ID code: '2GXX' 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' C A 1 alpha beta 4 21 9 7 39 C1' G A 2 alpha beta 35 55 40 38 72 C1' C A 3 alpha beta 68 85 73 71 102 C1' G A 4 alpha beta 98 118 103 101 135 C1' A A 5 alpha beta 131 150 136 134 167 C1' A A 6 alpha beta 163 182 168 166 199 C1' T A 7 alpha beta 195 215 200 198 231 C1' T A 8 alpha beta 227 247 232 230 263 C1' C A 9 alpha beta 259 276 264 262 293 C1' G A 10 alpha beta 289 309 294 292 326 C1' C A 11 alpha beta 322 339 327 325 356 C1' G A 12 alpha beta 352 373 357 355 388 C1' C B 13 alpha beta 384 401 389 387 419 C1' G B 14 alpha beta 415 435 420 418 452 C1' C B 15 alpha beta 448 465 453 451 482 C1' G B 16 alpha beta 478 498 483 481 515 C1' A B 17 alpha beta 511 530 516 514 547 C1' A B 18 alpha beta 543 562 548 546 579 C1' T B 19 alpha beta 575 595 580 578 611 C1' T B 20 alpha beta 607 627 612 610 643 C1' C B 21 alpha beta 639 656 644 642 673 C1' G B 22 alpha beta 669 689 674 672 706 C1' C B 23 alpha beta 702 719 707 705 736 C1' G B 24 alpha beta 732 753 737 735 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 8 5 27 28 38 C2' G A 2 OK OK 39 36 60 61 71 C2' C A 3 OK OK 72 69 90 91 101 C2' G A 4 OK OK 102 99 123 124 134 C2' A A 5 OK OK 135 132 155 156 166 C2' A A 6 OK OK 167 164 187 188 198 C2' T A 7 OK OK 199 196 213 214 230 C2' T A 8 OK OK 231 228 245 246 262 C2' C A 9 OK OK 263 260 281 282 292 C2' G A 10 OK OK 293 290 314 315 325 C2' C A 11 OK OK 326 323 344 345 355 C2' G A 12 OK OK 356 353 378 379 387 C2' C B 13 OK OK 388 385 407 408 418 C2' G B 14 OK OK 419 416 440 441 451 C2' C B 15 OK OK 452 449 470 471 481 C2' G B 16 OK OK 482 479 503 504 514 C2' A B 17 OK OK 515 512 535 536 546 C2' A B 18 OK OK 547 544 567 568 578 C2' T B 19 OK OK 579 576 593 594 610 C2' T B 20 OK OK 611 608 625 626 642 C2' C B 21 OK OK 643 640 661 662 672 C2' G B 22 OK OK 673 670 694 695 705 C2' C B 23 OK OK 706 703 724 725 735 C2' G B 24 OK OK 736 733 758 759 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 20 6 7 36 C3' G A 2 OK OK 34 54 37 38 69 C3' C A 3 OK OK 67 84 70 71 99 C3' G A 4 OK OK 97 117 100 101 132 C3' A A 5 OK OK 130 149 133 134 164 C3' A A 6 OK OK 162 181 165 166 196 C3' T A 7 OK OK 194 212 197 198 228 C3' T A 8 OK OK 226 244 229 230 260 C3' C A 9 OK OK 258 275 261 262 290 C3' G A 10 OK OK 288 308 291 292 323 C3' C A 11 OK OK 321 338 324 325 353 C3' G A 12 OK OK 351 371 354 355 385 C3' C B 13 OK OK 383 400 386 387 416 C3' G B 14 OK OK 414 434 417 418 449 C3' C B 15 OK OK 447 464 450 451 479 C3' G B 16 OK OK 477 497 480 481 512 C3' A B 17 OK OK 510 529 513 514 544 C3' A B 18 OK OK 542 561 545 546 576 C3' T B 19 OK OK 574 592 577 578 608 C3' T B 20 OK OK 606 624 609 610 640 C3' C B 21 OK OK 638 655 641 642 670 C3' G B 22 OK OK 668 688 671 672 703 C3' C B 23 OK OK 701 718 704 705 733 C3' G B 24 OK OK 731 751 734 735 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 19 2 4 34 C4' G