ID code: '2A43' 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 3 beta 4 10 7 32 C1' C A 4 beta 27 33 30 52 C1' G A 5 beta 47 53 50 75 C1' G A 6 beta 70 76 73 98 C1' C A 7 beta 93 99 96 118 C1' A A 8 beta 113 119 116 140 C1' C A 9 beta 135 141 138 160 C1' C A 10 beta 155 161 158 180 C1' G A 11 beta 175 181 178 203 C1' U A 12 beta 198 204 201 223 C1' C A 13 beta 218 224 221 243 C1' C A 14 beta 238 244 241 263 C1' G A 15 beta 258 264 261 286 C1' C A 16 beta 281 287 284 306 C1' U A 17 beta 301 307 304 326 C1' C A 18 beta 321 327 324 346 C1' A A 19 beta 341 347 344 368 C1' A A 20 beta 363 369 366 390 C1' A A 21 beta 385 391 388 412 C1' C A 22 beta 407 413 410 432 C1' A A 23 beta 427 433 430 454 C1' A A 24 beta 449 455 452 476 C1' A A 25 beta 471 477 474 498 C1' C A 26 beta 493 499 496 518 C1' G A 27 beta 513 519 516 541 C1' G A 28 beta 536 542 539 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 3 OK 9 5 8 30 C2' C A 4 OK 32 28 31 50 C2' G A 5 OK 52 48 51 73 C2' G A 6 OK 75 71 74 96 C2' C A 7 OK 98 94 97 116 C2' A A 8 OK 118 114 117 138 C2' C A 9 OK 140 136 139 158 C2' C A 10 OK 160 156 159 178 C2' G A 11 OK 180 176 179 201 C2' U A 12 OK 203 199 202 221 C2' C A 13 OK 223 219 222 241 C2' C A 14 OK 243 239 242 261 C2' G A 15 OK 263 259 262 284 C2' C A 16 OK 286 282 285 304 C2' U A 17 OK 306 302 305 324 C2' C A 18 OK 326 322 325 344 C2' A A 19 OK 346 342 345 366 C2' A A 20 OK 368 364 367 388 C2' A A 21 OK 390 386 389 410 C2' C A 22 OK 412 408 411 430 C2' A A 23 OK 432 428 431 452 C2' A A 24 OK 454 450 453 474 C2' A A 25 OK 476 472 475 496 C2' C A 26 OK 498 494 497 516 C2' G A 27 OK 518 514 517 539 C2' G A 28 OK 541 537 540 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 3 OK 3 6 7 28 C3' C A 4 OK 26 29 30 48 C3' G A 5 OK 46 49 50 71 C3' G A 6 OK 69 72 73 94 C3' C A 7 OK 92 95 96 114 C3' A A 8 OK 112 115 116 136 C3' C A 9 OK 134 137 138 156 C3' C A 10 OK 154 157 158 176 C3' G A 11 OK 174 177 178 199 C3' U A 12 OK 197 200 201 219 C3' C A 13 OK 217 220 221 239 C3' C A 14 OK 237 240 241 259 C3' G A 15 OK 257 260 261 282 C3' C A 16 OK 280 283 284 302 C3' U A 17 OK 300 303 304 322 C3' C A 18 OK 320 323 324 342 C3' A A 19 OK 340 343 344 364 C3' A A 20 OK 362 365 366 386 C3' A A 21 OK 384 387 388 408 C3' C A 22 OK 406 409 410 428 C3' A A 23 OK 426 429 430 450 C3' A A 24 OK 448 451 452 472 C3' A A 25 OK 470 473 474 494 C3' C A 26 OK 492 495 496 514 C3' G A 27 OK 512 515 516 537 C3' G A 28 OK 535 538 539 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 3 OK 5 2 4 26 C4' C A 4 OK 28 25 27 46 C4' G A 5 OK 48 45 47 69 C4' G A 6 OK 71 68 70 92 C4' C A 7 OK 94 91 93 112 C4' A A 8 OK 114 111 113 134 C4' C A 9 OK 136 133 135 154 C4' C A 10 OK 156 153 155 174 C4' G A 11 OK 176 173 175 197 C4' U A 12 OK 199 196 198 217 C4' C A 13 OK 219 216 218 237 C4' C A 14 OK 239 236 238 257 C4' G A 15 OK 259 256 258 280 C4' C A 16 OK 282 279 281 300 C4' U A 17 OK 302 299 301 320 C4' C A 18 OK 322 319 321 340 C4' A A 19 OK 342 339 341 362 C4' A A 20 OK 364 361 363 384 C4' A A 21 OK 386 383 385 406 C4' C A 22 OK 408 405 407 426 C4' A A 23 OK 428 425 427 448 C4' A A 24 OK 450 447 449 470 C4' A A 25 OK 472 469 471 492 C4' C A 26 OK 494 491 493 512 C4' G A 27 OK 514 511 513 535 C4' G A 28 OK 537 534 536 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 3 1 3 25 C5' C A 4 24 26 45 C5' G A 5 44 46 68 C5' G A 6 67 69 91 C5' C A 7 90 92 111 C5' A A 8 110 112 133 C5' C A 9 132 134 153 C5' C A 10 152 154 173 C5' G A 11 172 174 196 C5' U A 12 195 197 216 C5' C A 13 215 217 236 C5' C A 14 235 237 256 C5' G A 15 255 257 279 C5' C A 16 278 280 299 C5' U A 17 298 300 319 C5' C A 18 318 320 339 C5' A A 19 338 340 361 C5' A A 20 360 362 383 C5' A A 21 382 384 405 C5' C A 22 404 406 425 C5' A A 23 424 426 447 C5' A A 24 446 448 469 C5' A A 25 468 470 491 C5' C A 26 490 492 511 C5' G A 27 510 512 534 C5' G A 28 533 535 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 4 distorted distorted 6 22 23 24 41 P G A 5 distorted distorted 29 42 43 44 64 P G A 6 distorted distorted 49 65 66 67 87 P C A 7 distorted distorted 72 88 89 90 107 P A A 8 distorted distorted 95 108 109 110 129 P C A 9 distorted distorted 115 130 131 132 149 P C A 10 distorted distorted 137 150 151 152 169 P G A 11 distorted distorted 157 170 171 172 192 P U A 12 distorted distorted 177 193 194 195 212 P C A 13 distorted distorted 200 213 214 215 232 P C A 14 distorted distorted 220 233 234 235 252 P G A 15 distorted distorted 240 253 254 255 275 P C A 16 distorted distorted 260 276 277 278 295 P U A 17 distorted distorted 283 296 297 298 315 P C A 18 distorted distorted 303 316 317 318 335 P A A 19 distorted distorted 323 336 337 338 357 P A A 20 distorted distorted 343 358 359 360 379 P A A 21 distorted distorted 365 380 381 382 401 P C A 22 distorted distorted 387 402 403 404 421 P A A 23 distorted distorted 409 422 423 424 443 P A A 24 distorted distorted 429 444 445 446 465 P A A 25 distorted distorted 451 466 467 468 487 P C A 26 distorted distorted 473 488 489 490 507 P G A 27 distorted distorted 495 508 509 510 530 P G A 28 distorted distorted 515 531 532 533 ---------------------------------------------------------------------------------