Contacts of the helix formed by residues 677 - 705 (chain B) in PDB entry 1GKU
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 ASP 677 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLU* 2.6 20.9 + - - +
674B ARG* 4.2 8.9 - - - +
675B ASP 3.4 2.1 + - - +
676B VAL* 1.3 71.4 - - - +
678B GLU* 1.3 61.3 + - - +
679B ASN* 3.1 33.6 + - - +
680B LEU* 3.3 28.9 + - + +
681B VAL* 3.3 22.7 + - - +
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Residues in contact with GLU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B TRP* 3.7 31.3 + - - -
676B VAL* 3.4 14.1 + - - +
677B ASP* 1.3 71.6 + - - +
679B ASN* 1.3 61.6 + - - +
681B VAL* 3.3 7.3 + - + +
682B LYS* 2.9 59.6 + - + +
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Residues in contact with ASN 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B ASP* 3.1 16.6 + - - +
678B GLU* 1.3 78.0 - - - +
680B LEU* 1.3 64.5 + - - +
682B LYS* 3.4 6.9 + - - +
683B ALA* 3.1 19.4 + - - +
1032B ILE* 3.3 21.3 - - - +
1033B GLU* 3.4 22.7 + - - +
1034B ARG 4.5 3.2 + - - -
1035B GLY* 3.8 23.7 - - - +
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Residues in contact with LEU 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B PRO 6.1 0.4 - - - -
633B ASP* 4.6 14.6 - - - +
634B THR* 3.3 26.1 - - + +
637B GLU* 3.9 33.2 - - + +
674B ARG* 4.9 5.6 - - - +
677B ASP* 3.3 33.6 + - + +
678B GLU 3.3 0.2 - - - -
679B ASN* 1.3 78.8 - - - +
681B VAL* 1.3 62.9 - - - +
683B ALA* 3.3 2.5 + - - -
684B GLN* 3.1 19.8 + - - +
1033B GLU* 4.1 23.6 - - + +
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Residues in contact with VAL 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B THR 5.1 0.4 - - - -
637B GLU* 3.5 33.9 - - + +
638B LYS* 4.0 9.0 - - + +
641B TRP* 3.5 50.9 - - + -
676B VAL* 4.0 3.6 - - + -
677B ASP 3.3 12.5 + - - +
678B GLU* 3.3 12.3 + - + +
679B ASN 3.2 0.6 - - - -
680B LEU* 1.3 75.3 - - - +
682B LYS* 1.3 62.5 + - + +
684B GLN* 3.4 6.1 + - - +
685B VAL* 3.0 32.0 + - + +
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Residues in contact with LYS 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B GLU* 2.9 42.5 + - + +
679B ASN* 4.9 5.5 + - - +
681B VAL* 1.3 75.5 - - + +
683B ALA* 1.3 67.8 + - - +
685B VAL* 3.8 5.9 - - - +
686B VAL* 3.1 28.1 + - - +
1032B ILE* 3.3 21.3 - - + -
1039B TYR* 3.6 50.9 - - + -
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Residues in contact with ALA 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B THR* 4.0 1.3 - - + -
679B ASN 3.1 7.6 + - - +
680B LEU 3.3 10.3 - - - +
682B LYS* 1.3 79.3 - - - +
684B GLN* 1.3 63.2 + - - +
686B VAL* 3.1 3.5 + - - +
687B ARG* 3.0 24.0 + - - +
972B ARG* 5.6 3.1 - - - +
1029B MET* 4.0 5.8 - - + +
1032B ILE* 3.4 30.9 - - + +
1033B GLU* 3.6 30.3 - - + +
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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
----------------------------------------------------------
555B HIS* 4.8 4.8 - - - -
578B TYR* 5.2 0.2 + - - -
634B THR* 3.7 40.2 - - - +
635B GLU* 2.8 28.8 + - - +
638B LYS* 2.9 39.5 - - + +
680B LEU 3.1 4.5 + - - +
681B VAL 3.7 7.0 - - - +
683B ALA* 1.3 78.6 - - - +
685B VAL* 1.3 63.2 + - - +
687B ARG* 3.3 8.6 + - - +
688B ARG* 3.0 39.7 + - - +
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Residues in contact with VAL 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B PRO* 4.2 24.0 - - + -
578B TYR* 3.8 8.3 - - - +
638B LYS* 3.5 28.7 - - + -
641B TRP* 4.9 5.6 - - + -
681B VAL* 3.0 28.1 + - + +
682B LYS* 3.8 7.2 - - - +
684B GLN* 1.3 78.9 - - - +
686B VAL* 1.3 67.0 + - + +
688B ARG* 3.0 16.2 + - - +
689B ILE* 3.0 22.1 + - + +
1039B TYR* 5.4 9.0 - - + -
1043B LEU* 5.6 2.7 - - + -
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Residues in contact with VAL 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B LYS 3.1 17.6 + - - +
683B ALA* 3.6 4.9 - - - +
685B VAL* 1.3 77.3 - - + +
687B ARG* 1.3 57.7 + - - +
689B ILE* 3.2 2.9 + - - +
690B GLU* 2.8 28.1 + - - +
