Contacts of the helix formed by residues 467 - 490 (chain C) in PDB entry 1NYE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 467 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C VAL* 6.6 0.4 - - - -
454C TYR* 4.8 4.7 - - - -
458C THR* 4.1 10.1 - - - +
459C ARG* 4.5 8.7 - - + -
465C GLY 3.1 15.4 - - - +
466C THR* 1.3 79.0 - - - +
468C PRO* 1.3 76.6 - - + +
469C GLU* 3.3 13.0 + - - +
470C GLU* 2.9 50.6 + - - +
471C LEU* 3.2 17.5 + - - +
625D LYS* 2.9 39.6 + - - +
645D GLU* 4.6 0.3 - - - +
678D ALA* 5.8 0.7 - - - -
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Residues in contact with PRO 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C TYR* 4.8 8.7 - - + -
459C ARG* 3.1 41.3 - - - +
467C ASN* 1.3 86.2 - - + +
469C GLU* 1.3 64.4 + - - +
471C LEU* 3.1 5.8 + - + +
472C ILE* 3.0 27.6 + - - +
675D ALA* 3.6 17.0 - - + +
678D ALA* 4.1 9.4 - - + -
679D CYS* 3.6 33.7 - - + +
747D VAL* 4.1 6.3 - - + -
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Residues in contact with GLU 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ARG* 2.5 41.3 + - - +
467C ASN* 3.2 11.4 + - - +
468C PRO* 1.3 78.2 - - - +
470C GLU* 1.3 58.7 + - - +
472C ILE* 3.3 4.4 + - - +
473C GLY 2.9 25.1 + - - -
504C VAL* 3.5 32.9 - - + +
506C LEU* 3.7 34.1 - - + +
515C ILE* 3.6 20.0 - - + +
623D ILE* 5.8 2.0 - - + -
625D LYS* 3.7 17.3 - - + -
746D PRO* 4.7 2.1 - - - +
747D VAL* 5.2 0.2 - - - +
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Residues in contact with GLU 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C GLY 3.7 0.2 - - - +
466C THR* 2.9 29.7 - - - +
467C ASN* 2.9 29.7 - - - +
469C GLU* 1.3 72.4 - - - +
471C LEU* 1.3 63.6 + - + +
473C GLY* 3.3 1.9 + - - -
474C ALA* 3.0 22.7 + - - +
625D LYS* 3.8 10.5 - - + +
626D LYS 3.9 16.2 - - - +
627D GLY* 4.1 3.3 - - - -
644D THR* 2.8 31.9 + - - +
645D GLU* 3.5 7.3 - - - +
646D SER* 2.7 46.3 + - - -
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Residues in contact with LEU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C VAL* 4.6 8.7 - - + -
449C LEU* 4.3 17.7 - - + -
466C THR* 3.5 33.7 - - + -
467C ASN 3.2 8.6 + - - +
468C PRO 3.1 7.9 + - - +
470C GLU* 1.3 81.7 - - - +
472C ILE* 1.3 66.8 + - - +
474C ALA* 3.2 5.4 + - - +
475C ALA* 3.0 22.7 + - - +
644D THR* 4.1 7.9 - - + +
648D VAL* 6.1 0.2 - - + -
649D LEU* 4.9 12.1 - - + -
671D LEU* 3.9 19.2 - - + +
674D ALA* 4.1 21.3 - - + +
675D ALA* 3.8 19.5 - - + +
678D ALA* 5.6 0.9 - - + -
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Residues in contact with ILE 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C PRO 3.0 15.1 + - - +
469C GLU* 3.8 6.5 - - - +
471C LEU* 1.3 74.1 - - - +
473C GLY* 1.3 65.6 + - - +
475C ALA* 3.1 2.8 + - - +
476C HIS* 2.8 22.7 + - + +
504C VAL* 4.9 4.5 - - + -
515C ILE* 4.0 18.6 - - + -
518C ILE* 4.5 21.3 - - + -
551C LEU* 4.5 18.6 - - + -
672D ILE* 4.2 27.5 - - + +
675D ALA* 3.7 12.3 - - + -
747D VAL* 3.9 35.4 - - + -
750D VAL* 5.7 2.9 - - + -
751D LEU* 6.1 2.7 - - + -
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Residues in contact with GLY 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C GLU 2.9 11.1 + - - -
470C GLU 3.6 3.1 - - - -
472C ILE* 1.3 77.3 - - - +
474C ALA* 1.3 55.9 + - - +
476C HIS* 3.3 3.4 + - - +
477C ALA* 2.8 25.5 + - - +
502C ALA* 2.9 26.7 - - - +
504C VAL* 3.6 21.7 - - - +
627D GLY* 4.0 4.0 - - - -
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Residues in contact with ALA 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C GLU 3.0 13.6 + - - +
471C LEU* 3.6 9.4 - - - +
