Contacts of the helix formed by residues 690 - 719 (chain B) in PDB entry 6NYY
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 SER 690 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A GLU* 3.3 13.7 - - - -
694A ALA* 3.3 36.4 + - - -
695A ARG* 4.0 3.5 - - - -
698A ASP* 2.9 9.2 + - - +
687B LYS* 5.3 0.9 - - - +
689B TYR* 1.3 83.0 - - - +
691B GLU* 1.3 63.1 + - - +
692B ALA* 3.3 6.5 + - - +
693B THR* 2.8 31.7 + - - -
694B ALA* 3.2 18.4 + - - +
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Residues in contact with GLU 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A GLU* 2.5 32.4 + - + +
687B LYS* 5.1 4.3 + - - +
690B SER* 1.3 72.3 - - - +
692B ALA* 1.3 56.0 + - - +
694B ALA* 3.2 5.0 + - - +
695B ARG* 2.8 28.5 + - + +
689C TYR 5.3 0.3 - - - +
690C SER* 3.3 15.1 - - - -
691C GLU* 2.5 57.4 + - + +
692C ALA* 3.6 5.1 + - + +
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Residues in contact with ALA 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A GLU* 3.8 2.4 + - + +
695A ARG* 3.7 44.2 - - + +
699A ASP* 6.2 0.2 - - - +
690B SER* 3.3 4.4 + - - +
691B GLU* 1.3 76.2 - - - +
693B THR* 1.3 59.4 + - - +
695B ARG* 3.6 9.2 + - - +
696B LEU* 3.1 24.8 + - - +
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Residues in contact with THR 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A ASP* 3.3 20.8 + - - +
702A ARG* 3.6 20.9 + - - +
670B VAL* 5.1 2.5 - - + -
673B ILE* 5.1 6.1 - - + -
675B PHE* 4.9 6.3 - - + -
689B TYR* 3.8 23.1 - - + -
690B SER* 2.8 28.2 + - - -
692B ALA* 1.3 77.5 - - - +
694B ALA* 1.3 50.3 + - - +
696B LEU* 2.9 8.8 + - + +
697B ILE* 2.6 48.5 + - + +
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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
----------------------------------------------------------
687B LYS* 3.5 29.2 - - + +
689B TYR* 3.6 19.0 - - + +
690B SER 3.2 13.0 + - - +
691B GLU* 3.2 9.1 + - - +
693B THR* 1.3 76.3 - - - +
695B ARG* 1.3 58.6 + - - +
697B ILE* 4.2 4.3 - - - -
698B ASP* 3.1 36.8 + - - +
690C SER* 3.4 10.8 - - - -
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Residues in contact with ARG 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B GLU* 2.8 17.1 + - + +
692B ALA* 3.8 11.0 - - - +
694B ALA* 1.3 77.5 - - - +
696B LEU* 1.3 60.0 + - - +
698B ASP* 4.1 0.7 - - - +
699B ASP* 2.9 46.2 + - - +
690C SER* 3.9 8.4 - - - -
692C ALA* 3.7 29.9 - - + +
695C ARG* 4.5 15.9 - - - +
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Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ARG* 4.3 25.8 - - - +
669B LYS* 3.7 49.8 - - + +
670B VAL* 4.3 14.8 - - + -
692B ALA 3.1 15.1 + - - +
693B THR* 2.9 9.5 + - + +
695B ARG* 1.3 74.8 - - - +
697B ILE* 1.3 62.7 + - - +
699B ASP* 3.6 4.9 + - + +
700B GLU* 3.3 32.1 + - + +
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Residues in contact with ILE 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B TYR* 4.3 4.5 - - + -
661B ILE* 4.3 4.7 - - + +
662B VAL* 3.8 31.6 - - + -
