ID code: '1QNA' 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' T C 204 beta 63 68 66 87 C1' T C 205 beta 83 88 86 107 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 272 277 275 295 C1' T D 215 beta 291 296 294 315 C1' G D 216 beta 311 316 314 337 C1' C D 217 beta 333 338 336 356 C1' C D 218 beta 352 357 355 375 C1' C D 219 beta 371 376 374 394 C1' T D 220 beta 390 395 393 414 C1' T D 221 beta 410 415 413 434 C1' T D 222 beta 430 435 433 454 C1' T D 223 beta 450 455 453 474 C1' A D 224 beta 470 475 473 495 C1' A D 225 beta 491 496 494 516 C1' A D 226 beta 512 517 515 537 C1' G D 227 beta 533 538 536 559 C1' C D 228 beta 555 560 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' T C 204 67 64 86 C2' T C 205 87 84 106 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 214 276 273 294 C2' T D 215 295 292 314 C2' G D 216 315 312 336 C2' C D 217 337 334 355 C2' C D 218 356 353 374 C2' C D 219 375 372 393 C2' T D 220 394 391 413 C2' T D 221 414 411 433 C2' T D 222 434 431 453 C2' T D 223 454 451 473 C2' A D 224 474 471 494 C2' A D 225 495 492 515 C2' A D 226 516 513 536 C2' G D 227 537 534 558 C2' C D 228 559 556 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' T C 204 OK 62 65 66 84 C3' T C 205 OK 82 85 86 104 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 271 274 275 292 C3' T D 215 OK 290 293 294 312 C3' G D 216 OK 310 313 314 334 C3' C D 217 OK 332 335 336 353 C3' C D 218 OK 351 354 355 372 C3' C D 219 OK 370 373 374 391 C3' T D 220 OK 389 392 393 411 C3' T D 221 OK 409 412 413 431 C3' T D 222 OK 429 432 433 451 C3' T D 223 OK 449 452 453 471 C3' A D 224 OK 469 472 473 492 C3' A D 225 OK 490 493 494 513 C3' A D 226 OK 511 514 515 534 C3' G D 227 OK 532 535 536 556 C3' C D 228 OK 554 557 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' T C 204 OK 64 61 63 82 C4' T C 205 OK 84 81 83 102 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 273 270 272 290 C4' T D 215 OK 292 289 291 310 C4' G D 216 OK 312 309 311 332 C4' C D 217 OK 334 331 333 351 C4' C D 218 OK 353 350 352 370 C4' C D 219 OK 372 369 371 389 C4' T D 220 OK 391 388 390 409 C4' T D 221 OK 411 408 410 429 C4' T D 222 OK 431 428 430 449 C4' T D 223 OK 451 448 450 469 C4' A D 224 OK 471 468 470 490 C4' A D 225 OK 492 489 491 511 C4' A D 226 OK 513 510 512 532 C4' G D 227 OK 534 531 533 554 C4' C D 228 OK 556 553 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' T C 204 60 62 81 C5' T C 205 80 82 101 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 214 269 271 289 C5' T D 215 288 290 309 C5' G D 216 308 310 331 C5' C D 217 330 332 350 C5' C D 218 349 351 369 C5' C D 219 368 370 388 C5' T D 220 387 389 408 C5' T D 221 407 409 428 C5' T D 222 427 429 448 C5' T D 223 447 449 468 C5' A D 224 467 469 489 C5' A D 225 488 490 510 C5' A D 226 509 511 531 C5' G D 227 530 532 553 C5' C D 228 552 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 T C 204 OK OK 45 58 59 60 77 P T C 205 OK OK 65 78 79 80 97 P A C 206 OK OK 85 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 255 267 268 269 305 P G D 216 OK OK 293 306 307 308 327 P C D 217 OK OK 313 328 329 330 346 P C D 218 OK OK 335 347 348 349 365 P C D 219 OK OK 354 366 367 368 384 P T D 220 OK OK 373 385 386 387 404 P T D 221 OK OK 392 405 406 407 424 P T D 222 OK OK 412 425 426 427 444 P T D 223 OK OK 432 445 446 447 464 P A D 224 OK OK 452 465 466 467 485 P A D 225 OK OK 472 486 487 488 506 P A D 226 OK OK 493 507 508 509 527 P G D 227 OK OK 514 528 529 530 549 P C D 228 OK OK 535 550 551 552 ---------------------------------------------------------------------------------