ID code: '2ANR' 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' C B 201 beta 4 10 7 29 C1' 5BU B 202 beta 24 30 27 50 C1' C B 203 beta 45 51 48 70 C1' G B 204 beta 65 71 68 93 C1' C B 205 beta 88 94 91 113 C1' G B 206 beta 108 114 111 136 C1' G B 207 beta 131 137 134 159 C1' A B 208 beta 154 160 157 181 C1' U B 209 beta 176 182 179 201 C1' C B 210 beta 196 202 199 221 C1' A B 211 beta 216 222 219 243 C1' G B 212 beta 238 244 241 266 C1' U B 213 beta 261 267 264 286 C1' C B 214 beta 281 287 284 306 C1' A B 215 beta 301 307 304 328 C1' C B 216 beta 323 329 326 348 C1' C B 217 beta 343 349 346 368 C1' C B 218 beta 363 369 366 388 C1' A B 219 beta 383 389 386 410 C1' A B 220 beta 405 411 408 432 C1' G B 221 beta 427 433 430 455 C1' C B 222 beta 450 456 453 475 C1' G B 223 beta 470 476 473 498 C1' A B 224 beta 493 499 496 520 C1' G B 225 beta 515 521 518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C B 201 OK 9 5 8 27 C2' 5BU B 202 OK 29 25 28 48 C2' C B 203 OK 50 46 49 68 C2' G B 204 OK 70 66 69 91 C2' C B 205 OK 93 89 92 111 C2' G B 206 OK 113 109 112 134 C2' G B 207 OK 136 132 135 157 C2' A B 208 OK 159 155 158 179 C2' U B 209 OK 181 177 180 199 C2' C B 210 OK 201 197 200 219 C2' A B 211 OK 221 217 220 241 C2' G B 212 OK 243 239 242 264 C2' U B 213 OK 266 262 265 284 C2' C B 214 OK 286 282 285 304 C2' A B 215 OK 306 302 305 326 C2' C B 216 OK 328 324 327 346 C2' C B 217 OK 348 344 347 366 C2' C B 218 OK 368 364 367 386 C2' A B 219 OK 388 384 387 408 C2' A B 220 OK 410 406 409 430 C2' G B 221 OK 432 428 431 453 C2' C B 222 OK 455 451 454 473 C2' G B 223 OK 475 471 474 496 C2' A B 224 OK 498 494 497 518 C2' G B 225 OK 520 516 519 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C B 201 OK 3 6 7 25 C3' 5BU B 202 OK 23 26 27 46 C3' C B 203 OK 44 47 48 66 C3' G B 204 OK 64 67 68 89 C3' C B 205 OK 87 90 91 109 C3' G B 206 OK 107 110 111 132 C3' G B 207 OK 130 133 134 155 C3' A B 208 OK 153 156 157 177 C3' U B 209 OK 175 178 179 197 C3' C B 210 OK 195 198 199 217 C3' A B 211 OK 215 218 219 239 C3' G B 212 OK 237 240 241 262 C3' U B 213 OK 260 263 264 282 C3' C B 214 OK 280 283 284 302 C3' A B 215 OK 300 303 304 324 C3' C B 216 OK 322 325 326 344 C3' C B 217 OK 342 345 346 364 C3' C B 218 OK 362 365 366 384 C3' A B 219 OK 382 385 386 406 C3' A B 220 OK 404 407 408 428 C3' G B 221 OK 426 429 430 451 C3' C B 222 OK 449 452 453 471 C3' G B 223 OK 469 472 473 494 C3' A B 224 OK 492 495 496 516 C3' G B 225 OK 514 517 518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C B 201 OK 5 2 4 23 C4' 5BU B 202 OK 25 22 24 44 C4' C B 203 OK 46 43 45 64 C4' G B 204 OK 66 63 65 87 C4' C B 205 OK 89 86 88 107 C4' G B 206 OK 109 106 108 130 C4' G B 207 OK 132 129 131 153 C4' A B 208 OK 155 152 154 175 C4' U B 209 OK 177 174 176 195 C4' C B 210 OK 197 194 196 215 C4' A B 211 OK 217 214 216 237 C4' G B 212 OK 239 236 238 260 C4' U B 213 OK 262 259 261 280 C4' C B 214 OK 282 279 281 300 C4' A B 215 OK 302 299 301 322 C4' C B 216 OK 324 321 323 342 C4' C B 217 OK 344 341 343 362 C4' C B 218 OK 364 361 363 382 C4' A B 219 OK 384 381 383 404 C4' A B 220 OK 406 403 405 426 C4' G B 221 OK 428 425 427 449 C4' C B 222 OK 451 448 450 469 C4' G B 223 OK 471 468 470 492 C4' A B 224 OK 494 491 493 514 C4' G B 225 OK 516 513 515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C B 201 1 3 22 C5' 5BU B 202 21 23 43 C5' C B 203 42 44 63 C5' G B 204 62 64 86 C5' C B 205 85 87 106 C5' G B 206 105 107 129 C5' G B 207 128 130 152 C5' A B 208 151 153 174 C5' U B 209 173 175 194 C5' C B 210 193 195 214 C5' A B 211 213 215 236 C5' G B 212 235 237 259 C5' U B 213 258 260 279 C5' C B 214 278 280 299 C5' A B 215 298 300 321 C5' C B 216 320 322 341 C5' C B 217 340 342 361 C5' C B 218 360 362 381 C5' A B 219 380 382 403 C5' A B 220 402 404 425 C5' G B 221 424 426 448 C5' C B 222 447 449 468 C5' G B 223 467 469 491 C5' A B 224 490 492 513 C5' G B 225 512 514 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P 5BU B 202 distorted distorted 6 19 20 21 39 P C B 203 distorted distorted 26 40 41 42 59 P G B 204 distorted distorted 47 60 61 62 82 P C B 205 distorted distorted 67 83 84 85 102 P G B 206 distorted distorted 90 103 104 105 125 P G B 207 distorted distorted 110 126 127 128 148 P A B 208 distorted distorted 133 149 150 151 170 P U B 209 distorted distorted 156 171 172 173 190 P C B 210 distorted distorted 178 191 192 193 210 P A B 211 distorted distorted 198 211 212 213 232 P G B 212 distorted distorted 218 233 234 235 255 P U B 213 distorted distorted 240 256 257 258 275 P C B 214 distorted distorted 263 276 277 278 295 P A B 215 distorted distorted 283 296 297 298 317 P C B 216 distorted distorted 303 318 319 320 337 P C B 217 distorted distorted 325 338 339 340 357 P C B 218 distorted distorted 345 358 359 360 377 P A B 219 distorted distorted 365 378 379 380 399 P A B 220 distorted distorted 385 400 401 402 421 P G B 221 distorted distorted 407 422 423 424 444 P C B 222 distorted distorted 429 445 446 447 464 P G B 223 distorted distorted 452 465 466 467 487 P A B 224 distorted distorted 472 488 489 490 509 P G B 225 distorted distorted 495 510 511 512 ---------------------------------------------------------------------------------