ID code: '2R22' 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' C A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' U A 4 beta 70 76 73 95 C1' U A 5 beta 90 96 93 115 C1' U A 6 beta 110 116 113 135 C1' G A 7 beta 130 136 133 158 C1' A A 8 beta 153 159 156 180 C1' A A 9 beta 175 181 178 202 C1' A A 10 beta 197 203 200 224 C1' C A 11 beta 219 225 222 244 C1' G A 12 beta 239 245 242 267 C1' C A 13 beta 262 268 265 285 C1' G B 14 beta 280 286 283 308 C1' C B 15 beta 303 309 306 328 C1' G B 16 beta 323 329 326 351 C1' U B 17 beta 346 352 349 371 C1' U B 18 beta 366 372 369 391 C1' U B 19 beta 386 392 389 411 C1' G B 20 beta 406 412 409 434 C1' A B 21 beta 429 435 432 456 C1' A B 22 beta 451 457 454 478 C1' A B 23 beta 473 479 476 500 C1' C B 24 beta 495 501 498 520 C1' G B 25 beta 515 521 518 543 C1' C B 26 beta 538 544 541 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' U A 4 OK 75 71 74 93 C2' U A 5 OK 95 91 94 113 C2' U A 6 OK 115 111 114 133 C2' G A 7 OK 135 131 134 156 C2' A A 8 OK 158 154 157 178 C2' A A 9 OK 180 176 179 200 C2' A A 10 OK 202 198 201 222 C2' C A 11 OK 224 220 223 242 C2' G A 12 OK 244 240 243 265 C2' C A 13 OK 267 263 266 283 C2' G B 14 OK 285 281 284 306 C2' C B 15 OK 308 304 307 326 C2' G B 16 OK 328 324 327 349 C2' U B 17 OK 351 347 350 369 C2' U B 18 OK 371 367 370 389 C2' U B 19 OK 391 387 390 409 C2' G B 20 OK 411 407 410 432 C2' A B 21 OK 434 430 433 454 C2' A B 22 OK 456 452 455 476 C2' A B 23 OK 478 474 477 498 C2' C B 24 OK 500 496 499 518 C2' G B 25 OK 520 516 519 541 C2' C B 26 OK 543 539 542 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' U A 4 OK 69 72 73 91 C3' U A 5 OK 89 92 93 111 C3' U A 6 OK 109 112 113 131 C3' G A 7 OK 129 132 133 154 C3' A A 8 OK 152 155 156 176 C3' A A 9 OK 174 177 178 198 C3' A A 10 OK 196 199 200 220 C3' C A 11 OK 218 221 222 240 C3' G A 12 OK 238 241 242 263 C3' C A 13 OK 261 264 265 281 C3' G B 14 OK 279 282 283 304 C3' C B 15 OK 302 305 306 324 C3' G B 16 OK 322 325 326 347 C3' U B 17 OK 345 348 349 367 C3' U B 18 OK 365 368 369 387 C3' U B 19 OK 385 388 389 407 C3' G B 20 OK 405 408 409 430 C3' A B 21 OK 428 431 432 452 C3' A B 22 OK 450 453 454 474 C3' A B 23 OK 472 475 476 496 C3' C B 24 OK 494 497 498 516 C3' G B 25 OK 514 517 518 539 C3' C B 26 OK 537 540 541 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' U A 4 OK 71 68 70 89 C4' U A 5 OK 91 88 90 109 C4' U A 6 OK 111 108 110 129 C4' G A 7 OK 131 128 130 152 C4' A A 8 OK 154 151 153 174 C4' A A 9 OK 176 173 175 196 C4' A A 10 OK 198 195 197 218 C4' C A 11 OK 220 217 219 238 C4' G A 12 OK 240 237 239 261 C4' C A 13 OK 263 260 262 279 C4' G B 14 OK 281 278 280 302 C4' C B 15 OK 304 301 303 322 C4' G B 16 OK 324 321 323 345 C4' U B 17 OK 347 344 346 365 C4' U B 18 OK 367 364 366 385 C4' U B 19 OK 387 384 386 405 C4' G B 20 OK 407 404 406 428 C4' A B 21 OK 430 427 429 450 C4' A B 22 OK 452 449 451 472 C4' A B 23 OK 474 471 473 494 C4' C B 24 OK 496 493 495 514 C4' G B 25 OK 516 513 515 537 C4' C B 26 OK 539 536 538 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' G A 3 44 46 68 C5' U A 4 67 69 88 C5' U A 5 87 89 108 C5' U A 6 107 109 128 C5' G A 7 127 129 151 C5' A A 8 150 152 173 C5' A A 9 172 174 195 C5' A A 10 194 196 217 C5' C A 11 216 218 237 C5' G A 12 236 238 260 C5' C A 13 259 261 278 C5' G B 14 277 279 301 C5' C B 15 300 302 321 C5' G B 16 320 322 344 C5' U B 17 343 345 364 C5' U B 18 363 365 384 C5' U B 19 383 385 404 C5' G B 20 403 405 427 C5' A B 21 426 428 449 C5' A B 22 448 450 471 C5' A B 23 470 472 493 C5' C B 24 492 494 513 C5' G B 25 512 514 536 C5' C B 26 535 537 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P U A 4 distorted distorted 49 65 66 67 84 P U A 5 distorted distorted 72 85 86 87 104 P U A 6 distorted distorted 92 105 106 107 124 P G A 7 distorted distorted 112 125 126 127 147 P A A 8 distorted distorted 132 148 149 150 169 P A A 9 distorted distorted 155 170 171 172 191 P A A 10 distorted distorted 177 192 193 194 213 P C A 11 distorted distorted 199 214 215 216 233 P G A 12 distorted distorted 221 234 235 236 256 P C A 13 distorted distorted 241 257 258 259 297 P C B 15 distorted distorted 282 298 299 300 317 P G B 16 distorted distorted 305 318 319 320 340 P U B 17 distorted distorted 325 341 342 343 360 P U B 18 distorted distorted 348 361 362 363 380 P U B 19 distorted distorted 368 381 382 383 400 P G B 20 distorted distorted 388 401 402 403 423 P A B 21 distorted distorted 408 424 425 426 445 P A B 22 distorted distorted 431 446 447 448 467 P A B 23 distorted distorted 453 468 469 470 489 P C B 24 distorted distorted 475 490 491 492 509 P G B 25 distorted distorted 497 510 511 512 532 P C B 26 distorted distorted 517 533 534 535 ---------------------------------------------------------------------------------