ID code: '2GVO' 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' G A 3 alpha beta 72 95 78 75 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' G A 9 alpha beta 269 292 275 272 308 C1' A A 10 alpha beta 303 325 309 306 341 C1' U A 11 alpha beta 336 356 342 339 371 C1' G A 12 alpha beta 366 389 372 369 405 C1' G A 13 alpha beta 400 423 406 403 439 C1' A A 14 alpha beta 434 456 440 437 472 C1' U A 15 alpha beta 467 487 473 470 502 C1' C A 16 alpha beta 497 517 503 500 533 C1' U A 17 alpha beta 528 548 534 531 563 C1' C A 18 alpha beta 558 579 564 561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 77 73 93 76 109 C2' G A 4 OK OK 111 107 127 110 143 C2' U A 5 OK OK 145 141 158 144 173 C2' C A 6 OK OK 175 171 188 174 204 C2' G A 7 OK OK 206 202 222 205 238 C2' G A 8 OK OK 240 236 256 239 272 C2' G A 9 OK OK 274 270 290 273 306 C2' A A 10 OK OK 308 304 323 307 339 C2' U A 11 OK OK 341 337 354 340 369 C2' G A 12 OK OK 371 367 387 370 403 C2' G A 13 OK OK 405 401 421 404 437 C2' A A 14 OK OK 439 435 454 438 470 C2' U A 15 OK OK 472 468 485 471 500 C2' C A 16 OK OK 502 498 515 501 531 C2' U A 17 OK OK 533 529 546 532 561 C2' C A 18 OK OK 563 559 577 562 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 71 92 74 75 107 C3' G A 4 OK OK 105 126 108 109 141 C3' U A 5 OK OK 139 157 142 143 171 C3' C A 6 OK OK 169 187 172 173 202 C3' G A 7 OK OK 200 221 203 204 236 C3' G A 8 OK OK 234 255 237 238 270 C3' G A 9 OK OK 268 289 271 272 304 C3' A A 10 OK OK 302 322 305 306 337 C3' U A 11 OK OK 335 353 338 339 367 C3' G A 12 OK OK 365 386 368 369 401 C3' G A 13 OK OK 399 420 402 403 435 C3' A A 14 OK OK 433 453 436 437 468 C3' U A 15 OK OK 466 484 469 470 498 C3' C A 16 OK OK 496 514 499 500 529 C3' U A 17 OK OK 527 545 530 531 559 C3' C A 18 OK OK 557 575 560 561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 73 91 70 72 105 C4' G A 4 OK OK 107 125 104 106 139 C4' U A 5 OK OK 141 156 138 140 169 C4' C A 6 OK OK 171 186 168 170 200 C4' G A 7 OK OK 202 220 199 201 234 C4' G A 8 OK OK 236 254 233 235 268 C4' G A 9 OK OK 270 288 267 269 302 C4' A A 10 OK OK 304 321 301 303 335 C4' U A 11 OK OK 337 352 334 336 365 C4' G A 12 OK OK 367 385 364 366 399 C4' G A 13 OK OK 401 419 398 400 433 C4' A A 14 OK OK 435 452 432 434 466 C4' U A 15 OK OK 468 483 465 467 496 C4' C A 16 OK OK 498 513 495 497 527 C4' U A 17 OK OK 529 544 526 528 557 C4' C A 18 OK OK 559 574 556 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 69 89 90 71 104 C5' G A 4 OK OK 103 123 124 105 138 C5' U A 5 OK OK 137 154 155 139 168 C5' C A 6 OK OK 167 184 185 169 199 C5' G A 7 OK OK 198 218 219 200 233 C5' G A 8 OK OK 232 252 253 234 267 C5' G A 9 OK OK 266 286 287 268 301 C5' A A 10 OK OK 300 319 320 302 334 C5' U A 11 OK OK 333 350 351 335 364 C5' G A 12 OK OK 363 383 384 365 398 C5' G A 13 OK OK 397 417 418 399 432 C5' A A 14 OK OK 431 450 451 433 465 C5' U A 15 OK OK 464 481 482 466 495 C5' C A 16 OK OK 494 511 512 496 526 C5' U A 17 OK OK 525 542 543 527 556 C5' C A 18 OK OK 555 572 573 557 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P G A 4 distorted distorted 74 101 102 103 134 P U A 5 distorted distorted 108 135 136 137 164 P C A 6 distorted distorted 142 165 166 167 195 P G A 7 distorted distorted 172 196 197 198 229 P G A 8 distorted distorted 203 230 231 232 263 P G A 9 distorted distorted 237 264 265 266 297 P A A 10 distorted distorted 271 298 299 300 330 P U A 11 distorted distorted 305 331 332 333 360 P G A 12 distorted distorted 338 361 362 363 394 P G A 13 distorted distorted 368 395 396 397 428 P A A 14 distorted distorted 402 429 430 431 461 P U A 15 distorted distorted 436 462 463 464 491 P C A 16 distorted distorted 469 492 493 494 522 P U A 17 distorted distorted 499 523 524 525 552 P C A 18 distorted distorted 530 553 554 555 ---------------------------------------------------------------------------------