ID code: '1J4Y' 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' G A 4 alpha beta 107 130 113 110 146 C1' A A 5 alpha beta 141 163 147 144 179 C1' U A 6 alpha beta 174 194 180 177 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' A A 9 alpha beta 268 290 274 271 306 C1' A A 10 alpha beta 301 323 307 304 339 C1' A A 11 alpha beta 334 356 340 337 372 C1' A A 12 alpha beta 367 389 373 370 405 C1' U A 13 alpha beta 400 420 406 403 435 C1' C A 14 alpha beta 430 450 436 433 466 C1' C A 15 alpha beta 461 481 467 464 497 C1' C A 16 alpha beta 492 512 498 495 528 C1' C A 17 alpha beta 523 544 529 526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK OK 112 108 128 111 144 C2' A A 5 OK OK 146 142 161 145 177 C2' U A 6 OK OK 179 175 192 178 207 C2' U A 7 OK OK 209 205 222 208 237 C2' G A 8 OK OK 239 235 255 238 271 C2' A A 9 OK OK 273 269 288 272 304 C2' A A 10 OK OK 306 302 321 305 337 C2' A A 11 OK OK 339 335 354 338 370 C2' A A 12 OK OK 372 368 387 371 403 C2' U A 13 OK OK 405 401 418 404 433 C2' C A 14 OK OK 435 431 448 434 464 C2' C A 15 OK OK 466 462 479 465 495 C2' C A 16 OK OK 497 493 510 496 526 C2' C A 17 OK OK 528 524 542 527 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 106 127 109 110 142 C3' A A 5 OK OK 140 160 143 144 175 C3' U A 6 OK OK 173 191 176 177 205 C3' U A 7 OK OK 203 221 206 207 235 C3' G A 8 OK OK 233 254 236 237 269 C3' A A 9 OK OK 267 287 270 271 302 C3' A A 10 OK OK 300 320 303 304 335 C3' A A 11 OK OK 333 353 336 337 368 C3' A A 12 OK OK 366 386 369 370 401 C3' U A 13 OK OK 399 417 402 403 431 C3' C A 14 OK OK 429 447 432 433 462 C3' C A 15 OK OK 460 478 463 464 493 C3' C A 16 OK OK 491 509 494 495 524 C3' C A 17 OK OK 522 540 525 526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 108 126 105 107 140 C4' A A 5 OK OK 142 159 139 141 173 C4' U A 6 OK OK 175 190 172 174 203 C4' U A 7 OK OK 205 220 202 204 233 C4' G A 8 OK OK 235 253 232 234 267 C4' A A 9 OK OK 269 286 266 268 300 C4' A A 10 OK OK 302 319 299 301 333 C4' A A 11 OK OK 335 352 332 334 366 C4' A A 12 OK OK 368 385 365 367 399 C4' U A 13 OK OK 401 416 398 400 429 C4' C A 14 OK OK 431 446 428 430 460 C4' C A 15 OK OK 462 477 459 461 491 C4' C A 16 OK OK 493 508 490 492 522 C4' C A 17 OK OK 524 539 521 523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 104 124 125 106 139 C5' A A 5 OK OK 138 157 158 140 172 C5' U A 6 OK OK 171 188 189 173 202 C5' U A 7 OK OK 201 218 219 203 232 C5' G A 8 OK OK 231 251 252 233 266 C5' A A 9 OK OK 265 284 285 267 299 C5' A A 10 OK OK 298 317 318 300 332 C5' A A 11 OK OK 331 350 351 333 365 C5' A A 12 OK OK 364 383 384 366 398 C5' U A 13 OK OK 397 414 415 399 428 C5' C A 14 OK OK 427 444 445 429 459 C5' C A 15 OK OK 458 475 476 460 490 C5' C A 16 OK OK 489 506 507 491 521 C5' C A 17 OK OK 520 537 538 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 75 102 103 104 135 P A A 5 distorted distorted 109 136 137 138 168 P U A 6 distorted distorted 143 169 170 171 198 P U A 7 distorted distorted 176 199 200 201 228 P G A 8 distorted distorted 206 229 230 231 262 P A A 9 distorted distorted 236 263 264 265 295 P A A 10 distorted distorted 270 296 297 298 328 P A A 11 distorted distorted 303 329 330 331 361 P A A 12 distorted distorted 336 362 363 364 394 P U A 13 distorted distorted 369 395 396 397 424 P C A 14 distorted distorted 402 425 426 427 455 P C A 15 distorted distorted 432 456 457 458 486 P C A 16 distorted distorted 463 487 488 489 517 P C A 17 distorted distorted 494 518 519 520 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