670B VAL* 4.3 25.1 - - + -
673B ILE* 5.8 0.2 - - + -
675B PHE* 5.0 3.1 - - + -
689B TYR* 3.6 40.4 - - + +
693B THR* 2.6 32.2 + - + +
694B ALA* 4.1 4.9 - - - +
696B LEU* 1.3 73.6 - - + +
698B ASP* 1.3 67.6 + - - +
700B GLU* 3.0 5.7 + - - +
701B VAL* 3.0 41.6 + - + +
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Residues in contact with ASP 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B TYR* 2.6 37.1 + - - +
687B LYS* 4.9 0.5 + - - -
694B ALA* 3.1 18.8 + - - +
695B ARG 4.5 1.8 - - - +
697B ILE* 1.3 79.6 - - - +
699B ASP* 1.3 60.5 + - - +
701B VAL* 4.2 6.5 - - - +
702B ARG* 3.2 30.4 + - - +
689C TYR* 3.6 6.4 - - - +
690C SER* 2.9 31.5 + - - +
693C THR* 3.5 18.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ARG* 2.9 38.0 + - - +
696B LEU* 4.1 7.1 - - + +
697B ILE 3.2 0.8 - - - -
698B ASP* 1.3 78.5 - - - +
700B GLU* 1.3 61.9 + - + +
702B ARG* 2.7 33.4 + - - +
703B ILE* 3.3 28.0 + - + +
693C THR* 5.5 0.7 + - - -
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Residues in contact with GLU 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B ILE* 4.7 6.0 - - + +
667B ASN* 3.2 38.0 + - - +
669B LYS* 3.3 38.4 + - + +
670B VAL* 4.4 6.3 - - + -
696B LEU* 3.3 19.4 + - + +
697B ILE* 3.0 4.8 + - - +
699B ASP* 1.3 78.3 - - + +
701B VAL* 1.3 59.8 + - - +
702B ARG 3.2 1.3 - - - -
703B ILE* 3.1 29.5 + - - +
704B LEU* 2.8 29.0 + - - +
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Residues in contact with VAL 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B THR* 5.2 2.2 - - + +
657B ALA* 3.8 22.9 - - + +
658B TYR* 3.6 40.2 - - + +
661B ILE* 3.7 23.8 - - + -
697B ILE* 3.0 17.5 + - + +
698B ASP* 4.4 4.9 - - - +
700B GLU* 1.3 74.4 - - - +
702B ARG* 1.3 58.3 + - - +
704B LEU* 3.2 7.0 + - - +
705B ILE* 2.9 41.9 + - + +
673C ILE* 5.1 8.7 - - + -
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Residues in contact with ARG 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B ASP* 3.2 27.4 + - - +
699B ASP* 2.7 35.2 + - - +
700B GLU 3.2 0.2 - - - -
701B VAL* 1.3 81.8 - - - +
703B ILE* 1.3 60.7 + - + +
705B ILE* 4.5 2.0 - - - +
706B ASN* 2.8 40.3 + - - +
669C LYS 3.9 13.1 + - - -
670C VAL* 2.9 31.1 + - - +
671C GLY* 4.9 2.2 - - - -
673C ILE* 4.4 17.4 - - + +
693C THR* 3.7 33.1 + - - +
696C LEU* 4.5 15.9 - - - +
----------------------------------------------------------
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Residues in contact with ILE 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B ASP* 3.3 17.4 + - + +
700B GLU* 3.1 33.5 + - - +
702B ARG* 1.3 77.2 - - + +
704B LEU* 1.3 59.9 + - - +
706B ASN* 3.5 3.7 + - - +
707B ASP* 2.9 50.9 + - - +
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Residues in contact with LEU 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B LYS* 5.5 8.3 - - - -
622B LEU* 5.1 10.9 - - + +
625B MET* 4.1 9.1 - - - +
657B ALA* 3.8 23.8 - - + -
660B GLN* 3.7 35.9 - - - +
661B ILE* 4.0 24.2 - - + -
700B GLU 2.8 17.0 + - - +
