ID code: '2PY9' 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' A E 1 beta 4 10 7 31 C1' A E 2 beta 26 32 29 53 C1' C E 3 beta 48 54 51 73 C1' C E 4 beta 68 74 71 93 C1' C E 5 beta 88 94 91 113 C1' U E 6 beta 108 114 111 133 C1' A E 7 beta 128 134 131 155 C1' A E 8 beta 150 156 153 177 C1' C E 9 beta 172 178 175 197 C1' C E 10 beta 192 198 195 217 C1' C E 11 beta 212 218 215 237 C1' U E 12 beta 232 238 235 255 C1' A F 1 beta 250 256 253 277 C1' A F 2 beta 272 278 275 299 C1' C F 3 beta 294 300 297 319 C1' C F 4 beta 314 320 317 339 C1' C F 5 beta 334 340 337 359 C1' U F 6 beta 354 360 357 379 C1' A F 7 beta 374 380 377 401 C1' A F 8 beta 396 402 399 423 C1' C F 9 beta 418 424 421 443 C1' C F 10 beta 438 444 441 463 C1' C F 11 beta 458 464 461 483 C1' U F 12 beta 478 484 481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A E 1 OK 9 5 8 29 C2' A E 2 OK 31 27 30 51 C2' C E 3 OK 53 49 52 71 C2' C E 4 OK 73 69 72 91 C2' C E 5 OK 93 89 92 111 C2' U E 6 OK 113 109 112 131 C2' A E 7 OK 133 129 132 153 C2' A E 8 OK 155 151 154 175 C2' C E 9 OK 177 173 176 195 C2' C E 10 OK 197 193 196 215 C2' C E 11 OK 217 213 216 235 C2' U E 12 OK 237 233 236 253 C2' A F 1 OK 255 251 254 275 C2' A F 2 OK 277 273 276 297 C2' C F 3 OK 299 295 298 317 C2' C F 4 OK 319 315 318 337 C2' C F 5 OK 339 335 338 357 C2' U F 6 OK 359 355 358 377 C2' A F 7 OK 379 375 378 399 C2' A F 8 OK 401 397 400 421 C2' C F 9 OK 423 419 422 441 C2' C F 10 OK 443 439 442 461 C2' C F 11 OK 463 459 462 481 C2' U F 12 OK 483 479 482 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A E 1 OK 3 6 7 27 C3' A E 2 OK 25 28 29 49 C3' C E 3 OK 47 50 51 69 C3' C E 4 OK 67 70 71 89 C3' C E 5 OK 87 90 91 109 C3' U E 6 OK 107 110 111 129 C3' A E 7 OK 127 130 131 151 C3' A E 8 OK 149 152 153 173 C3' C E 9 OK 171 174 175 193 C3' C E 10 OK 191 194 195 213 C3' C E 11 OK 211 214 215 233 C3' U E 12 OK 231 234 235 251 C3' A F 1 OK 249 252 253 273 C3' A F 2 OK 271 274 275 295 C3' C F 3 OK 293 296 297 315 C3' C F 4 OK 313 316 317 335 C3' C F 5 OK 333 336 337 355 C3' U F 6 OK 353 356 357 375 C3' A F 7 OK 373 376 377 397 C3' A F 8 OK 395 398 399 419 C3' C F 9 OK 417 420 421 439 C3' C F 10 OK 437 440 441 459 C3' C F 11 OK 457 460 461 479 C3' U F 12 OK 477 480 481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A E 1 OK 5 2 4 25 C4' A E 2 OK 27 24 26 47 C4' C E 3 OK 49 46 48 67 C4' C E 4 OK 69 66 68 87 C4' C E 5 OK 89 86 88 107 C4' U E 6 OK 109 106 108 127 C4' A E 7 OK 129 126 128 149 C4' A E 8 OK 151 148 150 171 C4' C E 9 OK 173 170 172 191 C4' C E 10 OK 193 190 192 211 C4' C E 11 OK 213 210 212 231 C4' U E 12 OK 233 230 232 249 C4' A F 1 OK 251 248 250 271 C4' A F 2 OK 273 270 272 293 C4' C F 3 OK 295 292 294 313 C4' C F 4 OK 315 312 314 333 C4' C F 5 OK 335 332 334 353 C4' U F 6 OK 355 352 354 373 C4' A F 7 OK 375 372 374 395 C4' A F 8 OK 397 394 396 417 C4' C F 9 OK 419 416 418 437 C4' C F 10 OK 439 436 438 457 C4' C F 11 OK 459 456 458 477 C4' U F 12 OK 479 476 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A E 1 1 3 24 C5' A E 2 23 25 46 C5' C E 3 45 47 66 C5' C E 4 65 67 86 C5' C E 5 85 87 106 C5' U E 6 105 107 126 C5' A E 7 125 127 148 C5' A E 8 147 149 170 C5' C E 9 169 171 190 C5' C E 10 189 191 210 C5' C E 11 209 211 230 C5' U E 12 229 231 248 C5' A F 1 247 249 270 C5' A F 2 269 271 292 C5' C F 3 291 293 312 C5' C F 4 311 313 332 C5' C F 5 331 333 352 C5' U F 6 351 353 372 C5' A F 7 371 373 394 C5' A F 8 393 395 416 C5' C F 9 415 417 436 C5' C F 10 435 437 456 C5' C F 11 455 457 476 C5' U F 12 475 477 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A E 2 distorted distorted 6 21 22 23 42 P C E 3 distorted distorted 28 43 44 45 62 P C E 4 distorted distorted 50 63 64 65 82 P C E 5 distorted distorted 70 83 84 85 102 P U E 6 distorted distorted 90 103 104 105 122 P A E 7 distorted distorted 110 123 124 125 144 P A E 8 distorted distorted 130 145 146 147 166 P C E 9 distorted distorted 152 167 168 169 186 P C E 10 distorted distorted 174 187 188 189 206 P C E 11 distorted distorted 194 207 208 209 226 P U E 12 distorted distorted 214 227 228 229 266 P A F 2 distorted distorted 252 267 268 269 288 P C F 3 distorted distorted 274 289 290 291 308 P C F 4 distorted distorted 296 309 310 311 328 P C F 5 distorted distorted 316 329 330 331 348 P U F 6 distorted distorted 336 349 350 351 368 P A F 7 distorted distorted 356 369 370 371 390 P A F 8 distorted distorted 376 391 392 393 412 P C F 9 distorted distorted 398 413 414 415 432 P C F 10 distorted distorted 420 433 434 435 452 P C F 11 distorted distorted 440 453 454 455 472 P U F 12 distorted distorted 460 473 474 475 ---------------------------------------------------------------------------------