ID code: '1JTW' 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' U A 4 alpha beta 107 127 113 110 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' A A 8 alpha beta 236 258 242 239 274 C1' G A 9 alpha beta 269 292 275 272 308 C1' A A 10 alpha beta 303 325 309 306 341 C1' G A 11 alpha beta 336 359 342 339 375 C1' C A 12 alpha beta 370 390 376 373 406 C1' G A 13 alpha beta 401 424 407 404 440 C1' U A 14 alpha beta 435 455 441 438 470 C1' C A 15 alpha beta 465 485 471 468 501 C1' A A 16 alpha beta 496 519 502 499 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 4 OK OK 112 108 125 111 140 C2' G A 5 OK OK 142 138 158 141 174 C2' C A 6 OK OK 176 172 189 175 205 C2' G A 7 OK OK 207 203 223 206 239 C2' A A 8 OK OK 241 237 256 240 272 C2' G A 9 OK OK 274 270 290 273 306 C2' A A 10 OK OK 308 304 323 307 339 C2' G A 11 OK OK 341 337 357 340 373 C2' C A 12 OK OK 375 371 388 374 404 C2' G A 13 OK OK 406 402 422 405 438 C2' U A 14 OK OK 440 436 453 439 468 C2' C A 15 OK OK 470 466 483 469 499 C2' A A 16 OK OK 501 497 517 500 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 106 124 109 110 138 C3' G A 5 OK OK 136 157 139 140 172 C3' C A 6 OK OK 170 188 173 174 203 C3' G A 7 OK OK 201 222 204 205 237 C3' A A 8 OK OK 235 255 238 239 270 C3' G A 9 OK OK 268 289 271 272 304 C3' A A 10 OK OK 302 322 305 306 337 C3' G A 11 OK OK 335 356 338 339 371 C3' C A 12 OK OK 369 387 372 373 402 C3' G A 13 OK OK 400 421 403 404 436 C3' U A 14 OK OK 434 452 437 438 466 C3' C A 15 OK OK 464 482 467 468 497 C3' A A 16 OK OK 495 515 498 499 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 108 123 105 107 136 C4' G A 5 OK OK 138 156 135 137 170 C4' C A 6 OK OK 172 187 169 171 201 C4' G A 7 OK OK 203 221 200 202 235 C4' A A 8 OK OK 237 254 234 236 268 C4' G A 9 OK OK 270 288 267 269 302 C4' A A 10 OK OK 304 321 301 303 335 C4' G A 11 OK OK 337 355 334 336 369 C4' C A 12 OK OK 371 386 368 370 400 C4' G A 13 OK OK 402 420 399 401 434 C4' U A 14 OK OK 436 451 433 435 464 C4' C A 15 OK OK 466 481 463 465 495 C4' A A 16 OK OK 497 514 494 496 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 104 121 122 106 135 C5' G A 5 OK OK 134 154 155 136 169 C5' C A 6 OK OK 168 185 186 170 200 C5' G A 7 OK OK 199 219 220 201 234 C5' A A 8 OK OK 233 252 253 235 267 C5' G A 9 OK OK 266 286 287 268 301 C5' A A 10 OK OK 300 319 320 302 334 C5' G A 11 OK OK 333 353 354 335 368 C5' C A 12 OK OK 367 384 385 369 399 C5' G A 13 OK OK 398 418 419 400 433 C5' U A 14 OK OK 432 449 450 434 463 C5' C A 15 OK OK 462 479 480 464 494 C5' A A 16 OK OK 493 512 513 495 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 4 distorted distorted 75 102 103 104 131 P G A 5 distorted distorted 109 132 133 134 165 P C A 6 distorted distorted 139 166 167 168 196 P G A 7 distorted distorted 173 197 198 199 230 P A A 8 distorted distorted 204 231 232 233 263 P G A 9 distorted distorted 238 264 265 266 297 P A A 10 distorted distorted 271 298 299 300 330 P G A 11 distorted distorted 305 331 332 333 364 P C A 12 distorted distorted 338 365 366 367 395 P G A 13 distorted distorted 372 396 397 398 429 P U A 14 distorted distorted 403 430 431 432 459 P C A 15 distorted distorted 437 460 461 462 490 P A A 16 distorted distorted 467 491 492 493 ---------------------------------------------------------------------------------