701B VAL 3.2 5.1 + - - +
703B ILE* 1.3 77.5 - - - +
705B ILE* 1.3 56.9 + - - +
707B ASP* 3.5 9.5 + - + +
708B ALA* 3.1 25.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B MET* 3.9 12.8 - - + -
629B LEU* 4.0 4.8 - - + +
653B VAL* 3.8 41.1 - - + +
654B THR* 4.7 1.6 - - - -
657B ALA* 4.2 5.2 - - + -
701B VAL* 2.9 32.4 + - + +
702B ARG* 4.5 3.8 - - - +
704B LEU* 1.3 75.0 - - - +
706B ASN* 1.3 54.4 + - - +
708B ALA* 3.1 4.2 + - - +
709B TYR* 2.7 32.4 + - - +
672C GLN* 4.0 32.8 - - + +
673C ILE* 3.7 29.2 - - + -
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Residues in contact with ASN 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ARG* 2.8 34.0 + - - +
703B ILE* 4.1 3.8 - - - +
705B ILE* 1.3 79.0 - - - +
707B ASP* 1.3 60.6 + - - +
709B TYR* 3.8 19.3 - - - +
710B LYS* 2.9 46.4 + - - +
668C GLU 5.8 2.2 + - - -
671C GLY* 5.1 9.0 - - - -
672C GLN* 5.1 9.4 - - - +
----------------------------------------------------------
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Residues in contact with ASP 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B LEU* 5.0 5.6 - - + +
703B ILE* 2.9 39.2 + - - +
704B LEU* 3.8 10.7 - - + +
706B ASN* 1.3 78.4 - - - +
708B ALA* 1.3 61.7 + - - +
710B LYS* 4.4 8.5 + - - +
711B ARG* 3.5 24.1 + - - +
----------------------------------------------------------
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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
----------------------------------------------------------
622B LEU* 4.0 12.1 - - + +
625B MET* 3.8 31.9 - - + -
626B CYS* 3.4 17.5 - - - -
629B LEU* 3.7 11.6 - - + +
704B LEU 3.1 14.9 + - - +
705B ILE 3.1 7.6 + - - +
707B ASP* 1.3 75.7 - - - +
709B TYR* 1.3 61.0 + - - +
712B THR* 3.0 24.6 + - - -
----------------------------------------------------------
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Residues in contact with TYR 709 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B LEU* 3.8 16.8 - - + -
632B ARG* 5.4 6.6 - - + +
633B VAL* 3.6 23.2 - - + +
636B GLU* 2.3 36.0 + - - -
705B ILE 2.7 20.9 + - - +
706B ASN* 3.7 20.0 - - - +
707B ASP 3.2 0.2 - - - -
708B ALA* 1.3 73.3 - - - +
710B LYS* 1.3 65.7 + - + +
711B ARG 3.2 0.2 - - - -
712B THR* 3.2 4.5 + - - -
713B VAL* 3.0 52.4 + - + +
672C GLN* 4.0 37.4 + - + -
----------------------------------------------------------
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Residues in contact with LYS 710 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B ASN* 2.9 32.8 + - - +
707B ASP* 4.6 8.9 + - - +
709B TYR* 1.3 82.3 - - + +
711B ARG* 1.3 57.4 + - - +
713B VAL* 4.0 6.7 - - - +
714B ALA* 3.0 28.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B LEU* 3.5 22.9 - - + +
586B GLU 5.7 0.8 - - - +
622B LEU* 4.1 21.0 - - - +
623B ASP* 2.6 32.7 + - - -
626B CYS* 3.2 31.8 - - + -
707B ASP 3.5 17.8 + - - +
709B TYR 3.2 0.6 - - - -
710B LYS* 1.3 80.8 - - - +
712B THR* 1.3 56.4 + - - +
714B ALA* 3.6 6.1 + - - +
715B LEU* 3.0 26.1 + - + +
