ID code: '1QN9' 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' --------------------------------------------------------------------------------- 6 C1' G C 201 beta 2 7 5 28 C1' C C 202 beta 24 29 27 47 C1' T C 203 beta 43 48 46 67 C1' A C 204 beta 63 68 66 88 C1' C C 205 beta 84 89 87 107 C1' A C 206 beta 103 108 106 128 C1' A C 207 beta 124 129 127 149 C1' A C 208 beta 145 150 148 170 C1' A C 209 beta 166 171 169 191 C1' G C 210 beta 187 192 190 213 C1' G C 211 beta 209 214 212 235 C1' G C 212 beta 231 236 234 257 C1' C C 213 beta 253 258 256 276 C1' A C 214 beta 272 277 275 293 C1' T D 215 beta 289 294 292 313 C1' G D 216 beta 309 314 312 335 C1' C D 217 beta 331 336 334 354 C1' C D 218 beta 350 355 353 373 C1' C D 219 beta 369 374 372 392 C1' T D 220 beta 388 393 391 412 C1' T D 221 beta 408 413 411 432 C1' T D 222 beta 428 433 431 452 C1' T D 223 beta 448 453 451 472 C1' G D 224 beta 468 473 471 494 C1' T D 225 beta 490 495 493 514 C1' A D 226 beta 510 515 513 535 C1' G D 227 beta 531 536 534 557 C1' C D 228 beta 553 558 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5 C2' G C 201 6 3 27 C2' C C 202 28 25 46 C2' T C 203 47 44 66 C2' A C 204 67 64 87 C2' C C 205 88 85 106 C2' A C 206 107 104 127 C2' A C 207 128 125 148 C2' A C 208 149 146 169 C2' A C 209 170 167 190 C2' G C 210 191 188 212 C2' G C 211 213 210 234 C2' G C 212 235 232 256 C2' C C 213 257 254 275 C2' A C 214 276 273 292 C2' T D 215 293 290 312 C2' G D 216 313 310 334 C2' C D 217 335 332 353 C2' C D 218 354 351 372 C2' C D 219 373 370 391 C2' T D 220 392 389 411 C2' T D 221 412 409 431 C2' T D 222 432 429 451 C2' T D 223 452 449 471 C2' G D 224 472 469 493 C2' T D 225 494 491 513 C2' A D 226 514 511 534 C2' G D 227 535 532 556 C2' C D 228 557 554 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3 C3' G C 201 OK 1 4 5 25 C3' C C 202 OK 23 26 27 44 C3' T C 203 OK 42 45 46 64 C3' A C 204 OK 62 65 66 85 C3' C C 205 OK 83 86 87 104 C3' A C 206 OK 102 105 106 125 C3' A C 207 OK 123 126 127 146 C3' A C 208 OK 144 147 148 167 C3' A C 209 OK 165 168 169 188 C3' G C 210 OK 186 189 190 210 C3' G C 211 OK 208 211 212 232 C3' G C 212 OK 230 233 234 254 C3' C C 213 OK 252 255 256 273 C3' A C 214 OK 271 274 275 290 C3' T D 215 OK 288 291 292 310 C3' G D 216 OK 308 311 312 332 C3' C D 217 OK 330 333 334 351 C3' C D 218 OK 349 352 353 370 C3' C D 219 OK 368 371 372 389 C3' T D 220 OK 387 390 391 409 C3' T D 221 OK 407 410 411 429 C3' T D 222 OK 427 430 431 449 C3' T D 223 OK 447 450 451 469 C3' G D 224 OK 467 470 471 491 C3' T D 225 OK 489 492 493 511 C3' A D 226 OK 509 512 513 532 C3' G D 227 OK 530 533 534 554 C3' C D 228 OK 552 555 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1 C4' G C 201 3 2 23 C4' C C 202 OK 25 22 24 42 C4' T C 203 OK 44 41 43 62 C4' A C 204 OK 64 61 63 83 C4' C C 205 OK 85 82 84 102 C4' A C 206 OK 104 101 103 123 C4' A C 207 OK 125 122 124 144 C4' A C 208 OK 146 143 145 165 C4' A C 209 OK 167 164 166 186 C4' G C 210 OK 188 185 187 208 C4' G C 211 OK 210 207 209 230 C4' G C 212 OK 232 229 231 252 C4' C C 213 OK 254 251 253 271 C4' A C 214 OK 273 270 272 288 C4' T D 215 290 289 308 C4' G D 216 OK 310 307 309 330 C4' C D 217 OK 332 329 331 349 C4' C D 218 OK 351 348 350 368 C4' C D 219 OK 370 367 369 387 C4' T D 220 OK 389 386 388 407 C4' T D 221 OK 409 406 408 427 C4' T D 222 OK 429 426 428 447 C4' T D 223 OK 449 446 448 467 C4' G D 224 OK 469 466 468 489 C4' T D 225 OK 491 488 490 509 C4' A D 226 OK 511 508 510 530 C4' G D 227 OK 532 529 531 552 C4' C D 228 OK 554 551 553 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 22 C5' C C 202 21 23 41 C5' T C 203 40 42 61 C5' A C 204 60 62 82 C5' C C 205 81 83 101 C5' A C 206 100 102 122 C5' A C 207 121 123 143 C5' A C 208 142 144 164 C5' A C 209 163 165 185 C5' G C 210 184 186 207 C5' G C 211 206 208 229 C5' G C 212 228 230 251 C5' C C 213 250 252 270 C5' A C 214 269 271 307 C5' G D 216 306 308 329 C5' C D 217 328 330 348 C5' C D 218 347 349 367 C5' C D 219 366 368 386 C5' T D 220 385 387 406 C5' T D 221 405 407 426 C5' T D 222 425 427 446 C5' T D 223 445 447 466 C5' G D 224 465 467 488 C5' T D 225 487 489 508 C5' A D 226 507 509 529 C5' G D 227 528 530 551 C5' C D 228 550 552 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C C 202 OK OK 4 19 20 21 37 P T C 203 OK OK 26 38 39 40 57 P A C 204 OK OK 45 58 59 60 78 P C C 205 OK OK 65 79 80 81 97 P A C 206 OK OK 86 98 99 100 118 P A C 207 OK OK 105 119 120 121 139 P A C 208 OK OK 126 140 141 142 160 P A C 209 OK OK 147 161 162 163 181 P G C 210 OK OK 168 182 183 184 203 P G C 211 OK OK 189 204 205 206 225 P G C 212 OK OK 211 226 227 228 247 P C C 213 OK OK 233 248 249 250 266 P A C 214 OK OK 255 267 268 269 303 P G D 216 OK OK 291 304 305 306 325 P C D 217 OK OK 311 326 327 328 344 P C D 218 OK OK 333 345 346 347 363 P C D 219 OK OK 352 364 365 366 382 P T D 220 OK OK 371 383 384 385 402 P T D 221 OK OK 390 403 404 405 422 P T D 222 OK OK 410 423 424 425 442 P T D 223 OK OK 430 443 444 445 462 P G D 224 OK OK 450 463 464 465 484 P T D 225 OK OK 470 485 486 487 504 P A D 226 OK OK 492 505 506 507 525 P G D 227 OK OK 512 526 527 528 547 P C D 228 OK OK 533 548 549 550 ---------------------------------------------------------------------------------