ID code: '1OO7' 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' G A 1 alpha beta 4 27 10 7 44 C1' A A 2 alpha beta 39 61 45 42 77 C1' A A 3 alpha beta 72 94 78 75 110 C1' G A 4 alpha beta 105 128 111 108 144 C1' A A 5 alpha beta 139 161 145 142 177 C1' G A 6 alpha beta 172 195 178 175 211 C1' A A 7 alpha beta 206 228 212 209 244 C1' A A 8 alpha beta 239 261 245 242 277 C1' G A 9 alpha beta 272 295 278 275 311 C1' C A 10 alpha beta 306 327 312 309 340 C1' DG B 1 alpha beta 336 358 341 339 374 C1' 5PC B 2 alpha beta 370 392 375 373 409 C1' PDU B 3 alpha beta 405 427 410 408 443 C1' PDU B 4 alpha beta 439 461 444 442 477 C1' 5PC B 5 alpha beta 473 495 478 476 512 C1' PDU B 6 alpha beta 508 530 513 511 546 C1' 5PC B 7 alpha beta 542 564 547 545 581 C1' PDU B 8 alpha beta 577 599 582 580 615 C1' PDU B 9 alpha beta 611 633 616 614 649 C1' DC B 10 alpha beta 645 665 650 648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' A A 2 OK OK 44 40 59 43 75 C2' A A 3 OK OK 77 73 92 76 108 C2' G A 4 OK OK 110 106 126 109 142 C2' A A 5 OK OK 144 140 159 143 175 C2' G A 6 OK OK 177 173 193 176 209 C2' A A 7 OK OK 211 207 226 210 242 C2' A A 8 OK OK 244 240 259 243 275 C2' G A 9 OK OK 277 273 293 276 309 C2' C A 10 OK OK 311 307 325 310 339 C2' DG B 1 OK OK 340 337 356 357 373 C2' 5PC B 2 OK OK 374 371 390 391 408 C2' PDU B 3 OK OK 409 406 426 425 442 C2' PDU B 4 OK OK 443 440 460 459 476 C2' 5PC B 5 OK OK 477 474 493 494 511 C2' PDU B 6 OK OK 512 509 529 528 545 C2' 5PC B 7 OK OK 546 543 562 563 580 C2' PDU B 8 OK OK 581 578 598 597 614 C2' PDU B 9 OK OK 615 612 632 631 648 C2' DC B 10 OK OK 649 646 663 664 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' A A 3 OK OK 71 91 74 75 106 C3' G A 4 OK OK 104 125 107 108 140 C3' A A 5 OK OK 138 158 141 142 173 C3' G A 6 OK OK 171 192 174 175 207 C3' A A 7 OK OK 205 225 208 209 240 C3' A A 8 OK OK 238 258 241 242 273 C3' G A 9 OK OK 271 292 274 275 307 C3' C A 10 OK OK 305 323 308 309 337 C3' DG B 1 OK OK 335 355 338 339 371 C3' 5PC B 2 OK OK 369 389 372 373 406 C3' PDU B 3 OK OK 404 424 407 408 440 C3' PDU B 4 OK OK 438 458 441 442 474 C3' 5PC B 5 OK OK 472 492 475 476 509 C3' PDU B 6 OK OK 507 527 510 511 543 C3' 5PC B 7 OK OK 541 561 544 545 578 C3' PDU B 8 OK OK 576 596 579 580 612 C3' PDU B 9 OK OK 610 630 613 614 646 C3' DC B 10 OK OK 644 661 647 648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' A A 3 OK OK 73 90 70 72 104 C4' G A 4 OK OK 106 124 103 105 138 C4' A A 5 OK OK 140 157 137 139 171 C4' G A 6 OK OK 173 191 170 172 205 C4' A A 7 OK OK 207 224 204 206 238 C4' A A 8 OK OK 240 257 237 239 271 C4' G A 9 OK OK 273 291 270 272 305 C4' C A 10 OK OK 307 322 304 306 335 C4' DG B 1 OK OK 337 354 334 336 369 C4' 5PC B 2 OK OK 371 388 367 370 404 C4' PDU B 3 OK OK 406 423 403 405 438 C4' PDU B 4 OK OK 440 457 437 439 472 C4' 5PC B 5 OK OK 474 491 470 473 507 C4' PDU B 6 OK OK 509 526 506 508 541 C4' 5PC B 7 OK OK 543 560 539 542 576 C4' PDU B 8 OK OK 578 595 575 577 610 C4' PDU B 9 OK OK 612 629 609 611 644 C4' DC B 10 OK OK 646 660 643 645 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' A A 2 OK OK 36 55 56 38 70 C5' A A 3 OK OK 69 88 89 71 103 C5' G A 4 OK OK 102 122 123 104 137 C5' A A 5 OK OK 136 155 156 138 170 C5' G A 6 OK OK 169 189 190 171 204 C5' A A 7 OK OK 203 222 223 205 237 C5' A A 8 OK OK 236 255 256 238 270 C5' G A 9 OK OK 269 289 290 271 304 C5' C A 10 OK OK 303 320 321 305 334 C5' DG B 1 OK OK 333 352 353 335 367 C5' 5PC B 2 OK OK 368 386 387 369 403 C5' PDU B 3 OK OK 402 421 422 404 437 C5' PDU B 4 OK OK 436 455 456 438 470 C5' 5PC B 5 OK OK 471 489 490 472 506 C5' PDU B 6 OK OK 505 524 525 507 539 C5' 5PC B 7 OK OK 540 558 559 541 575 C5' PDU B 8 OK OK 574 593 594 576 609 C5' PDU B 9 OK OK 608 627 628 610 643 C5' DC B 10 OK OK 642 658 659 644 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P A A 3 distorted distorted 41 67 68 69 99 P G A 4 distorted distorted 74 100 101 102 133 P A A 5 distorted distorted 107 134 135 136 166 P G A 6 distorted distorted 141 167 168 169 200 P A A 7 distorted distorted 174 201 202 203 233 P A A 8 distorted distorted 208 234 235 236 266 P G A 9 distorted distorted 241 267 268 269 300 P C A 10 distorted distorted 274 301 302 303 364 P 5PC B 2 distorted distorted 338 365 366 368 399 P PDU B 3 distorted distorted 372 401 400 402 433 P PDU B 4 distorted distorted 407 435 434 436 467 P 5PC B 5 distorted distorted 441 468 469 471 502 P PDU B 6 distorted distorted 475 504 503 505 536 P 5PC B 7 distorted distorted 510 537 538 540 571 P PDU B 8 distorted distorted 544 573 572 574 605 P PDU B 9 distorted distorted 579 607 606 608 639 P DC B 10 distorted distorted 613 640 641 642 ---------------------------------------------------------------------------------