ID code: '1ATV' 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' G A 3 alpha beta 73 96 79 76 112 C1' A A 4 alpha beta 107 129 113 110 145 C1' C A 5 alpha beta 140 160 146 143 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' A A 7 alpha beta 202 224 208 205 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' A A 9 alpha beta 269 291 275 272 307 C1' A A 10 alpha beta 302 324 308 305 340 C1' G A 11 alpha beta 335 358 341 338 374 C1' G A 12 alpha beta 369 392 375 372 408 C1' U A 13 alpha beta 403 423 409 406 438 C1' C A 14 alpha beta 433 453 439 436 469 C1' C A 15 alpha beta 464 484 470 467 500 C1' C A 16 alpha beta 495 515 501 498 531 C1' G A 17 alpha beta 526 550 532 529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' A A 4 OK OK 112 108 127 111 143 C2' C A 5 OK OK 145 141 158 144 174 C2' C A 6 OK OK 176 172 189 175 205 C2' A A 7 OK OK 207 203 222 206 238 C2' G A 8 OK OK 240 236 256 239 272 C2' A A 9 OK OK 274 270 289 273 305 C2' A A 10 OK OK 307 303 322 306 338 C2' G A 11 OK OK 340 336 356 339 372 C2' G A 12 OK OK 374 370 390 373 406 C2' U A 13 OK OK 408 404 421 407 436 C2' C A 14 OK OK 438 434 451 437 467 C2' C A 15 OK OK 469 465 482 468 498 C2' C A 16 OK OK 500 496 513 499 529 C2' G A 17 OK OK 531 527 548 530 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' A A 4 OK OK 106 126 109 110 141 C3' C A 5 OK OK 139 157 142 143 172 C3' C A 6 OK OK 170 188 173 174 203 C3' A A 7 OK OK 201 221 204 205 236 C3' G A 8 OK OK 234 255 237 238 270 C3' A A 9 OK OK 268 288 271 272 303 C3' A A 10 OK OK 301 321 304 305 336 C3' G A 11 OK OK 334 355 337 338 370 C3' G A 12 OK OK 368 389 371 372 404 C3' U A 13 OK OK 402 420 405 406 434 C3' C A 14 OK OK 432 450 435 436 465 C3' C A 15 OK OK 463 481 466 467 496 C3' C A 16 OK OK 494 512 497 498 527 C3' G A 17 OK OK 525 546 528 529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' A A 4 OK OK 108 125 105 107 139 C4' C A 5 OK OK 141 156 138 140 170 C4' C A 6 OK OK 172 187 169 171 201 C4' A A 7 OK OK 203 220 200 202 234 C4' G A 8 OK OK 236 254 233 235 268 C4' A A 9 OK OK 270 287 267 269 301 C4' A A 10 OK OK 303 320 300 302 334 C4' G A 11 OK OK 336 354 333 335 368 C4' G A 12 OK OK 370 388 367 369 402 C4' U A 13 OK OK 404 419 401 403 432 C4' C A 14 OK OK 434 449 431 433 463 C4' C A 15 OK OK 465 480 462 464 494 C4' C A 16 OK OK 496 511 493 495 525 C4' G A 17 OK OK 527 545 524 526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' A A 4 OK OK 104 123 124 106 138 C5' C A 5 OK OK 137 154 155 139 169 C5' C A 6 OK OK 168 185 186 170 200 C5' A A 7 OK OK 199 218 219 201 233 C5' G A 8 OK OK 232 252 253 234 267 C5' A A 9 OK OK 266 285 286 268 300 C5' A A 10 OK OK 299 318 319 301 333 C5' G A 11 OK OK 332 352 353 334 367 C5' G A 12 OK OK 366 386 387 368 401 C5' U A 13 OK OK 400 417 418 402 431 C5' C A 14 OK OK 430 447 448 432 462 C5' C A 15 OK OK 461 478 479 463 493 C5' C A 16 OK OK 492 509 510 494 524 C5' G A 17 OK OK 523 543 544 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P A A 4 distorted distorted 75 102 103 104 134 P C A 5 distorted distorted 109 135 136 137 165 P C A 6 distorted distorted 142 166 167 168 196 P A A 7 distorted distorted 173 197 198 199 229 P G A 8 distorted distorted 204 230 231 232 263 P A A 9 distorted distorted 237 264 265 266 296 P A A 10 distorted distorted 271 297 298 299 329 P G A 11 distorted distorted 304 330 331 332 363 P G A 12 distorted distorted 337 364 365 366 397 P U A 13 distorted distorted 371 398 399 400 427 P C A 14 distorted distorted 405 428 429 430 458 P C A 15 distorted distorted 435 459 460 461 489 P C A 16 distorted distorted 466 490 491 492 520 P G A 17 distorted distorted 497 521 522 523 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