ID code: '4U3R' 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' U A 1 alpha beta 4 24 10 7 40 C1' C A 2 alpha beta 35 55 41 38 71 C1' G A 3 alpha beta 66 89 72 69 105 C1' U A 4 alpha beta 100 120 106 103 135 C1' A A 5 alpha beta 130 152 136 133 168 C1' C A 6 alpha beta 163 183 169 166 199 C1' G A 7 alpha beta 194 217 200 197 233 C1' A A 8 alpha beta 228 251 234 231 265 C1' U B 1 alpha beta 260 280 266 263 296 C1' C B 2 alpha beta 291 311 297 294 327 C1' G B 3 alpha beta 322 345 328 325 361 C1' U B 4 alpha beta 356 376 362 359 391 C1' A B 5 alpha beta 386 408 392 389 424 C1' C B 6 alpha beta 419 439 425 422 455 C1' G B 7 alpha beta 450 473 456 453 489 C1' A B 8 alpha beta 484 507 490 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK OK 9 5 22 8 38 C2' C A 2 OK OK 40 36 53 39 69 C2' G A 3 OK OK 71 67 87 70 103 C2' U A 4 OK OK 105 101 118 104 133 C2' A A 5 OK OK 135 131 150 134 166 C2' C A 6 OK OK 168 164 181 167 197 C2' G A 7 OK OK 199 195 215 198 231 C2' A A 8 OK OK 233 229 249 232 263 C2' U B 1 OK OK 265 261 278 264 294 C2' C B 2 OK OK 296 292 309 295 325 C2' G B 3 OK OK 327 323 343 326 359 C2' U B 4 OK OK 361 357 374 360 389 C2' A B 5 OK OK 391 387 406 390 422 C2' C B 6 OK OK 424 420 437 423 453 C2' G B 7 OK OK 455 451 471 454 487 C2' A B 8 OK OK 489 485 505 488 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK OK 3 21 6 7 36 C3' C A 2 OK OK 34 52 37 38 67 C3' G A 3 OK OK 65 86 68 69 101 C3' U A 4 OK OK 99 117 102 103 131 C3' A A 5 OK OK 129 149 132 133 164 C3' C A 6 OK OK 162 180 165 166 195 C3' G A 7 OK OK 193 214 196 197 229 C3' A A 8 OK OK 227 247 230 231 261 C3' U B 1 OK OK 259 277 262 263 292 C3' C B 2 OK OK 290 308 293 294 323 C3' G B 3 OK OK 321 342 324 325 357 C3' U B 4 OK OK 355 373 358 359 387 C3' A B 5 OK OK 385 405 388 389 420 C3' C B 6 OK OK 418 436 421 422 451 C3' G B 7 OK OK 449 470 452 453 485 C3' A B 8 OK OK 483 503 486 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK OK 5 20 2 4 34 C4' C A 2 OK OK 36 51 33 35 65 C4' G A 3 OK OK 67 85 64 66 99 C4' U A 4 OK OK 101 116 98 100 129 C4' A A 5 OK OK 131 148 128 130 162 C4' C A 6 OK OK 164 179 161 163 193 C4' G A 7 OK OK 195 213 192 194 227 C4' A A 8 OK OK 229 246 226 228 259 C4' U B 1 OK OK 261 276 258 260 290 C4' C B 2 OK OK 292 307 289 291 321 C4' G B 3 OK OK 323 341 320 322 355 C4' U B 4 OK OK 357 372 354 356 385 C4' A B 5 OK OK 387 404 384 386 418 C4' C B 6 OK OK 420 435 417 419 449 C4' G B 7 OK OK 451 469 448 450 483 C4' A B 8 OK OK 485 502 482 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 OK OK 1 18 19 3 33 C5' C A 2 OK OK 32 49 50 34 64 C5' G A 3 OK OK 63 83 84 65 98 C5' U A 4 OK OK 97 114 115 99 128 C5' A A 5 OK OK 127 146 147 129 161 C5' C A 6 OK OK 160 177 178 162 192 C5' G A 7 OK OK 191 211 212 193 226 C5' A A 8 OK OK 225 244 245 227 258 C5' U B 1 OK OK 257 274 275 259 289 C5' C B 2 OK OK 288 305 306 290 320 C5' G B 3 OK OK 319 339 340 321 354 C5' U B 4 OK OK 353 370 371 355 384 C5' A B 5 OK OK 383 402 403 385 417 C5' C B 6 OK OK 416 433 434 418 448 C5' G B 7 OK OK 447 467 468 449 482 C5' A B 8 OK OK 481 500 501 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P C A 2 distorted distorted 6 30 31 32 60 P G A 3 distorted distorted 37 61 62 63 94 P U A 4 distorted distorted 68 95 96 97 124 P A A 5 distorted distorted 102 125 126 127 157 P C A 6 distorted distorted 132 158 159 160 188 P G A 7 distorted distorted 165 189 190 191 222 P A A 8 distorted distorted 196 223 224 225 285 P C B 2 distorted distorted 262 286 287 288 316 P G B 3 distorted distorted 293 317 318 319 350 P U B 4 distorted distorted 324 351 352 353 380 P A B 5 distorted distorted 358 381 382 383 413 P C B 6 distorted distorted 388 414 415 416 444 P G B 7 distorted distorted 421 445 446 447 478 P A B 8 distorted distorted 452 479 480 481 ---------------------------------------------------------------------------------