ID code: '5AY4' 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 beta 4 10 7 32 C1' G A 2 beta 27 33 30 55 C1' A A 3 beta 50 56 53 77 C1' C A 4 beta 72 78 75 97 C1' U A 5 beta 92 98 95 123 C1' CBR A 6 beta 122 111 119 137 C1' G A 7 beta 132 138 135 160 C1' A A 8 beta 155 161 158 182 C1' C A 9 beta 177 183 180 202 C1' U A 10 beta 197 203 200 222 C1' C A 11 beta 217 223 220 242 C1' C A 12 beta 237 243 240 260 C1' G B 1 beta 255 261 258 283 C1' G B 2 beta 278 284 281 306 C1' A B 3 beta 301 307 304 328 C1' C B 4 beta 323 329 326 348 C1' U B 5 beta 343 349 346 374 C1' CBR B 6 beta 373 362 370 388 C1' G B 7 beta 383 389 386 411 C1' A B 8 beta 406 412 409 433 C1' C B 9 beta 428 434 431 453 C1' U B 10 beta 448 454 451 473 C1' C B 11 beta 468 474 471 493 C1' C B 12 beta 488 494 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' G A 2 OK 32 28 31 53 C2' A A 3 OK 55 51 54 75 C2' C A 4 OK 77 73 76 95 C2' U A 5 OK 97 93 96 119 C2' CBR A 6 123 124 135 C2' G A 7 OK 137 133 136 158 C2' A A 8 OK 160 156 159 180 C2' C A 9 OK 182 178 181 200 C2' U A 10 OK 202 198 201 220 C2' C A 11 OK 222 218 221 240 C2' C A 12 OK 242 238 241 258 C2' G B 1 OK 260 256 259 281 C2' G B 2 OK 283 279 282 304 C2' A B 3 OK 306 302 305 326 C2' C B 4 OK 328 324 327 346 C2' U B 5 OK 348 344 347 370 C2' CBR B 6 374 375 386 C2' G B 7 OK 388 384 387 409 C2' A B 8 OK 411 407 410 431 C2' C B 9 OK 433 429 432 451 C2' U B 10 OK 453 449 452 471 C2' C B 11 OK 473 469 472 491 C2' C B 12 OK 493 489 492 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' A A 3 OK 49 52 53 73 C3' C A 4 OK 71 74 75 93 C3' U A 5 OK 91 94 95 124 C3' CBR A 6 OK 121 125 119 133 C3' G A 7 OK 131 134 135 156 C3' A A 8 OK 154 157 158 178 C3' C A 9 OK 176 179 180 198 C3' U A 10 OK 196 199 200 218 C3' C A 11 OK 216 219 220 238 C3' C A 12 OK 236 239 240 256 C3' G B 1 OK 254 257 258 279 C3' G B 2 OK 277 280 281 302 C3' A B 3 OK 300 303 304 324 C3' C B 4 OK 322 325 326 344 C3' U B 5 OK 342 345 346 375 C3' CBR B 6 OK 372 376 370 384 C3' G B 7 OK 382 385 386 407 C3' A B 8 OK 405 408 409 429 C3' C B 9 OK 427 430 431 449 C3' U B 10 OK 447 450 451 469 C3' C B 11 OK 467 470 471 489 C3' C B 12 OK 487 490 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' A A 3 OK 51 48 50 71 C4' C A 4 OK 73 70 72 91 C4' U A 5 OK 93 90 92 121 C4' CBR A 6 OK 124 120 122 131 C4' G A 7 OK 133 130 132 154 C4' A A 8 OK 156 153 155 176 C4' C A 9 OK 178 175 177 196 C4' U A 10 OK 198 195 197 216 C4' C A 11 OK 218 215 217 236 C4' C A 12 OK 238 235 237 254 C4' G B 1 OK 256 253 255 277 C4' G B 2 OK 279 276 278 300 C4' A B 3 OK 302 299 301 322 C4' C B 4 OK 324 321 323 342 C4' U B 5 OK 344 341 343 372 C4' CBR B 6 OK 375 371 373 382 C4' G B 7 OK 384 381 383 405 C4' A B 8 OK 407 404 406 427 C4' C B 9 OK 429 426 428 447 C4' U B 10 OK 449 446 448 467 C4' C B 11 OK 469 466 468 487 C4' C B 12 OK 489 486 488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' A A 3 47 49 70 C5' C A 4 69 71 90 C5' U A 5 89 91 120 C5' CBR A 6 110 121 130 C5' G A 7 129 131 153 C5' A A 8 152 154 175 C5' C A 9 174 176 195 C5' U A 10 194 196 215 C5' C A 11 214 216 235 C5' C A 12 234 236 253 C5' G B 1 252 254 276 C5' G B 2 275 277 299 C5' A B 3 298 300 321 C5' C B 4 320 322 341 C5' U B 5 340 342 371 C5' CBR B 6 361 372 381 C5' G B 7 380 382 404 C5' A B 8 403 405 426 C5' C B 9 425 427 446 C5' U B 10 445 447 466 C5' C B 11 465 467 486 C5' C B 12 485 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P A A 3 distorted distorted 29 45 46 47 66 P C A 4 distorted distorted 52 67 68 69 86 P U A 5 distorted distorted 74 87 88 89 107 P CBR A 6 distorted distorted 94 108 109 110 126 P G A 7 distorted distorted 125 127 128 129 149 P A A 8 distorted distorted 134 150 151 152 171 P C A 9 distorted distorted 157 172 173 174 191 P U A 10 distorted distorted 179 192 193 194 211 P C A 11 distorted distorted 199 212 213 214 231 P C A 12 distorted distorted 219 232 233 234 272 P G B 2 distorted distorted 257 273 274 275 295 P A B 3 distorted distorted 280 296 297 298 317 P C B 4 distorted distorted 303 318 319 320 337 P U B 5 distorted distorted 325 338 339 340 358 P CBR B 6 distorted distorted 345 359 360 361 377 P G B 7 distorted distorted 376 378 379 380 400 P A B 8 distorted distorted 385 401 402 403 422 P C B 9 distorted distorted 408 423 424 425 442 P U B 10 distorted distorted 430 443 444 445 462 P C B 11 distorted distorted 450 463 464 465 482 P C B 12 distorted distorted 470 483 484 485 ---------------------------------------------------------------------------------