ID code: '2DRA' 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' --------------------------------------------------------------------------------- 13 C1' G B 1 beta 8 14 11 36 C1' G B 2 beta 31 37 34 59 C1' C B 3 beta 54 60 57 79 C1' C B 4 beta 74 80 77 99 C1' C B 5 beta 94 100 97 119 C1' G B 6 beta 114 120 117 142 C1' G B 7 beta 137 143 140 165 C1' G B 8 beta 160 166 163 188 C1' G B 9 beta 183 189 186 211 C1' C B 10 beta 206 212 209 231 C1' G B 11 beta 226 232 229 254 C1' G B 12 beta 249 255 252 277 C1' U B 13 beta 272 278 275 297 C1' U B 14 beta 292 298 295 317 C1' C B 15 beta 312 318 315 337 C1' G B 16 beta 332 338 335 360 C1' A B 17 beta 355 361 358 382 C1' U B 18 beta 377 383 380 402 C1' U B 19 beta 397 403 400 422 C1' C B 20 beta 417 423 420 442 C1' C B 21 beta 437 443 440 462 C1' G B 22 beta 457 463 460 485 C1' C B 23 beta 480 486 483 505 C1' C B 24 beta 500 506 503 525 C1' C B 25 beta 520 526 523 545 C1' U B 26 beta 540 546 543 565 C1' G B 27 beta 560 566 563 588 C1' G B 28 beta 583 589 586 611 C1' G B 29 beta 606 612 609 634 C1' C B 30 beta 629 635 632 654 C1' C B 31 beta 649 655 652 674 C1' A B 32 beta 669 675 672 696 C1' C B 33 beta 691 697 694 716 C1' C B 34 beta 711 717 714 4383 C1' ATP A 501 beta 4378 4384 4381 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G B 1 OK 13 9 12 34 C2' G B 2 OK 36 32 35 57 C2' C B 3 OK 59 55 58 77 C2' C B 4 OK 79 75 78 97 C2' C B 5 OK 99 95 98 117 C2' G B 6 OK 119 115 118 140 C2' G B 7 OK 142 138 141 163 C2' G B 8 OK 165 161 164 186 C2' G B 9 OK 188 184 187 209 C2' C B 10 OK 211 207 210 229 C2' G B 11 OK 231 227 230 252 C2' G B 12 OK 254 250 253 275 C2' U B 13 OK 277 273 276 295 C2' U B 14 OK 297 293 296 315 C2' C B 15 OK 317 313 316 335 C2' G B 16 OK 337 333 336 358 C2' A B 17 OK 360 356 359 380 C2' U B 18 OK 382 378 381 400 C2' U B 19 OK 402 398 401 420 C2' C B 20 OK 422 418 421 440 C2' C B 21 OK 442 438 441 460 C2' G B 22 OK 462 458 461 483 C2' C B 23 OK 485 481 484 503 C2' C B 24 OK 505 501 504 523 C2' C B 25 OK 525 521 524 543 C2' U B 26 OK 545 541 544 563 C2' G B 27 OK 565 561 564 586 C2' G B 28 OK 588 584 587 609 C2' G B 29 OK 611 607 610 632 C2' C B 30 OK 634 630 633 652 C2' C B 31 OK 654 650 653 672 C2' A B 32 OK 674 670 673 694 C2' C B 33 OK 696 692 695 714 C2' C B 34 OK 716 712 715 4381 C2' ATP A 501 OK 4383 4379 4382 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G B 1 OK 7 10 11 32 C3' G B 2 OK 30 33 34 55 C3' C B 3 OK 53 56 57 75 C3' C B 4 OK 73 76 77 95 C3' C B 5 OK 93 96 97 115 C3' G B 6 OK 113 116 117 138 C3' G B 7 OK 136 139 140 161 C3' G B 8 OK 159 162 163 184 C3' G B 9 OK 182 185 186 207 C3' C B 10 OK 205 208 209 227 C3' G B 11 OK 225 228 229 250 C3' G B 12 OK 248 251 252 273 C3' U B 13 OK 271 274 275 293 C3' U B 14 OK 291 294 295 313 C3' C B 15 OK 311 314 315 333 C3' G B 16 OK 331 334 335 356 C3' A B 17 OK 354 357 358 378 C3' U B 18 OK 376 379 380 398 C3' U B 19 OK 396 399 400 418 C3' C B 20 OK 416 419 420 438 C3' C B 21 OK 436 439 440 458 C3' G B 22 OK 456 459 460 481 C3' C B 23 OK 479 482 483 501 C3' C B 24 OK 499 502 503 521 C3' C B 25 OK 519 522 523 541 C3' U B 26 OK 539 542 543 561 C3' G B 27 OK 559 562 563 584 C3' G B 28 OK 582 585 586 607 C3' G B 29 OK 605 608 609 630 C3' C B 30 OK 628 631 632 650 C3' C B 31 OK 648 651 652 670 C3' A B 32 OK 668 671 672 692 C3' C B 33 OK 690 693 694 712 C3' C B 34 OK 710 713 714 4379 C3' ATP A 501 OK 4377 4380 4381 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G B 1 OK 9 6 8 30 C4' G B 2 OK 32 29 31 53 C4' C B 3 OK 55 52 54 73 C4' C B 