472C ILE 3.2 0.2 - - - -
473C GLY* 1.3 72.7 - - - +
475C ALA* 1.3 67.2 + - - +
477C ALA* 3.2 2.4 + - - +
478C ALA* 2.8 27.1 + - - +
627D GLY* 3.7 11.8 - - - -
628D GLN 4.4 3.8 - - - +
629D ALA* 4.7 0.3 - - - +
642D VAL* 4.4 4.9 - - + +
643D SER 4.0 18.4 - - - +
644D THR* 4.4 7.0 - - - +
649D LEU* 4.5 15.5 - - + -
671D LEU* 4.4 6.3 - - + -
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Residues in contact with ALA 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C LEU 3.0 6.9 + - - +
472C ILE 3.5 7.4 - - - +
474C ALA* 1.3 76.1 - - - +
476C HIS* 1.3 53.5 + - - +
478C ALA* 3.3 2.6 - - - +
479C CYS* 2.8 36.2 + - - +
547C VAL* 4.5 2.0 - - + -
668D PRO* 3.5 35.1 - - + +
671D LEU* 3.5 22.1 - - + +
672D ILE* 3.6 18.8 - - + -
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Residues in contact with HIS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C ILE* 2.8 17.1 + - + +
473C GLY* 3.5 7.6 - - - +
475C ALA* 1.3 75.2 - - - +
477C ALA* 1.3 67.6 + - - +
479C CYS 3.3 0.2 + - - -
480C PHE* 2.9 23.0 + - + +
502C ALA* 4.7 2.5 - - + -
518C ILE* 3.7 16.5 - - + +
520C LEU* 3.8 18.3 - - + +
545C CYS* 4.1 6.3 - - - -
547C VAL* 3.7 26.4 - - + +
548C SER* 2.6 31.1 + - - -
551C LEU* 3.5 25.4 - - + +
555C ILE* 3.8 26.2 - - + -
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Residues in contact with ALA 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C GLY 2.8 19.4 + - - +
474C ALA 3.8 2.7 - - - +
476C HIS* 1.3 73.3 - - - +
478C ALA* 1.3 64.3 + - - +
480C PHE* 3.7 4.0 - - - +
481C SER* 2.9 27.5 + - - -
500C THR* 3.5 19.4 + - - +
501C THR 4.5 0.4 - - - -
502C ALA* 4.0 13.6 - - + +
520C LEU* 4.7 4.0 - - - -
627D GLY 4.2 0.9 - - - +
628D GLN 3.9 4.7 - - - -
629D ALA* 3.3 26.5 - - + +
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Residues in contact with ALA 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C ALA 2.8 18.1 + - - +
475C ALA* 3.3 6.3 - - - +
477C ALA* 1.3 79.3 - - - +
479C CYS* 1.3 67.7 + - - +
482C MET* 3.2 7.3 + - - +
629D ALA* 3.1 5.7 - - - +
642D VAL* 3.3 26.5 - - + -
654D TYR* 2.7 38.0 + - + -
667D ASN 5.8 0.2 - - - -
668D PRO* 4.3 8.7 - - + -
671D LEU* 5.3 1.1 - - + -
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Residues in contact with CYS 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C ALA 2.8 12.9 + - - +
476C HIS 3.8 1.8 - - - +
478C ALA* 1.3 69.9 - - - +
480C PHE* 1.3 63.8 + - - +
482C MET* 2.8 17.2 + - - +
483C ALA* 2.9 11.8 + - - -
545C CYS* 3.5 12.3 - - - -
546C PRO* 3.4 33.4 - - - -
547C VAL* 3.3 33.7 - - + -
659D ARG* 3.6 20.4 - - - +
668D PRO* 3.8 13.5 - - + +
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Residues in contact with PHE 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C HIS* 2.9 25.0 + - + +
477C ALA* 3.7 3.4 - - - +
479C CYS* 1.3 74.0 - - - +
481C SER* 1.3 60.5 + - - +
483C ALA* 3.4 1.2 + - - +
484C LEU* 2.8 46.0 + - + +
500C THR* 4.1 25.1 - - + -
520C LEU* 4.2 18.4 - - + -
522C SER* 4.4 9.2 - - - -
538C ILE* 3.8 26.9 - - + -
541C ALA* 3.0 33.0 - - + -
542C LYS* 3.5 24.0 - - + -
545C CYS* 4.0 18.3 - - - -
557C LEU* 4.6 12.3 - - + -
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Residues in contact with SER 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C ALA 2.9 20.8 + - - -
478C ALA 3.6 4.5 - - - -
480C PHE* 1.3 76.8 - - - +
482C MET* 1.3 63.4 + - - +
484C LEU* 3.4 3.3 + - - +
485C SER* 3.1 22.3 + - - -
498C ILE* 3.7 19.4 - - - +
500C THR* 3.2 27.9 + - - +
629D ALA* 3.9 10.7 + - - +
630D HIS 4.8 0.4 - - - -
631D TRP* 4.2 13.0 - - - -
654D TYR* 3.8 9.9 - - - -
