ID code: '3DW7' 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' --------------------------------------------------------------------------------- 10 C1' U A2647 beta 4 11 8 121 C1' U A2650 beta 116 122 119 141 C1' C A2651 beta 136 142 139 161 C1' C A2652 beta 156 162 159 181 C1' U A2653 beta 176 182 179 207 C1' A A2654 beta 202 208 205 229 C1' G A2655 beta 224 230 227 252 C1' UMS A2656 beta 247 254 250 273 C1' A A2657 beta 268 274 271 295 C1' C A2658 beta 290 296 293 315 C1' G A2659 beta 310 316 313 338 C1' A A2660 beta 333 339 336 360 C1' G A2661 beta 355 361 358 383 C1' A A2662 beta 378 384 381 405 C1' G A2663 beta 400 406 403 428 C1' G A2664 beta 423 429 426 451 C1' A A2665 beta 446 452 449 473 C1' C A2666 beta 468 474 471 493 C1' C A2667 beta 488 494 491 564 C1' G A2669 beta 559 565 562 587 C1' A A2670 beta 582 588 585 609 C1' G A2671 beta 604 610 607 632 C1' U A2672 beta 627 633 630 652 C1' G A2673 beta 647 653 650 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8 C2' U A2647 OK 10 5 9 119 C2' U A2650 OK 121 117 120 139 C2' C A2651 OK 141 137 140 159 C2' C A2652 OK 161 157 160 179 C2' U A2653 OK 181 177 180 205 C2' A A2654 OK 207 203 206 227 C2' G A2655 OK 229 225 228 250 C2' UMS A2656 252 248 271 C2' A A2657 OK 273 269 272 293 C2' C A2658 OK 295 291 294 313 C2' G A2659 OK 315 311 314 336 C2' A A2660 OK 338 334 337 358 C2' G A2661 OK 360 356 359 381 C2' A A2662 OK 383 379 382 403 C2' G A2663 OK 405 401 404 426 C2' G A2664 OK 428 424 427 449 C2' A A2665 OK 451 447 450 471 C2' C A2666 OK 473 469 472 491 C2' C A2667 OK 493 489 492 562 C2' G A2669 OK 564 560 563 585 C2' A A2670 OK 587 583 586 607 C2' G A2671 OK 609 605 608 630 C2' U A2672 OK 632 628 631 650 C2' G A2673 OK 652 648 651 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A2647 3 8 117 C3' U A2650 OK 115 118 119 137 C3' C A2651 OK 135 138 139 157 C3' C A2652 OK 155 158 159 177 C3' U A2653 OK 175 178 179 203 C3' A A2654 204 205 225 C3' G A2655 OK 223 226 227 248 C3' UMS A2656 OK 246 249 250 269 C3' A A2657 OK 267 270 271 291 C3' C A2658 OK 289 292 293 311 C3' G A2659 OK 309 312 313 334 C3' A A2660 OK 332 335 336 356 C3' G A2661 OK 354 357 358 379 C3' A A2662 OK 377 380 381 401 C3' G A2663 OK 399 402 403 424 C3' G A2664 OK 422 425 426 447 C3' A A2665 OK 445 448 449 469 C3' C A2666 OK 467 470 471 489 C3' C A2667 OK 487 490 491 560 C3' G A2669 OK 558 561 562 583 C3' A A2670 OK 581 584 585 605 C3' G A2671 OK 603 606 607 628 C3' U A2672 OK 626 629 630 648 C3' G A2673 OK 646 649 650 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A2647 OK 5 2 4 115 C4' U A2650 117 116 135 C4' C A2651 OK 137 134 136 155 C4' C A2652 OK 157 154 156 175 C4' U A2653 OK 177 174 176 223 C4' G A2655 OK 225 222 224 246 C4' UMS A2656 OK 248 245 247 267 C4' A A2657 OK 269 266 268 289 C4' C A2658 OK 291 288 290 309 C4' G A2659 OK 311 308 310 332 C4' A A2660 OK 334 331 333 354 C4' G A2661 OK 356 353 355 377 C4' A A2662 OK 379 376 378 399 C4' G A2663 OK 401 398 400 422 C4' G A2664 OK 424 421 423 445 C4' A A2665 OK 447 444 446 467 C4' C A2666 OK 469 466 468 487 C4' C A2667 OK 489 486 488 558 C4' G A2669 560 559 581 C4' A A2670 OK 583 580 582 603 C4' G A2671 OK 605 602 604 626 C4' U A2672 OK 628 625 627 646 C4' G A2673 OK 648 645 647 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A2647 1 3 134 C5' C A2651 133 135 154 C5' C A2652 153 155 174 C5' U A2653 173 175 222 C5' G A2655 221 223 245 C5' UMS A2656 244 246 266 C5' A A2657 265 267 288 C5' C A2658 287 289 308 C5' G A2659 307 309 331 C5' A A2660 330 332 353 C5' G A2661 352 354 376 C5' A A2662 375 377 398 C5' G A2663 397 399 421 C5' G A2664 420 422 444 C5' A A2665 443 445 466 C5' C A2666 465 467 486 C5' C A2667 485 487 580 C5' A A2670 579 581 602 C5' G A2671 601 603 625 C5' U A2672 624 626 645 C5' G A2673 644 646 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P G A2648 20 P G A2648 65 P C A2649 66 P C A2649 105 P U A2650 106 P U A2650 130 P C A2651 distorted distorted 118 131 132 133 150 P C A2652 distorted distorted 138 151 152 153 170 P U A2653 distorted distorted 158 171 172 173 190 P A A2654 178 191 P A A2654 178 218 P G A2655 distorted distorted 204 219 220 221 241 P UMS A2656 distorted distorted 226 242 243 244 262 P A A2657 distorted distorted 249 263 264 265 284 P C A2658 distorted distorted 270 285 286 287 304 P G A2659 distorted distorted 292 305 306 307 327 P A A2660 distorted distorted 312 328 329 330 349 P G A2661 distorted distorted 335 350 351 352 372 P A A2662 distorted distorted 357 373 374 375 394 P G A2663 distorted distorted 380 395 396 397 417 P G A2664 distorted distorted 402 418 419 420 440 P A A2665 distorted distorted 425 441 442 443 462 P C A2666 distorted distorted 448 463 464 465 482 P C A2667 distorted distorted 470 483 484 485 502 P G A2668 490 503 P G A2668 490 548 P G A2669 549 P G A2669 576 P A A2670 distorted distorted 561 577 578 579 598 P G A2671 distorted distorted 584 599 600 601 621 P U A2672 distorted distorted 606 622 623 624 641 P G A2673 distorted distorted 629 642 643 644 ---------------------------------------------------------------------------------