A 2 OK OK 36 53 33 35 67 C4' C A 3 OK OK 69 83 66 68 97 C4' G A 4 OK OK 99 116 96 98 130 C4' A A 5 OK OK 132 148 129 131 162 C4' A A 6 OK OK 164 180 161 163 194 C4' T A 7 OK OK 196 211 193 195 226 C4' T A 8 OK OK 228 243 225 227 258 C4' C A 9 OK OK 260 274 257 259 288 C4' G A 10 OK OK 290 307 287 289 321 C4' C A 11 OK OK 323 337 320 322 351 C4' G A 12 OK OK 353 370 350 352 383 C4' C B 13 OK OK 385 399 382 384 414 C4' G B 14 OK OK 416 433 413 415 447 C4' C B 15 OK OK 449 463 446 448 477 C4' G B 16 OK OK 479 496 476 478 510 C4' A B 17 OK OK 512 528 509 511 542 C4' A B 18 OK OK 544 560 541 543 574 C4' T B 19 OK OK 576 591 573 575 606 C4' T B 20 OK OK 608 623 605 607 638 C4' C B 21 OK OK 640 654 637 639 668 C4' G B 22 OK OK 670 687 667 669 701 C4' C B 23 OK OK 703 717 700 702 731 C4' G B 24 OK OK 733 750 730 732 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 17 18 3 33 C5' G A 2 OK OK 32 51 52 34 66 C5' C A 3 OK OK 65 81 82 67 96 C5' G A 4 OK OK 95 114 115 97 129 C5' A A 5 OK OK 128 146 147 130 161 C5' A A 6 OK OK 160 178 179 162 193 C5' T A 7 OK OK 192 209 210 194 225 C5' T A 8 OK OK 224 241 242 226 257 C5' C A 9 OK OK 256 272 273 258 287 C5' G A 10 OK OK 286 305 306 288 320 C5' C A 11 OK OK 319 335 336 321 350 C5' G A 12 OK OK 349 368 369 351 382 C5' C B 13 OK OK 381 397 398 383 413 C5' G B 14 OK OK 412 431 432 414 446 C5' C B 15 OK OK 445 461 462 447 476 C5' G B 16 OK OK 475 494 495 477 509 C5' A B 17 OK OK 508 526 527 510 541 C5' A B 18 OK OK 540 558 559 542 573 C5' T B 19 OK OK 572 589 590 574 605 C5' T B 20 OK OK 604 621 622 606 637 C5' C B 21 OK OK 636 652 653 638 667 C5' G B 22 OK OK 666 685 686 668 700 C5' C B 23 OK OK 699 715 716 701 730 C5' G B 24 OK OK 729 748 749 731 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P G A 2 distorted distorted 6 30 31 32 62 P C A 3 distorted distorted 37 63 64 65 92 P G A 4 distorted distorted 70 93 94 95 125 P A A 5 distorted distorted 100 126 127 128 157 P A A 6 distorted distorted 133 158 159 160 189 P T A 7 distorted distorted 165 190 191 192 221 P T A 8 distorted distorted 197 222 223 224 253 P C A 9 distorted distorted 229 254 255 256 283 P G A 10 distorted distorted 261 284 285 286 316 P C A 11 distorted distorted 291 317 318 319 346 P G A 12 distorted distorted 324 347 348 349 409 P G B 14 distorted distorted 386 410 411 412 442 P C B 15 distorted distorted 417 443 444 445 472 P G B 16 distorted distorted 450 473 474 475 505 P A B 17 distorted distorted 480 506 507 508 537 P A B 18 distorted distorted 513 538 539 540 569 P T B 19 distorted distorted 545 570 571 572 601 P T B 20 distorted distorted 577 602 603 604 633 P C B 21 distorted distorted 609 634 635 636 663 P G B 22 distorted distorted 641 664 665 666 696 P C B 23 distorted distorted 671 697 698 699 726 P G B 24 distorted distorted 704 727 728 729 ---------------------------------------------------------------------------------