----------------------------------------------------------
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Residues in contact with THR 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ALA* 4.9 3.4 - - + -
626B CYS* 2.8 38.1 + - - +
629B LEU* 4.6 2.3 - - - +
630B GLY* 3.7 23.3 - - - +
633B VAL* 3.8 14.1 - - + -
708B ALA 3.0 16.7 + - - -
709B TYR* 3.2 5.6 + - - -
711B ARG* 1.3 76.5 - - - +
713B VAL* 1.3 57.0 + - - +
714B ALA 3.2 0.2 - - - -
715B LEU* 3.0 6.7 + - + -
716B LEU* 2.8 45.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B VAL* 3.7 24.5 - - + -
636B GLU* 5.5 0.9 - - - +
637B ILE* 5.3 4.5 - - + -
709B TYR* 3.0 46.2 + - + +
710B LYS* 4.1 6.5 - - - +
712B THR* 1.3 75.2 - - - +
714B ALA* 1.3 61.7 + - - +
717B THR* 2.5 38.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B LYS 3.0 19.9 + - - +
711B ARG* 3.8 6.5 - - - +
713B VAL* 1.3 77.8 - - - +
715B LEU* 1.3 60.9 + - - +
717B THR* 4.2 2.0 - - - -
718B GLU* 3.8 23.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B VAL 4.9 0.2 - - - +
581B ALA* 4.1 31.4 - - + +
584B TYR* 4.0 26.9 - - + +
585B LEU* 4.1 26.2 - - + -
626B CYS* 5.8 0.9 - - + +
711B ARG 3.0 16.1 + - - +
712B THR* 3.0 11.7 + - + +
714B ALA* 1.3 78.7 - - - +
716B LEU* 1.3 64.1 + - + +
717B THR 3.2 1.5 + - - -
718B GLU* 3.6 4.6 + - - +
719B LYS* 3.1 45.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B GLY* 3.8 15.5 - - - +
580B VAL* 3.8 32.5 - - + -
581B ALA* 4.1 12.6 - - + +
630B GLY* 3.4 26.5 - - - +
633B VAL* 4.2 5.6 - - + -
634B SER* 4.5 6.1 - - - +
637B ILE* 3.4 22.0 - - + +
638B PHE* 6.0 0.7 - - - -
712B THR* 2.8 35.0 + - + +
715B LEU* 1.3 78.3 - - + +
717B THR* 1.3 60.0 + - - +
719B LYS* 4.1 6.6 - - + +
720B LYS* 3.8 16.3 - - - +
723B VAL* 3.9 13.6 - - + +
----------------------------------------------------------
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Residues in contact with THR 717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B ILE* 3.5 22.8 - - + +
713B VAL* 2.5 30.4 + - - +
714B ALA* 4.7 2.2 - - - -
715B LEU 3.2 1.0 - - - -
716B LEU* 1.3 77.4 - - - +
718B GLU* 1.3 64.2 + - - +
719B LYS 3.2 0.9 - - - -
720B LYS* 3.4 21.9 - - + +
----------------------------------------------------------
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Residues in contact with GLU 718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714B ALA 3.8 18.2 + - - +
715B LEU* 3.6 6.5 + - - +
717B THR* 1.3 79.2 - - - +
719B LYS* 1.3 78.0 + - + +
720B LYS 3.3 3.3 + - - -
721B ALA 5.2 0.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B VAL* 4.4 7.4 - - + -
584B TYR* 3.6 51.3 + - + -
715B LEU* 3.1 27.0 + - + +
716B LEU* 4.2 5.4 - - - -
717B THR 3.2 0.2 - - - -
718B GLU* 1.3 98.4 + - + +
720B LYS* 1.3 61.5 + - - +
721B ALA 3.4 2.2 - - - -
722B ASP* 3.3 23.5 + - - +
723B VAL* 3.3 15.6 + - - +
----------------------------------------------------------
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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