Contacts of the helix formed by residues 683 - 713 (chain B) in PDB entry 1JQI
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 LEU 683 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A FAD 3.7 55.9 - - + +
675B ALA* 4.9 11.4 - - + +
676B PHE* 5.6 5.2 - - + -
679B PRO 4.6 2.7 - - - +
680B LEU* 2.9 37.5 + - + +
682B LYS* 1.3 79.7 - - + +
684B GLN* 1.3 65.6 + - - +
685B ASN 4.6 0.7 - - - +
686B ILE* 3.1 23.4 + - + +
687B GLN* 3.1 14.2 + - - +
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Residues in contact with GLN 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B LYS 3.5 4.2 + - - -
683B LEU* 1.3 70.5 - - - +
685B ASN* 1.3 63.8 + - - +
687B GLN* 3.0 18.6 + - + +
688B PHE* 3.0 53.3 + - + -
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Residues in contact with ASN 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU* 3.2 30.2 - - - +
399A FAD 4.2 18.9 + - + -
683B LEU* 3.3 0.8 - - - +
684B GLN* 1.3 77.1 - - - +
686B ILE* 1.3 65.9 + - - +
688B PHE* 3.3 10.1 + - - +
689B LYS* 3.1 45.0 + - - +
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Residues in contact with ILE 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A FAD 3.9 30.5 - - - +
670B ALA* 4.4 11.7 - - + -
680B LEU* 3.4 38.4 - - + +
681B THR* 4.3 7.0 - - - +
683B LEU* 3.1 20.0 + - + +
685B ASN* 1.3 84.6 - - - +
687B GLN* 1.3 63.2 + - - +
689B LYS* 3.3 8.6 + - + +
690B LEU* 3.1 36.3 + - + +
742B ILE* 4.4 23.8 - - + -
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Residues in contact with GLN 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B THR* 3.2 29.3 + - - +
682B LYS* 3.5 24.9 + - - +
683B LEU 3.5 7.3 + - - +
684B GLN* 3.0 15.7 + - - +
686B ILE* 1.3 79.6 - - - +
688B PHE* 1.3 61.1 + - + +
690B LEU* 3.4 11.3 + - + +
691B ALA* 3.0 27.7 + - - +
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Residues in contact with PHE 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B GLN* 3.0 45.1 + - + +
685B ASN* 3.6 11.9 - - - +
687B GLN* 1.3 80.1 - - + +
689B LYS* 1.3 65.5 + - + +
691B ALA* 3.4 7.8 + - + +
692B ASP* 3.0 31.6 + - - +
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Residues in contact with LYS 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU* 2.8 37.3 + - - +
399A FAD 5.2 0.9 - - - -
685B ASN* 3.1 39.2 + - - +
686B ILE* 3.7 15.5 - - + +
687B GLN 3.3 0.2 - - - -
688B PHE* 1.3 72.5 - - + +
690B LEU* 1.3 62.1 + - - +
692B ASP* 3.2 7.7 + - - +
693B MET* 2.8 37.8 + - + +
738B GLN* 2.9 38.2 - - + +
741B GLN* 4.4 6.0 - - - +
742B ILE* 4.2 25.8 - - + -
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Residues in contact with LEU 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LEU* 4.1 9.7 - - + +
666B ALA* 4.2 8.3 - - + -
667B VAL* 4.0 31.9 - - + +
670B ALA* 4.9 3.8 - - + -
681B THR* 4.7 16.4 - - + -
686B ILE* 3.1 31.0 + - + +
687B GLN* 3.7 8.7 - - + +
689B LYS* 1.3 76.1 - - - +
691B ALA* 1.3 58.7 + - - +
693B MET* 3.3 11.7 + - - +
694B ALA* 2.9 31.2 + - - +
742B ILE* 4.1 20.0 - - + -
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Residues in contact with ALA 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B GLN 3.0 17.4 + - - +
688B PHE* 3.6 8.7 - - + +
690B LEU* 1.3 77.4 - - - +
692B ASP* 1.3 62.0 + - - +
694B ALA* 3.3 6.7 + - - +
695B LEU* 3.0 29.7 + - - +
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Residues in contact with ASP 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B PHE* 3.0 21.7 + - - +
689B LYS* 3.7 6.4 - - - +
691B ALA* 1.3 77.0 - - - +
693B MET* 1.3 66.2 + - + +
695B LEU* 3.8 11.1 - - - +
696B ALA* 3.1 25.8 + - - +
----------------------------------------------------------
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Residues in contact with MET 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LEU* 3.7 25.4 - - + -
666B ALA* 3.9 21.3 - - + -
689B LYS 2.8 33.6 + - - +
690B LEU* 3.5 10.5 - - - +
692B ASP* 1.3 79.6 - - + +
694B ALA* 1.3 62.1 + - - +
696B ALA* 3.6 0.4 + - - -
697B LEU* 3.2 19.4 + - - +
735B ILE* 3.4 60.3 - - + +
738B GLN* 3.9 24.2 - - + -
739B ALA* 4.4 5.4 - - + +
