ID code: '4FSJ' 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' --------------------------------------------------------------------------------- 7407 C1' U R 2 beta 7402 7408 7405 7427 C1' U R 3 beta 7422 7428 7425 7447 C1' C R 4 beta 7442 7448 7445 7467 C1' U R 5 beta 7462 7468 7465 7487 C1' C R 6 beta 7482 7488 7485 7507 C1' U R 7 beta 7502 7508 7505 7527 C1' U R 8 beta 7522 7528 7525 7547 C1' U R 9 beta 7542 7548 7545 7567 C1' U R 10 beta 7562 7568 7565 7587 C1' A R 11 beta 7582 7588 7585 7609 C1' U R 12 beta 7604 7610 7607 7629 C1' C R 13 beta 7624 7630 7627 7649 C1' U R 14 beta 7644 7650 7647 7669 C1' U R 15 beta 7664 7670 7667 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7405 C2' U R 2 OK 7407 7403 7406 7425 C2' U R 3 OK 7427 7423 7426 7445 C2' C R 4 OK 7447 7443 7446 7465 C2' U R 5 OK 7467 7463 7466 7485 C2' C R 6 OK 7487 7483 7486 7505 C2' U R 7 OK 7507 7503 7506 7525 C2' U R 8 OK 7527 7523 7526 7545 C2' U R 9 OK 7547 7543 7546 7565 C2' U R 10 OK 7567 7563 7566 7585 C2' A R 11 OK 7587 7583 7586 7607 C2' U R 12 OK 7609 7605 7608 7627 C2' C R 13 OK 7629 7625 7628 7647 C2' U R 14 OK 7649 7645 7648 7667 C2' U R 15 OK 7669 7665 7668 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7403 C3' U R 2 OK 7401 7404 7405 7423 C3' U R 3 OK 7421 7424 7425 7443 C3' C R 4 OK 7441 7444 7445 7463 C3' U R 5 OK 7461 7464 7465 7483 C3' C R 6 OK 7481 7484 7485 7503 C3' U R 7 OK 7501 7504 7505 7523 C3' U R 8 OK 7521 7524 7525 7543 C3' U R 9 OK 7541 7544 7545 7563 C3' U R 10 OK 7561 7564 7565 7583 C3' A R 11 OK 7581 7584 7585 7605 C3' U R 12 OK 7603 7606 7607 7625 C3' C R 13 OK 7623 7626 7627 7645 C3' U R 14 OK 7643 7646 7647 7665 C3' U R 15 OK 7663 7666 7667 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7401 C4' U R 2 OK 7403 7400 7402 7421 C4' U R 3 OK 7423 7420 7422 7441 C4' C R 4 OK 7443 7440 7442 7461 C4' U R 5 OK 7463 7460 7462 7481 C4' C R 6 OK 7483 7480 7482 7501 C4' U R 7 OK 7503 7500 7502 7521 C4' U R 8 OK 7523 7520 7522 7541 C4' U R 9 OK 7543 7540 7542 7561 C4' U R 10 OK 7563 7560 7562 7581 C4' A R 11 OK 7583 7580 7582 7603 C4' U R 12 OK 7605 7602 7604 7623 C4' C R 13 OK 7625 7622 7624 7643 C4' U R 14 OK 7645 7642 7644 7663 C4' U R 15 OK 7665 7662 7664 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7400 C5' U R 2 7399 7401 7420 C5' U R 3 7419 7421 7440 C5' C R 4 7439 7441 7460 C5' U R 5 7459 7461 7480 C5' C R 6 7479 7481 7500 C5' U R 7 7499 7501 7520 C5' U R 8 7519 7521 7540 C5' U R 9 7539 7541 7560 C5' U R 10 7559 7561 7580 C5' A R 11 7579 7581 7602 C5' U R 12 7601 7603 7622 C5' C R 13 7621 7623 7642 C5' U R 14 7641 7643 7662 C5' U R 15 7661 7663 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7396 P U R 2 distorted distorted 7397 7398 7399 7416 P U R 3 distorted distorted 7404 7417 7418 7419 7436 P C R 4 distorted distorted 7424 7437 7438 7439 7456 P U R 5 distorted distorted 7444 7457 7458 7459 7476 P C R 6 distorted distorted 7464 7477 7478 7479 7496 P U R 7 distorted distorted 7484 7497 7498 7499 7516 P U R 8 distorted distorted 7504 7517 7518 7519 7536 P U R 9 distorted distorted 7524 7537 7538 7539 7556 P U R 10 distorted distorted 7544 7557 7558 7559 7576 P A R 11 distorted distorted 7564 7577 7578 7579 7598 P U R 12 distorted distorted 7584 7599 7600 7601 7618 P C R 13 distorted distorted 7606 7619 7620 7621 7638 P U R 14 distorted distorted 7626 7639 7640 7641 7658 P U R 15 distorted distorted 7646 7659 7660 7661 ---------------------------------------------------------------------------------