------------------