742B ILE* 4.0 11.0 - - - -
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Residues in contact with ALA 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LEU* 4.3 19.4 - - + +
690B LEU 2.9 17.4 + - - +
691B ALA* 3.6 6.3 - - - +
693B MET* 1.3 77.4 - - - +
695B LEU* 1.3 62.9 + - - +
697B LEU* 3.3 2.7 + - - +
698B GLU* 3.0 42.6 + - - +
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Residues in contact with LEU 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B ALA 3.0 16.8 + - - +
692B ASP* 3.8 11.4 - - - +
694B ALA* 1.3 77.4 - - - +
696B ALA* 1.3 66.3 + - + +
698B GLU* 4.2 2.6 - - - +
699B SER* 2.9 40.8 + - - +
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Residues in contact with ALA 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B ASP 3.1 16.6 + - - +
693B MET 4.0 3.4 - - - +
695B LEU* 1.3 85.6 - - + +
697B LEU* 1.3 57.3 + - - +
699B SER* 3.8 3.3 - - - -
700B ALA* 3.1 29.3 + - - +
727B ALA 5.2 0.2 - - - +
731B ALA* 4.2 20.6 - - + +
735B ILE* 4.5 7.0 - - + -
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Residues in contact with LEU 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B LEU* 3.8 36.4 - - + +
659B ALA* 3.9 15.5 - - + +
660B GLN* 3.5 42.6 - - - +
663B LEU* 4.3 16.2 - - + -
693B MET 3.2 15.3 + - - +
694B ALA* 3.8 3.8 - - - +
695B LEU 3.2 0.2 - - - -
696B ALA* 1.3 75.7 - - - +
698B GLU* 1.3 67.2 + - + +
699B SER 3.2 1.1 - - - -
700B ALA* 3.3 3.4 + - - -
701B ARG* 3.0 34.9 + - - +
731B ALA* 5.1 2.0 - - + -
735B ILE* 3.9 9.1 - - + +
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Residues in contact with GLU 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B VAL 4.7 3.8 - - - +
405B TYR* 4.1 23.8 - - + +
406B GLN 5.2 2.8 + - - +
694B ALA* 3.0 28.3 + - - +
695B LEU* 4.4 2.5 - - - +
697B LEU* 1.3 78.7 - - + +
699B SER* 1.3 61.8 + - - +
701B ARG* 3.3 24.0 + - - +
702B LEU* 3.1 30.2 + - + +
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Residues in contact with SER 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B LEU* 2.9 30.6 + - - +
696B ALA* 3.8 6.1 - - - -
698B GLU* 1.3 79.6 - - - +
700B ALA* 1.3 61.5 + - - +
702B LEU* 3.3 17.9 + - - +
703B LEU* 3.4 21.0 + - - +
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Residues in contact with ALA 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B LEU* 3.8 8.7 - - + -
696B ALA 3.1 19.4 + - - +
697B LEU* 3.8 4.3 - - - +
699B SER* 1.3 74.9 - - - +
701B ARG* 1.3 63.6 + - - +
703B LEU* 3.4 13.1 + - - +
704B THR* 2.8 28.4 + - - -
724B ALA* 5.0 1.1 - - - +
727B ALA* 4.1 9.2 - - + +
728B ALA* 3.8 32.7 - - - +
731B ALA* 4.7 2.2 - - + -
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Residues in contact with ARG 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 3.3 54.8 - - - +
479B GLU* 2.9 34.9 + - - -
656B LEU* 3.5 18.8 - - + +
660B GLN* 3.2 23.2 + - - +
697B LEU* 3.0 33.0 + - - +
698B GLU* 3.6 28.1 - - - +
699B SER 3.2 0.4 - - - -
700B ALA* 1.3 74.3 - - - +
702B LEU* 1.3 60.5 + - + +
704B THR* 3.2 2.4 + - - -
705B TRP* 2.9 56.2 + - + +
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Residues in contact with LEU 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B GLU* 3.1 17.0 + - + +
699B SER* 3.3 11.0 + - - +
700B ALA 3.3 0.2 - - - -
701B ARG* 1.3 81.7 - - + +
703B LEU* 1.3 57.8 + - + +
705B TRP* 3.9 18.3 - - + +
706B ARG* 3.0 29.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B SER* 3.4 17.8 + - - +
700B ALA* 3.7 7.9 - - - +
701B ARG 3.3 0.4 - - - -
702B LEU* 1.3 77.5 - - + +
704B THR* 1.3 61.8 + - - +
706B ARG* 3.3 38.0 + - - +
707B ALA* 3.1 22.3 + - - +
720B GLU 4.3 2.8 - - - +
723B MET* 4.3 18.6 - - + +
724B ALA* 3.9 14.9 - - + +
727B ALA* 3.6 29.6 - - + -
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Residues in contact with THR 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B SER* 3.4 23.6 - - - +
649B ILE* 4.0 9.1 - - + +
652B ALA* 3.6 26.9 - - + +
653B SER* 3.6 13.2 - - - +
656B LEU* 3.6 17.5 - - + +
700B ALA 2.8 18.9 + - - -
701B ARG 3.2 8.0 + - - -
703B LEU* 1.3 74.0 - - - +
705B TRP* 1.3 65.6 + - + +
