ID code: '1IKD' 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' G A 3 beta 50 56 53 78 C1' G A 4 beta 73 79 76 101 C1' C A 5 beta 96 102 99 121 C1' U A 6 beta 116 122 119 141 C1' C A 7 beta 136 142 139 161 C1' U A 8 beta 156 162 159 181 C1' U A 9 beta 176 182 179 201 C1' C A 10 beta 196 202 199 221 C1' G A 11 beta 216 222 219 244 C1' G A 12 beta 239 245 242 267 C1' A A 13 beta 262 268 265 289 C1' G A 14 beta 284 290 287 312 C1' C A 15 beta 307 313 310 332 C1' U A 16 beta 327 333 330 352 C1' C A 17 beta 347 353 350 372 C1' C A 18 beta 367 373 370 392 C1' A A 19 beta 387 393 390 414 C1' C A 20 beta 409 415 412 434 C1' C A 21 beta 429 435 432 454 C1' A A 22 beta 449 455 452 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK 55 51 54 76 C2' G A 4 OK 78 74 77 99 C2' C A 5 OK 101 97 100 119 C2' U A 6 OK 121 117 120 139 C2' C A 7 OK 141 137 140 159 C2' U A 8 OK 161 157 160 179 C2' U A 9 OK 181 177 180 199 C2' C A 10 OK 201 197 200 219 C2' G A 11 OK 221 217 220 242 C2' G A 12 OK 244 240 243 265 C2' A A 13 OK 267 263 266 287 C2' G A 14 OK 289 285 288 310 C2' C A 15 OK 312 308 311 330 C2' U A 16 OK 332 328 331 350 C2' C A 17 OK 352 348 351 370 C2' C A 18 OK 372 368 371 390 C2' A A 19 OK 392 388 391 412 C2' C A 20 OK 414 410 413 432 C2' C A 21 OK 434 430 433 452 C2' A A 22 OK 454 450 453 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK 49 52 53 74 C3' G A 4 OK 72 75 76 97 C3' C A 5 OK 95 98 99 117 C3' U A 6 OK 115 118 119 137 C3' C A 7 OK 135 138 139 157 C3' U A 8 OK 155 158 159 177 C3' U A 9 OK 175 178 179 197 C3' C A 10 OK 195 198 199 217 C3' G A 11 OK 215 218 219 240 C3' G A 12 OK 238 241 242 263 C3' A A 13 OK 261 264 265 285 C3' G A 14 OK 283 286 287 308 C3' C A 15 OK 306 309 310 328 C3' U A 16 OK 326 329 330 348 C3' C A 17 OK 346 349 350 368 C3' C A 18 OK 366 369 370 388 C3' A A 19 OK 386 389 390 410 C3' C A 20 OK 408 411 412 430 C3' C A 21 OK 428 431 432 450 C3' A A 22 OK 448 451 452 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK 51 48 50 72 C4' G A 4 OK 74 71 73 95 C4' C A 5 OK 97 94 96 115 C4' U A 6 OK 117 114 116 135 C4' C A 7 OK 137 134 136 155 C4' U A 8 OK 157 154 156 175 C4' U A 9 OK 177 174 176 195 C4' C A 10 OK 197 194 196 215 C4' G A 11 OK 217 214 216 238 C4' G A 12 OK 240 237 239 261 C4' A A 13 OK 263 260 262 283 C4' G A 14 OK 285 282 284 306 C4' C A 15 OK 308 305 307 326 C4' U A 16 OK 328 325 327 346 C4' C A 17 OK 348 345 347 366 C4' C A 18 OK 368 365 367 386 C4' A A 19 OK 388 385 387 408 C4' C A 20 OK 410 407 409 428 C4' C A 21 OK 430 427 429 448 C4' A A 22 OK 450 447 449 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 47 49 71 C5' G A 4 70 72 94 C5' C A 5 93 95 114 C5' U A 6 113 115 134 C5' C A 7 133 135 154 C5' U A 8 153 155 174 C5' U A 9 173 175 194 C5' C A 10 193 195 214 C5' G A 11 213 215 237 C5' G A 12 236 238 260 C5' A A 13 259 261 282 C5' G A 14 281 283 305 C5' C A 15 304 306 325 C5' U A 16 324 326 345 C5' C A 17 344 346 365 C5' C A 18 364 366 385 C5' A A 19 384 386 407 C5' C A 20 406 408 427 C5' C A 21 426 428 447 C5' A A 22 446 448 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P G A 3 distorted distorted 29 45 46 47 67 P G A 4 distorted distorted 52 68 69 70 90 P C A 5 distorted distorted 75 91 92 93 110 P U A 6 distorted distorted 98 111 112 113 130 P C A 7 distorted distorted 118 131 132 133 150 P U A 8 distorted distorted 138 151 152 153 170 P U A 9 distorted distorted 158 171 172 173 190 P C A 10 distorted distorted 178 191 192 193 210 P G A 11 distorted distorted 198 211 212 213 233 P G A 12 distorted distorted 218 234 235 236 256 P A A 13 distorted distorted 241 257 258 259 278 P G A 14 distorted distorted 264 279 280 281 301 P C A 15 distorted distorted 286 302 303 304 321 P U A 16 distorted distorted 309 322 323 324 341 P C A 17 distorted distorted 329 342 343 344 361 P C A 18 distorted distorted 349 362 363 364 381 P A A 19 distorted distorted 369 382 383 384 403 P C A 20 distorted distorted 389 404 405 406 423 P C A 21 distorted distorted 411 424 425 426 443 P A A 22 distorted distorted 431 444 445 446 ---------------------------------------------------------------------------------