ID code: '1QNE' 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' --------------------------------------------------------------------------------- 3 C1' G C 201 beta 2 4 15 25 C1' C C 202 beta 24 26 34 44 C1' T C 203 beta 43 45 54 64 C1' A C 204 beta 63 65 75 85 C1' T C 205 beta 84 86 95 105 C1' A C 206 beta 104 106 116 126 C1' A C 207 beta 125 127 137 147 C1' A C 208 beta 146 148 158 168 C1' A C 209 beta 167 169 179 189 C1' G C 210 beta 188 190 201 211 C1' G C 211 beta 210 212 223 233 C1' G C 212 beta 232 234 245 255 C1' C C 213 beta 254 256 264 274 C1' A C 214 beta 273 275 285 293 C1' T D 215 beta 292 294 303 313 C1' G D 216 beta 312 314 325 335 C1' C D 217 beta 334 336 344 354 C1' C D 218 beta 353 355 363 373 C1' C D 219 beta 372 374 382 392 C1' T D 220 beta 391 393 402 412 C1' T D 221 beta 411 413 422 432 C1' T D 222 beta 431 433 442 452 C1' T D 223 beta 451 453 462 472 C1' A D 224 beta 471 473 483 493 C1' T D 225 beta 492 494 503 513 C1' A D 226 beta 512 514 524 534 C1' G D 227 beta 533 535 546 556 C1' C D 228 beta 555 557 565 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 15 C2' G C 201 3 16 34 C2' C C 202 25 35 54 C2' T C 203 44 55 75 C2' A C 204 64 76 95 C2' T C 205 85 96 116 C2' A C 206 105 117 137 C2' A C 207 126 138 158 C2' A C 208 147 159 179 C2' A C 209 168 180 201 C2' G C 210 189 202 223 C2' G C 211 211 224 245 C2' G C 212 233 246 264 C2' C C 213 255 265 285 C2' A C 214 274 286 303 C2' T D 215 293 304 325 C2' G D 216 313 326 344 C2' C D 217 335 345 363 C2' C D 218 354 364 382 C2' C D 219 373 383 402 C2' T D 220 392 403 422 C2' T D 221 412 423 442 C2' T D 222 432 443 462 C2' T D 223 452 463 483 C2' A D 224 472 484 503 C2' T D 225 493 504 524 C2' A D 226 513 525 546 C2' G D 227 534 547 565 C2' C D 228 556 566 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 16 C3' G C 201 OK 1 17 15 35 C3' C C 202 OK 23 36 34 55 C3' T C 203 OK 42 56 54 76 C3' A C 204 OK 62 77 75 96 C3' T C 205 OK 83 97 95 117 C3' A C 206 OK 103 118 116 138 C3' A C 207 OK 124 139 137 159 C3' A C 208 OK 145 160 158 180 C3' A C 209 OK 166 181 179 202 C3' G C 210 OK 187 203 201 224 C3' G C 211 OK 209 225 223 246 C3' G C 212 OK 231 247 245 265 C3' C C 213 OK 253 266 264 286 C3' A C 214 OK 272 287 285 304 C3' T D 215 OK 291 305 303 326 C3' G D 216 OK 311 327 325 345 C3' C D 217 OK 333 346 344 364 C3' C D 218 OK 352 365 363 383 C3' C D 219 OK 371 384 382 403 C3' T D 220 OK 390 404 402 423 C3' T D 221 OK 410 424 422 443 C3' T D 222 OK 430 444 442 463 C3' T D 223 OK 450 464 462 484 C3' A D 224 OK 470 485 483 504 C3' T D 225 OK 491 505 503 525 C3' A D 226 OK 511 526 524 547 C3' G D 227 OK 532 548 546 566 C3' C D 228 OK 554 567 565 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1 C4' G C 201 16 2 23 C4' C C 202 OK 35 22 24 42 C4' T C 203 OK 55 41 43 62 C4' A C 204 OK 76 61 63 83 C4' T C 205 OK 96 82 84 103 C4' A C 206 OK 117 102 104 124 C4' A C 207 OK 138 123 125 145 C4' A C 208 OK 159 144 146 166 C4' A C 209 OK 180 165 167 187 C4' G C 210 OK 202 186 188 209 C4' G C 211 OK 224 208 210 231 C4' G C 212 OK 246 230 232 253 C4' C C 213 OK 265 252 254 272 C4' A C 214 OK 286 271 273 291 C4' T D 215 OK 304 290 292 311 C4' G D 216 OK 326 310 312 333 C4' C D 217 OK 345 332 334 352 C4' C D 218 OK 364 351 353 371 C4' C D 219 OK 383 370 372 390 C4' T D 220 OK 403 389 391 410 C4' T D 221 OK 423 409 411 430 C4' T D 222 OK 443 429 431 450 C4' T D 223 OK 463 449 451 470 C4' A D 224 OK 484 469 471 491 C4' T D 225 OK 504 490 492 511 C4' A D 226 OK 525 510 512 532 C4' G D 227 OK 547 531 533 554 C4' C D 228 OK 566 553 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A C 204 60 62 82 C5' T C 205 81 83 102 C5' A C 206 101 103 123 C5' A C 207 122 124 144 C5' A C 208 143 145 165 C5' A C 209 164 166 186 C5' G C 210 185 187 208 C5' G C 211 207 209 230 C5' G C 212 229 231 252 C5' C C 213 251 253 271 C5' A C 214 270 272 290 C5' T D 215 289 291 310 C5' G D 216 309 311 332 C5' C D 217 331 333 351 C5' C D 218 350 352 370 C5' C D 219 369 371 389 C5' T D 220 388 390 409 C5' T D 221 408 410 429 C5' T D 222 428 430 449 C5' T D 223 448 450 469 C5' A D 224 468 470 490 C5' T D 225 489 491 510 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 17 19 20 21 37 P T C 203 OK OK 36 38 39 40 57 P A C 204 OK OK 56 58 59 60 78 P T C 205 OK OK 77 79 80 81 98 P A C 206 OK OK 97 99 100 101 119 P A C 207 OK OK 118 120 121 122 140 P A C 208 OK OK 139 141 142 143 161 P A C 209 OK OK 160 162 163 164 182 P G C 210 OK OK 181 183 184 185 204 P G C 211 OK OK 203 205 206 207 226 P G C 212 OK OK 225 227 228 229 248 P C C 213 OK OK 247 249 250 251 267 P A C 214 OK OK 266 268 269 270 306 P G D 216 OK OK 305 307 308 309 328 P C D 217 OK OK 327 329 330 331 347 P C D 218 OK OK 346 348 349 350 366 P C D 219 OK OK 365 367 368 369 385 P T D 220 OK OK 384 386 387 388 405 P T D 221 OK OK 404 406 407 408 425 P T D 222 OK OK 424 426 427 428 445 P T D 223 OK OK 444 446 447 448 465 P A D 224 OK OK 464 466 467 468 486 P T D 225 OK OK 485 487 488 489 506 P A D 226 OK OK 505 507 508 509 527 P G D 227 OK OK 526 528 529 530 549 P C D 228 OK OK 548 550 551 552 ---------------------------------------------------------------------------------