ID code: '4E58' 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 C 1 beta 4 10 7 32 C1' C C 2 beta 27 33 30 52 C1' C C 3 beta 47 53 50 76 C1' LCG C 4 beta 79 67 73 96 C1' C C 5 beta 91 97 94 116 C1' C C 6 beta 111 117 114 136 C1' G C 7 beta 131 137 134 159 C1' C C 8 beta 154 160 157 177 C1' G E 1 beta 172 178 175 200 C1' C E 2 beta 195 201 198 220 C1' C E 3 beta 215 221 218 244 C1' LCG E 4 beta 247 235 241 264 C1' C E 5 beta 259 265 262 284 C1' C E 6 beta 279 285 282 304 C1' G E 7 beta 299 305 302 330 C1' G D 1 beta 325 331 328 353 C1' C D 2 beta 348 354 351 373 C1' C D 3 beta 368 374 371 397 C1' LCG D 4 beta 400 388 394 417 C1' C D 5 beta 412 418 415 437 C1' C D 6 beta 432 438 435 457 C1' G D 7 beta 452 458 455 480 C1' C D 8 beta 475 481 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 1 OK 9 5 8 30 C2' C C 2 OK 32 28 31 50 C2' C C 3 OK 52 48 51 73 C2' LCG C 4 OK 76 65 83 94 C2' C C 5 OK 96 92 95 114 C2' C C 6 OK 116 112 115 134 C2' G C 7 OK 136 132 135 157 C2' C C 8 OK 159 155 158 175 C2' G E 1 OK 177 173 176 198 C2' C E 2 OK 200 196 199 218 C2' C E 3 OK 220 216 219 241 C2' LCG E 4 OK 244 233 251 262 C2' C E 5 OK 264 260 263 282 C2' C E 6 OK 284 280 283 302 C2' G E 7 OK 304 300 303 328 C2' G D 1 OK 330 326 329 351 C2' C D 2 OK 353 349 352 371 C2' C D 3 OK 373 369 372 394 C2' LCG D 4 OK 397 386 404 415 C2' C D 5 OK 417 413 416 435 C2' C D 6 OK 437 433 436 455 C2' G D 7 OK 457 453 456 478 C2' C D 8 OK 480 476 479 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 1 OK 3 6 7 28 C3' C C 2 OK 26 29 30 48 C3' C C 3 OK 46 49 50 65 C3' LCG C 4 OK 75 84 73 92 C3' C C 5 OK 90 93 94 112 C3' C C 6 OK 110 113 114 132 C3' G C 7 OK 130 133 134 155 C3' C C 8 OK 153 156 157 173 C3' G E 1 OK 171 174 175 196 C3' C E 2 OK 194 197 198 216 C3' C E 3 OK 214 217 218 233 C3' LCG E 4 OK 243 252 241 260 C3' C E 5 OK 258 261 262 280 C3' C E 6 OK 278 281 282 300 C3' G E 7 OK 298 301 302 326 C3' G D 1 OK 324 327 328 349 C3' C D 2 OK 347 350 351 369 C3' C D 3 OK 367 370 371 386 C3' LCG D 4 OK 396 405 394 413 C3' C D 5 OK 411 414 415 433 C3' C D 6 OK 431 434 435 453 C3' G D 7 OK 451 454 455 476 C3' C D 8 OK 474 477 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 1 OK 5 2 4 26 C4' C C 2 OK 28 25 27 46 C4' C C 3 OK 48 45 47 75 C4' LCG C 4 OK 65 64 79 90 C4' C C 5 OK 92 89 91 110 C4' C C 6 OK 112 109 111 130 C4' G C 7 OK 132 129 131 153 C4' C C 8 OK 155 152 154 171 C4' G E 1 OK 173 170 172 194 C4' C E 2 OK 196 193 195 214 C4' C E 3 OK 216 213 215 243 C4' LCG E 4 OK 233 232 247 258 C4' C E 5 OK 260 257 259 278 C4' C E 6 OK 280 277 279 298 C4' G E 7 OK 300 297 299 324 C4' G D 1 OK 326 323 325 347 C4' C D 2 OK 349 346 348 367 C4' C D 3 OK 369 366 368 396 C4' LCG D 4 OK 386 385 400 411 C4' C D 5 OK 413 410 412 431 C4' C D 6 OK 433 430 432 451 C4' G D 7 OK 453 450 452 474 C4' C D 8 OK 476 473 475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 1 1 3 25 C5' C C 2 24 26 45 C5' C C 3 44 46 64 C5' LCG C 4 63 75 89 C5' C C 5 88 90 109 C5' C C 6 108 110 129 C5' G C 7 128 130 152 C5' C C 8 151 153 170 C5' G E 1 169 171 193 C5' C E 2 192 194 213 C5' C E 3 212 214 232 C5' LCG E 4 231 243 257 C5' C E 5 256 258 277 C5' C E 6 276 278 297 C5' G E 7 296 298 320 C5' C E 8 319 323 C5' G D 1 322 324 346 C5' C D 2 345 347 366 C5' C D 3 365 367 385 C5' LCG D 4 384 396 410 C5' C D 5 409 411 430 C5' C D 6 429 431 450 C5' G D 7 449 451 473 C5' C D 8 472 474 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C C 2 distorted distorted 6 22 23 24 41 P C C 3 distorted distorted 29 42 43 44 61 P LCG C 4 OK OK 49 62 80 63 85 P C C 5 distorted distorted 84 86 87 88 105 P C C 6 distorted distorted 93 106 107 108 125 P G C 7 distorted distorted 113 126 127 128 148 P C C 8 distorted distorted 133 149 150 151 189 P C E 2 distorted distorted 174 190 191 192 209 P C E 3 distorted distorted 197 210 211 212 229 P LCG E 4 OK OK 217 230 248 231 253 P C E 5 distorted distorted 252 254 255 256 273 P C E 6 distorted distorted 261 274 275 276 293 P G E 7 distorted distorted 281 294 295 296 316 P C E 8 distorted distorted 301 317 318 319 342 P C D 2 distorted distorted 327 343 344 345 362 P C D 3 distorted distorted 350 363 364 365 382 P LCG D 4 OK OK 370 383 401 384 406 P C D 5 distorted distorted 405 407 408 409 426 P C D 6 distorted distorted 414 427 428 429 446 P G D 7 distorted distorted 434 447 448 449 469 P C D 8 distorted distorted 454 470 471 472 ---------------------------------------------------------------------------------