ID code: '1R7Q' 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' --------------------------------------------------------------------------------- 12 C1' G C 1 alpha beta 7 29 13 10 45 C1' G C 2 alpha beta 40 62 46 43 78 C1' C C 3 alpha beta 73 92 79 76 108 C1' G C 4 alpha beta 103 125 109 106 141 C1' G C 5 alpha beta 136 158 142 139 174 C1' U C 6 alpha beta 169 188 175 172 203 C1' U C 7 alpha beta 198 217 204 201 232 C1' G C 8 alpha beta 227 249 233 230 265 C1' C C 9 alpha beta 260 279 266 263 295 C1' A C 10 alpha beta 290 311 296 293 327 C1' G C 11 alpha beta 322 344 328 325 360 C1' G C 12 alpha beta 355 377 361 358 393 C1' U C 13 alpha beta 388 407 394 391 422 C1' C C 14 alpha beta 417 436 423 420 452 C1' U C 15 alpha beta 447 466 453 450 481 C1' G C 16 alpha beta 476 498 482 479 514 C1' C C 17 alpha beta 509 528 515 512 544 C1' A C 18 alpha beta 539 560 545 542 576 C1' C C 19 alpha beta 571 590 577 574 606 C1' C C 20 alpha beta 601 620 607 604 636 C1' G C 21 alpha beta 631 653 637 634 669 C1' C C 22 alpha beta 664 683 670 667 699 C1' C C 23 alpha beta 694 713 700 697 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G C 1 OK OK 12 8 28 11 43 C2' G C 2 OK OK 45 41 61 44 76 C2' C C 3 OK OK 78 74 91 77 106 C2' G C 4 OK OK 108 104 124 107 139 C2' G C 5 OK OK 141 137 157 140 172 C2' U C 6 OK OK 174 170 187 173 201 C2' U C 7 OK OK 203 199 216 202 230 C2' G C 8 OK OK 232 228 248 231 263 C2' C C 9 OK OK 265 261 278 264 293 C2' A C 10 OK OK 295 291 310 294 325 C2' G C 11 OK OK 327 323 343 326 358 C2' G C 12 OK OK 360 356 376 359 391 C2' U C 13 OK OK 393 389 406 392 420 C2' C C 14 OK OK 422 418 435 421 450 C2' U C 15 OK OK 452 448 465 451 479 C2' G C 16 OK OK 481 477 497 480 512 C2' C C 17 OK OK 514 510 527 513 542 C2' A C 18 OK OK 544 540 559 543 574 C2' C C 19 OK OK 576 572 589 575 604 C2' C C 20 OK OK 606 602 619 605 634 C2' G C 21 OK OK 636 632 652 635 667 C2' C C 22 OK OK 669 665 682 668 697 C2' C C 23 OK OK 699 695 712 698 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G C 1 OK OK 6 27 9 10 41 C3' G C 2 OK OK 39 60 42 43 74 C3' C C 3 OK OK 72 90 75 76 104 C3' G C 4 OK OK 102 123 105 106 137 C3' G C 5 OK OK 135 156 138 139 170 C3' U C 6 OK OK 168 186 171 172 199 C3' U C 7 OK OK 197 215 200 201 228 C3' G C 8 OK OK 226 247 229 230 261 C3' C C 9 OK OK 259 277 262 263 291 C3' A C 10 OK OK 289 309 292 293 323 C3' G C 11 OK OK 321 342 324 325 356 C3' G C 12 OK OK 354 375 357 358 389 C3' U C 13 OK OK 387 405 390 391 418 C3' C C 14 OK OK 416 434 419 420 448 C3' U C 15 OK OK 446 464 449 450 477 C3' G C 16 OK OK 475 496 478 479 510 C3' C C 17 OK OK 508 526 511 512 540 C3' A C 18 OK OK 538 558 541 542 572 C3' C C 19 OK OK 570 588 573 574 602 C3' C C 20 OK OK 600 618 603 604 632 C3' G C 21 OK OK 630 651 633 634 665 C3' C C 22 OK OK 663 681 666 667 695 C3' C C 23 OK OK 693 711 696 697 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G C 1 OK