707B ALA* 3.3 4.5 + - - +
708B ALA* 3.1 21.0 + - - +
724B ALA* 3.6 12.4 + - - +
728B ALA* 4.6 0.5 - - - +
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Residues in contact with TRP 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 3.6 37.0 - + - -
407B SER* 3.3 26.2 - - - -
408B VAL* 5.8 2.7 - - + -
410B LEU* 3.5 26.0 - - + -
472B LEU* 4.0 15.0 - - + +
475B SER* 3.7 21.4 + - - -
476B ILE* 3.7 26.6 - - + +
479B GLU* 4.7 5.9 + - - -
656B LEU* 5.3 0.8 - - + +
701B ARG* 2.9 41.5 + - + +
702B LEU* 3.9 18.2 - - + +
704B THR* 1.3 77.4 - - + +
706B ARG* 1.3 57.5 + - - +
708B ALA* 3.3 6.4 + - - +
709B MET* 2.9 48.6 + - + +
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Residues in contact with ARG 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B LEU 3.0 18.9 + - - +
703B LEU* 3.4 27.4 + - - +
704B THR 3.2 0.2 - - - -
705B TRP* 1.3 77.5 - - - +
707B ALA* 1.3 63.0 + - - +
709B MET* 3.2 14.8 + - + +
710B LEU* 2.9 41.1 + - + +
719B LYS* 5.4 4.9 - - - +
720B GLU* 3.7 31.0 + - - +
723B MET* 3.5 29.3 - - - -
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Residues in contact with ALA 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B ILE* 3.7 25.3 - - + +
703B LEU 3.1 6.1 + - - +
704B THR 3.6 7.9 - - - +
706B ARG* 1.3 77.9 - - - +
708B ALA* 1.3 61.4 + - - +
710B LEU* 3.4 5.5 + - - +
711B LYS* 3.0 23.7 + - - +
717B PHE* 4.0 5.0 - - - +
720B GLU* 3.8 33.8 - - - +
721B SER* 3.9 7.6 - - - +
724B ALA* 4.7 2.9 - - + -
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Residues in contact with ALA 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B TYR* 3.6 31.6 - - + +
472B LEU* 3.8 8.3 - - - -
475B SER* 4.5 3.8 - - - -
649B ILE* 4.0 17.2 - - + +
704B THR 3.1 13.6 + - - +
705B TRP* 3.5 11.9 - - - +
707B ALA* 1.3 77.4 - - - +
709B MET* 1.3 56.7 + - - +
711B LYS* 3.2 4.9 + - - +
712B ASP* 2.9 32.2 + - - -
----------------------------------------------------------
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Residues in contact with MET 709 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B LEU* 4.0 25.1 - - + -
705B TRP* 2.9 44.1 + - + +
706B ARG* 3.7 10.3 - - - +
708B ALA* 1.3 72.7 - - - +
710B LEU* 1.3 62.9 + - + +
712B ASP* 3.2 8.0 + - + +
713B ASN* 2.9 38.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 710 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B ARG* 2.9 30.1 + - + +
707B ALA 3.7 4.0 - - - +
709B MET* 1.3 74.5 - - + +
711B LYS* 1.3 66.6 + - - +
713B ASN* 3.1 5.7 + - + +
714B LYS 3.0 5.2 + - - -
715B LYS* 2.9 46.2 + - + +
716B PRO 3.8 11.0 - - - +
717B PHE* 3.9 8.5 - - + -
720B GLU* 3.4 46.2 - - + +
----------------------------------------------------------
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Residues in contact with LYS 711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ASP* 2.8 30.3 + - - -
471B TYR* 4.0 23.7 - - + -
504B LEU* 6.2 0.2 - - - +
646B MET* 3.8 27.7 - - + -
649B ILE* 4.4 2.2 - - + -
707B ALA 3.0 14.3 + - - +
708B ALA* 3.3 12.3 - - - +
710B LEU* 1.3 76.0 - - - +
712B ASP* 1.3 67.2 + - - +
714B LYS* 3.1 37.7 + - - +
715B LYS 4.6 0.4 - - - -
717B PHE* 3.5 40.6 - - + -
----------------------------------------------------------
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Residues in contact with ASP 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ASP* 5.0 1.9 - - - +
470B ASP* 3.2 34.3 - - + +
471B TYR* 2.9 24.0 + - - +
472B LEU* 3.2 21.3 + - - +
708B ALA 2.9 14.8 + - - +
709B MET* 3.6 10.2 - - - +
711B LYS* 1.3 82.1 + - - +
713B ASN* 1.3 63.6 + - - +
714B LYS* 3.2 17.9 - - - +
----------------------------------------------------------
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Residues in contact with ASN 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B MET* 2.9 22.5 + - - +
710B LEU* 3.1 7.5 + - + +
712B ASP* 1.3 82.8 + - - +
714B LYS* 1.3 72.1 + - - +
715B LYS* 3.3 26.0 - - + +
----------------------------------------------------------
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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