ID code: '2B7G' 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' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' C A 6 alpha beta 174 194 180 177 210 C1' U A 7 alpha beta 205 225 211 208 240 C1' C A 8 alpha beta 235 255 241 238 271 C1' U A 9 alpha beta 266 286 272 269 301 C1' G A 10 alpha beta 296 319 302 299 335 C1' G A 11 alpha beta 330 353 336 333 369 C1' C A 12 alpha beta 364 384 370 367 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' G A 14 alpha beta 428 451 434 431 467 C1' C A 15 alpha beta 462 482 468 465 498 C1' U A 16 alpha beta 493 513 499 496 528 C1' U A 17 alpha beta 523 543 529 526 558 C1' U A 18 alpha beta 553 573 559 556 588 C1' C A 19 alpha beta 583 604 589 586 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' G A 5 OK OK 145 141 161 144 177 C2' C A 6 OK OK 179 175 192 178 208 C2' U A 7 OK OK 210 206 223 209 238 C2' C A 8 OK OK 240 236 253 239 269 C2' U A 9 OK OK 271 267 284 270 299 C2' G A 10 OK OK 301 297 317 300 333 C2' G A 11 OK OK 335 331 351 334 367 C2' C A 12 OK OK 369 365 382 368 398 C2' A A 13 OK OK 400 396 415 399 431 C2' G A 14 OK OK 433 429 449 432 465 C2' C A 15 OK OK 467 463 480 466 496 C2' U A 16 OK OK 498 494 511 497 526 C2' U A 17 OK OK 528 524 541 527 556 C2' U A 18 OK OK 558 554 571 557 586 C2' C A 19 OK OK 588 584 602 587 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' G A 5 OK OK 139 160 142 143 175 C3' C A 6 OK OK 173 191 176 177 206 C3' U A 7 OK OK 204 222 207 208 236 C3' C A 8 OK OK 234 252 237 238 267 C3' U A 9 OK OK 265 283 268 269 297 C3' G A 10 OK OK 295 316 298 299 331 C3' G A 11 OK OK 329 350 332 333 365 C3' C A 12 OK OK 363 381 366 367 396 C3' A A 13 OK OK 394 414 397 398 429 C3' G A 14 OK OK 427 448 430 431 463 C3' C A 15 OK OK 461 479 464 465 494 C3' U A 16 OK OK 492 510 495 496 524 C3' U A 17 OK OK 522 540 525 526 554 C3' U A 18 OK OK 552 570 555 556 584 C3' C A 19 OK OK 582 600 585 586 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' G A 5 OK OK 141 159 138 140 173 C4' C A 6 OK OK 175 190 172 174 204 C4' U A 7 OK OK 206 221 203 205 234 C4' C A 8 OK OK 236 251 233 235 265 C4' U A 9 OK OK 267 282 264 266 295 C4' G A 10 OK OK 297 315 294 296 329 C4' G A 11 OK OK 331 349 328 330 363 C4' C A 12 OK OK 365 380 362 364 394 C4' A A 13 OK OK 396 413 393 395 427 C4' G A 14 OK OK 429 447 426 428 461 C4' C A 15 OK OK 463 478 460 462 492 C4' U A 16 OK OK 494 509 491 493 522 C4' U A 17 OK OK 524 539 521 523 552 C4' U A 18 OK OK 554 569 551 553 582 C4' C A 19 OK OK 584 599 581 583 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' G A 5 OK OK 137 157 158 139 172 C5' C A 6 OK OK 171 188 189 173 203 C5' U A 7 OK OK 202 219 220 204 233 C5' C A 8 OK OK 232 249 250 234 264 C5' U A 9 OK OK 263 280 281 265 294 C5' G A 10 OK OK 293 313 314 295 328 C5' G A 11 OK OK 327 347 348 329 362 C5' C A 12 OK OK 361 378 379 363 393 C5' A A 13 OK OK 392 411 412 394 426 C5' G A 14 OK OK 425 445 446 427 460 C5' C A 15 OK OK 459 476 477 461 491 C5' U A 16 OK OK 490 507 508 492 521 C5' U A 17 OK OK 520 537 538 522 551 C5' U A 18 OK OK 550 567 568 552 581 C5' C A 19 OK OK 580 597 598 582 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P G A 5 distorted distorted 108 135 136 137 168 P C A 6 distorted distorted 142 169 170 171 199 P U A 7 distorted distorted 176 200 201 202 229 P C A 8 distorted distorted 207 230 231 232 260 P U A 9 distorted distorted 237 261 262 263 290 P G A 10 distorted distorted 268 291 292 293 324 P G A 11 distorted distorted 298 325 326 327 358 P C A 12 distorted distorted 332 359 360 361 389 P A A 13 distorted distorted 366 390 391 392 422 P G A 14 distorted distorted 397 423 424 425 456 P C A 15 distorted distorted 430 457 458 459 487 P U A 16 distorted distorted 464 488 489 490 517 P U A 17 distorted distorted 495 518 519 520 547 P U A 18 distorted distorted 525 548 549 550 577 P C A 19 distorted distorted 555 578 579 580 ---------------------------------------------------------------------------------