ID code: '2ANN' 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' --------------------------------------------------------------------------------- 12 C1' C B 3 beta 7 13 10 32 C1' G B 4 beta 27 33 30 55 C1' C B 5 beta 50 56 53 75 C1' G B 6 beta 70 76 73 98 C1' G B 7 beta 93 99 96 121 C1' A B 8 beta 116 122 119 143 C1' U B 9 beta 138 144 141 163 C1' C B 10 beta 158 164 161 183 C1' A B 11 beta 178 184 181 205 C1' G B 12 beta 200 206 203 228 C1' U B 13 beta 223 229 226 248 C1' C B 14 beta 243 249 246 268 C1' A B 15 beta 263 269 266 290 C1' C B 16 beta 285 291 288 310 C1' C B 17 beta 305 311 308 330 C1' C B 18 beta 325 331 328 350 C1' A B 19 beta 345 351 348 372 C1' A B 20 beta 367 373 370 394 C1' G B 21 beta 389 395 392 417 C1' C B 22 beta 412 418 415 437 C1' G B 23 beta 432 438 435 460 C1' C B 24 beta 455 461 458 480 C1' G B 25 beta 475 481 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C B 3 OK 12 8 11 30 C2' G B 4 OK 32 28 31 53 C2' C B 5 OK 55 51 54 73 C2' G B 6 OK 75 71 74 96 C2' G B 7 OK 98 94 97 119 C2' A B 8 OK 121 117 120 141 C2' U B 9 OK 143 139 142 161 C2' C B 10 OK 163 159 162 181 C2' A B 11 OK 183 179 182 203 C2' G B 12 OK 205 201 204 226 C2' U B 13 OK 228 224 227 246 C2' C B 14 OK 248 244 247 266 C2' A B 15 OK 268 264 267 288 C2' C B 16 OK 290 286 289 308 C2' C B 17 OK 310 306 309 328 C2' C B 18 OK 330 326 329 348 C2' A B 19 OK 350 346 349 370 C2' A B 20 OK 372 368 371 392 C2' G B 21 OK 394 390 393 415 C2' C B 22 OK 417 413 416 435 C2' G B 23 OK 437 433 436 458 C2' C B 24 OK 460 456 459 478 C2' G B 25 OK 480 476 479 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C B 3 OK 6 9 10 28 C3' G B 4 OK 26 29 30 51 C3' C B 5 OK 49 52 53 71 C3' G B 6 OK 69 72 73 94 C3' G B 7 OK 92 95 96 117 C3' A B 8 OK 115 118 119 139 C3' U B 9 OK 137 140 141 159 C3' C B 10 OK 157 160 161 179 C3' A B 11 OK 177 180 181 201 C3' G B 12 OK 199 202 203 224 C3' U B 13 OK 222 225 226 244 C3' C B 14 OK 242 245 246 264 C3' A B 15 OK 262 265 266 286 C3' C B 16 OK 284 287 288 306 C3' C B 17 OK 304 307 308 326 C3' C B 18 OK 324 327 328 346 C3' A B 19 OK 344 347 348 368 C3' A B 20 OK 366 369 370 390 C3' G B 21 OK 388 391 392 413 C3' C B 22 OK 411 414 415 433 C3' G B 23 OK 431 434 435 456 C3' C B 24 OK 454 457 458 476 C3' G B 25 OK 474 477 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C B 3 OK 8 5 7 26 C4' G B 4 OK 28 25 27 49 C4' C B 5 OK 51 48 50 69 C4' G B 6 OK 71 68 70 92 C4' G B 7 OK 94 91 93 115 C4' A B 8 OK 117 114 116 137 C4' U B 9 OK 139 136 138 157 C4' C B 10 OK 159 156 158 177 C4' A B 11 OK 179 176 178 199 C4' G B 12 OK 201 198 200 222 C4' U B 13 OK 224 221 223 242 C4' C B 14 OK 244 241 243 262 C4' A B 15 OK 264 261 263 284 C4' C B 16 OK 286 283 285 304 C4' C B 17 OK 306 303 305 324 C4' C B 18 OK 326 323 325 344 C4' A B 19 OK 346 343 345 366 C4' A B 20 OK 368 365 367 388 C4' G B 21 OK 390 387 389 411 C4' C B 22 OK 413 410 412 431 C4' G B 23 OK 433 430 432 454 C4' C B 24 OK 456 453 455 474 C4' G B 25 OK 476 473 475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C B 3 4 6 25 C5' G B 4 24 26 48 C5' C B 5 47 49 68 C5' G B 6 67 69 91 C5' G B 7 90 92 114 C5' A B 8 113 115 136 C5' U B 9 135 137 156 C5' C B 10 155 157 176 C5' A B 11 175 177 198 C5' G B 12 197 199 221 C5' U B 13 220 222 241 C5' C B 14 240 242 261 C5' A B 15 260 262 283 C5' C B 16 282 284 303 C5' C B 17 302 304 323 C5' C B 18 322 324 343 C5' A B 19 342 344 365 C5' A B 20 364 366 387 C5' G B 21 386 388 410 C5' C B 22 409 411 430 C5' G B 23 429 431 453 C5' C B 24 452 454 473 C5' G B 25 472 474 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C B 3 distorted distorted 2 3 4 21 P G B 4 distorted distorted 9 22 23 24 44 P C B 5 distorted distorted 29 45 46 47 64 P G B 6 distorted distorted 52 65 66 67 87 P G B 7 distorted distorted 72 88 89 90 110 P A B 8 distorted distorted 95 111 112 113 132 P U B 9 distorted distorted 118 133 134 135 152 P C B 10 distorted distorted 140 153 154 155 172 P A B 11 distorted distorted 160 173 174 175 194 P G B 12 distorted distorted 180 195 196 197 217 P U B 13 distorted distorted 202 218 219 220 237 P C B 14 distorted distorted 225 238 239 240 257 P A B 15 distorted distorted 245 258 259 260 279 P C B 16 distorted distorted 265 280 281 282 299 P C B 17 distorted distorted 287 300 301 302 319 P C B 18 distorted distorted 307 320 321 322 339 P A B 19 distorted distorted 327 340 341 342 361 P A B 20 distorted distorted 347 362 363 364 383 P G B 21 distorted distorted 369 384 385 386 406 P C B 22 distorted distorted 391 407 408 409 426 P G B 23 distorted distorted 414 427 428 429 449 P C B 24 distorted distorted 434 450 451 452 469 P G B 25 distorted distorted 457 470 471 472 ---------------------------------------------------------------------------------