OK 8 26 5 7 39 C4' G C 2 OK OK 41 59 38 40 72 C4' C C 3 OK OK 74 89 71 73 102 C4' G C 4 OK OK 104 122 101 103 135 C4' G C 5 OK OK 137 155 134 136 168 C4' U C 6 OK OK 170 185 167 169 197 C4' U C 7 OK OK 199 214 196 198 226 C4' G C 8 OK OK 228 246 225 227 259 C4' C C 9 OK OK 261 276 258 260 289 C4' A C 10 OK OK 291 308 288 290 321 C4' G C 11 OK OK 323 341 320 322 354 C4' G C 12 OK OK 356 374 353 355 387 C4' U C 13 OK OK 389 404 386 388 416 C4' C C 14 OK OK 418 433 415 417 446 C4' U C 15 OK OK 448 463 445 447 475 C4' G C 16 OK OK 477 495 474 476 508 C4' C C 17 OK OK 510 525 507 509 538 C4' A C 18 OK OK 540 557 537 539 570 C4' C C 19 OK OK 572 587 569 571 600 C4' C C 20 OK OK 602 617 599 601 630 C4' G C 21 OK OK 632 650 629 631 663 C4' C C 22 OK OK 665 680 662 664 693 C4' C C 23 OK OK 695 710 692 694 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G C 1 OK OK 4 24 25 6 38 C5' G C 2 OK OK 37 57 58 39 71 C5' C C 3 OK OK 70 87 88 72 101 C5' G C 4 OK OK 100 120 121 102 134 C5' G C 5 OK OK 133 153 154 135 167 C5' U C 6 OK OK 166 183 184 168 196 C5' U C 7 OK OK 195 212 213 197 225 C5' G C 8 OK OK 224 244 245 226 258 C5' C C 9 OK OK 257 274 275 259 288 C5' A C 10 OK OK 287 306 307 289 320 C5' G C 11 OK OK 319 339 340 321 353 C5' G C 12 OK OK 352 372 373 354 386 C5' U C 13 OK OK 385 402 403 387 415 C5' C C 14 OK OK 414 431 432 416 445 C5' U C 15 OK OK 444 461 462 446 474 C5' G C 16 OK OK 473 493 494 475 507 C5' C C 17 OK OK 506 523 524 508 537 C5' A C 18 OK OK 536 555 556 538 569 C5' C C 19 OK OK 568 585 586 570 599 C5' C C 20 OK OK 598 615 616 600 629 C5' G C 21 OK OK 628 648 649 630 662 C5' C C 22 OK OK 661 678 679 663 692 C5' C C 23 OK OK 691 708 709 693 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G C 1 distorted distorted 2 3 4 34 P G C 2 distorted distorted 9 35 36 37 67 P C C 3 distorted distorted 42 68 69 70 97 P G C 4 distorted distorted 75 98 99 100 130 P G C 5 distorted distorted 105 131 132 133 163 P U C 6 distorted distorted 138 164 165 166 192 P U C 7 distorted distorted 171 193 194 195 221 P G C 8 distorted distorted 200 222 223 224 254 P C C 9 distorted distorted 229 255 256 257 284 P A C 10 distorted distorted 262 285 286 287 316 P G C 11 distorted distorted 292 317 318 319 349 P G C 12 distorted distorted 324 350 351 352 382 P U C 13 distorted distorted 357 383 384 385 411 P C C 14 distorted distorted 390 412 413 414 441 P U C 15 distorted distorted 419 442 443 444 470 P G C 16 distorted distorted 449 471 472 473 503 P C C 17 distorted distorted 478 504 505 506 533 P A C 18 distorted distorted 511 534 535 536 565 P C C 19 distorted distorted 541 566 567 568 595 P C C 20 distorted distorted 573 596 597 598 625 P G C 21 distorted distorted 603 626 627 628 658 P C C 22 distorted distorted 633 659 660 661 688 P C C 23 distorted distorted 666 689 690 691 ---------------------------------------------------------------------------------