4 OK 75 72 74 93 C4' C B 5 OK 95 92 94 113 C4' G B 6 OK 115 112 114 136 C4' G B 7 OK 138 135 137 159 C4' G B 8 OK 161 158 160 182 C4' G B 9 OK 184 181 183 205 C4' C B 10 OK 207 204 206 225 C4' G B 11 OK 227 224 226 248 C4' G B 12 OK 250 247 249 271 C4' U B 13 OK 273 270 272 291 C4' U B 14 OK 293 290 292 311 C4' C B 15 OK 313 310 312 331 C4' G B 16 OK 333 330 332 354 C4' A B 17 OK 356 353 355 376 C4' U B 18 OK 378 375 377 396 C4' U B 19 OK 398 395 397 416 C4' C B 20 OK 418 415 417 436 C4' C B 21 OK 438 435 437 456 C4' G B 22 OK 458 455 457 479 C4' C B 23 OK 481 478 480 499 C4' C B 24 OK 501 498 500 519 C4' C B 25 OK 521 518 520 539 C4' U B 26 OK 541 538 540 559 C4' G B 27 OK 561 558 560 582 C4' G B 28 OK 584 581 583 605 C4' G B 29 OK 607 604 606 628 C4' C B 30 OK 630 627 629 648 C4' C B 31 OK 650 647 649 668 C4' A B 32 OK 670 667 669 690 C4' C B 33 OK 692 689 691 710 C4' C B 34 OK 712 709 711 4377 C4' ATP A 501 OK 4379 4376 4378 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G B 1 5 7 29 C5' G B 2 28 30 52 C5' C B 3 51 53 72 C5' C B 4 71 73 92 C5' C B 5 91 93 112 C5' G B 6 111 113 135 C5' G B 7 134 136 158 C5' G B 8 157 159 181 C5' G B 9 180 182 204 C5' C B 10 203 205 224 C5' G B 11 223 225 247 C5' G B 12 246 248 270 C5' U B 13 269 271 290 C5' U B 14 289 291 310 C5' C B 15 309 311 330 C5' G B 16 329 331 353 C5' A B 17 352 354 375 C5' U B 18 374 376 395 C5' U B 19 394 396 415 C5' C B 20 414 416 435 C5' C B 21 434 436 455 C5' G B 22 454 456 478 C5' C B 23 477 479 498 C5' C B 24 497 499 518 C5' C B 25 517 519 538 C5' U B 26 537 539 558 C5' G B 27 557 559 581 C5' G B 28 580 582 604 C5' G B 29 603 605 627 C5' C B 30 626 628 647 C5' C B 31 646 648 667 C5' A B 32 666 668 689 C5' C B 33 688 690 709 C5' C B 34 708 710 4376 C5' ATP A 501 4375 4377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G B 1 distorted distorted 3 4 5 25 P G B 2 distorted distorted 10 26 27 28 48 P C B 3 distorted distorted 33 49 50 51 68 P C B 4 distorted distorted 56 69 70 71 88 P C B 5 distorted distorted 76 89 90 91 108 P G B 6 distorted distorted 96 109 110 111 131 P G B 7 distorted distorted 116 132 133 134 154 P G B 8 distorted distorted 139 155 156 157 177 P G B 9 distorted distorted 162 178 179 180 200 P C B 10 distorted distorted 185 201 202 203 220 P G B 11 distorted distorted 208 221 222 223 243 P G B 12 distorted distorted 228 244 245 246 266 P U B 13 distorted distorted 251 267 268 269 286 P U B 14 distorted distorted 274 287 288 289 306 P C B 15 distorted distorted 294 307 308 309 326 P G B 16 distorted distorted 314 327 328 329 349 P A B 17 distorted distorted 334 350 351 352 371 P U B 18 distorted distorted 357 372 373 374 391 P U B 19 distorted distorted 379 392 393 394 411 P C B 20 distorted distorted 399 412 413 414 431 P C B 21 distorted distorted 419 432 433 434 451 P G B 22 distorted distorted 439 452 453 454 474 P C B 23 distorted distorted 459 475 476 477 494 P C B 24 distorted distorted 482 495 496 497 514 P C B 25 distorted distorted 502 515 516 517 534 P U B 26 distorted distorted 522 535 536 537 554 P G B 27 distorted distorted 542 555 556 557 577 P G B 28 distorted distorted 562 578 579 580 600 P G B 29 distorted distorted 585 601 602 603 623 P C B 30 distorted distorted 608 624 625 626 643 P C B 31 distorted distorted 631 644 645 646 663 P A B 32 distorted distorted 651 664 665 666 685 P C B 33 distorted distorted 671 686 687 688 705 P C B 34 distorted distorted 693 706 707 708 ---------------------------------------------------------------------------------