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Residues in contact with MET 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ALA 3.2 6.9 + - - +
479C CYS* 2.8 15.1 + - - +
481C SER* 1.3 71.2 - - - +
483C ALA* 1.3 67.8 + - - +
485C SER* 3.0 5.9 + - - -
486C LEU* 2.9 21.8 + - + +
631D TRP* 3.6 34.1 - - + -
635D ILE* 4.8 11.0 - - + +
654D TYR* 3.6 26.8 + - + -
655D GLY 3.7 24.0 - - - +
656D PHE* 3.9 7.0 - - + +
659D ARG* 3.6 38.6 - - + +
660D PHE* 4.2 12.1 - - - -
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Residues in contact with ALA 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C CYS* 2.9 7.3 + - - +
480C PHE 3.6 5.2 - - - +
482C MET* 1.3 75.8 - - - +
484C LEU* 1.3 64.5 + - - +
486C LEU* 3.0 12.0 + - - +
487C MET* 2.8 27.4 + - + +
541C ALA* 4.0 10.5 - - + -
545C CYS* 3.6 34.1 - - + -
546C PRO* 5.0 5.2 - - + -
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Residues in contact with LEU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C PHE* 2.8 34.2 + - + +
481C SER* 3.5 6.3 - - - +
482C MET 3.1 0.2 + - - -
483C ALA* 1.3 71.6 - - - +
485C SER* 1.3 65.9 + - - +
487C MET* 2.9 14.6 + - - +
488C LEU* 3.0 23.1 + - + +
498C ILE* 3.5 23.6 - - + -
524C VAL* 3.7 19.7 - - + -
534C PHE* 5.3 0.2 - - + -
537C ILE* 3.7 15.7 - - + -
538C ILE* 3.3 48.9 - - + -
541C ALA* 3.7 10.9 - - + +
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Residues in contact with SER 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C SER 3.1 7.4 + - - -
482C MET 3.0 8.6 + - - -
484C LEU* 1.3 78.3 - - - +
486C LEU* 1.3 57.2 + - - +
488C LEU* 3.3 4.3 + - - +
489C GLY 3.0 18.4 + - - -
493C PHE 4.9 0.2 - - - +
495C PRO* 4.0 18.9 - - - +
498C ILE* 4.1 1.3 - - - +
631D TRP* 3.2 27.5 + - - -
633D GLY 2.9 23.7 + - - -
635D ILE* 2.9 25.4 + - - +
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C MET* 2.9 12.2 + - + +
483C ALA* 3.1 15.0 - - - +
485C SER* 1.3 77.5 - - - +
487C MET* 1.3 68.4 + - - +
489C GLY* 2.9 17.0 + - - -
490C GLU* 3.1 41.0 + - + +
635D ILE* 3.2 36.3 - - + +
656D PHE* 5.9 1.8 - - + -
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Residues in contact with MET 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ALA* 2.8 22.8 + - + +
484C LEU* 2.9 3.8 + - - +
486C LEU* 1.3 78.9 - - - +
488C LEU* 1.3 63.1 + - - +
490C GLU* 3.3 30.4 + - - +
491C ALA* 3.3 12.0 + - - +
537C ILE* 3.4 28.8 - - + +
540C LYS* 3.1 48.2 - - + +
541C ALA* 3.7 18.4 - - + +
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Residues in contact with LEU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C LEU* 3.0 29.4 + - + +
485C SER 3.6 5.8 - - - +
487C MET* 1.3 76.0 - - - +
489C GLY* 1.3 58.4 + - - +
491C ALA* 3.0 17.4 + - + +
492C GLY 3.0 0.2 + - - -
493C PHE* 2.9 37.4 + - + +
495C PRO* 3.6 36.1 - - + -
498C ILE* 4.6 1.3 - - + -
524C VAL* 4.8 0.2 - - + -
526C VAL* 3.9 14.6 - - + -
529C ILE* 4.0 22.4 - - + -
534C PHE* 4.3 10.5 - - + -
537C ILE* 3.4 30.5 - - + -
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Residues in contact with GLY 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C SER 3.0 10.6 + - - -
486C LEU 2.9 9.5 + - - -
488C LEU* 1.3 73.3 - - - +
490C GLU* 1.3 57.7 + - - +
491C ALA 2.9 8.7 + - - -
492C GLY* 3.2 13.3 + - - -
493C PHE 3.5 9.2 + - - -
494C THR* 5.7 0.9 - - - -
634D ASP* 6.1 1.3 - - - -
635D ILE* 4.4 10.8 - - - -
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Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C LEU* 3.1 37.8 + - + +
487C MET* 3.3 22.9 + - - +
489C GLY* 1.3 75.2 - - - +
491C ALA* 1.3 57.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il