1029B MET* 4.2 15.3 - - + -
1032B ILE* 5.2 5.6 - - + -
1039B TYR* 4.1 28.0 - - + +
1042B ALA* 4.4 13.2 - - + -
1043B LEU* 3.7 28.3 - - + -
1046B MET* 3.7 23.5 - - + +
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Residues in contact with ARG 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B ALA 3.0 16.4 + - - +
684B GLN* 3.7 8.1 - - - +
686B VAL* 1.3 77.8 - - - +
688B ARG* 1.3 61.9 + - - +
690B GLU* 4.2 9.4 + - - +
691B ASP* 2.6 58.7 + - - +
972B ARG* 3.7 18.8 - - - +
975B THR* 4.9 14.2 + - - -
1026B GLU* 5.4 1.8 - - - -
1029B MET* 3.3 37.0 - - + -
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Residues in contact with ARG 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B ASP* 3.0 38.1 + - - +
559B LEU* 4.4 14.6 - - + +
578B TYR* 5.6 5.6 - - + +
684B GLN* 3.0 32.2 + - - +
685B VAL* 3.0 11.9 + - - +
687B ARG* 1.3 80.0 - - - +
689B ILE* 1.3 61.8 + - + +
691B ASP* 3.4 15.5 - - - +
692B ARG* 3.0 56.0 + - - +
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Residues in contact with ILE 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LEU* 3.9 26.0 - - + -
568B VAL* 3.8 22.0 - - + -
576B PRO* 4.6 11.7 - - + -
578B TYR* 5.8 0.2 - - - +
685B VAL* 3.0 24.4 + - + +
686B VAL* 3.2 7.2 + - - +
688B ARG* 1.3 77.0 - - + +
690B GLU* 1.3 58.4 + - - +
691B ASP 3.0 1.1 - - - -
692B ARG* 2.9 4.6 + - + +
693B TRP* 2.7 79.4 + - + +
1043B LEU* 4.5 17.3 - - + -
1046B MET* 4.9 0.4 - - - -
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Residues in contact with GLU 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B VAL 2.8 18.4 + - - +
687B ARG* 3.9 24.5 + - - +
689B ILE* 1.3 77.7 - - - +
691B ASP* 1.3 64.1 + - - +
694B ILE* 3.2 40.2 + - - +
695B GLY 4.0 0.3 + - - -
715B ARG* 2.8 40.5 + - - +
1025B LEU* 4.1 10.0 - - - +
1029B MET* 4.3 9.8 - - + +
1046B MET* 3.3 25.5 - - + +
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Residues in contact with ASP 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B ARG* 2.6 52.0 + - - +
688B ARG* 3.4 20.2 + - - +
689B ILE 3.0 0.4 - - - -
690B GLU* 1.3 81.7 - - - +
692B ARG* 1.3 61.7 + - - +
695B GLY* 3.5 19.8 + - - +
982B ARG* 6.0 0.2 + - - -
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Residues in contact with ARG 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B ASP* 4.7 1.6 + - - -
559B LEU* 3.0 37.3 + - + +
560B ILE 2.7 32.7 + - - -
561B THR* 3.5 17.4 - - - +
566B HIS* 2.8 40.8 + - + +
568B VAL* 5.9 1.1 - - + -
688B ARG* 3.0 43.8 + - - +
689B ILE* 2.9 8.0 + - + +
691B ASP* 1.3 76.6 - - - +
693B TRP* 1.3 70.1 + - + +
696B PHE* 3.1 22.0 + - + +
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Residues in contact with TRP 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 3.1 55.7 + + + -
566B HIS* 4.4 10.3 - - + -
568B VAL* 3.6 30.0 - - + +
570B VAL* 4.3 1.6 - - + -
574B PHE* 3.3 30.1 - + - -
689B ILE* 2.7 39.6 + - + +
692B ARG* 1.3 74.9 - - + +
694B ILE* 1.3 73.2 + - + +
695B GLY 3.0 0.4 - - - -
696B PHE* 2.9 5.6 + - - +
697B VAL* 2.8 28.8 + - + +
1043B LEU* 4.2 5.8 - - + -
1046B MET* 4.1 25.1 - - + -
1047B TYR* 3.7 30.3 - + + -
1050B ILE* 4.1 13.2 - - + -
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Residues in contact with ILE 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B GLU* 3.2 29.3 + - - +
693B TRP* 1.3 81.4 - - + +
695B GLY* 1.3 67.7 + - - +
697B VAL* 4.1 8.5 - - - -
698B LEU* 2.9 56.3 + - + +
714B GLY* 5.0 0.2 - - - -
715B ARG* 3.4 47.1 - - + +
1016B PHE* 5.7 1.8 - - + +
1046B MET* 4.3 10.3 - - + -
1049B GLU* 4.0 4.9 - - - +
1050B ILE* 3.3 25.3 - - + +
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Residues in contact with GLY 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B GLU 4.0 0.4 + - - -
691B ASP* 3.5 21.1 + - - -
693B TRP 3.0 1.6 + - - -
694B ILE* 1.3 85.7 - - - +
696B PHE* 1.3 55.5 + - - +
698B LEU* 4.0 0.3 - - - +
699B SER* 2.9 32.5 + - - -
713B ALA 3.7 18.3 - - - +
714B GLY* 5.2 1.8 - - - -
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Residues in contact with PHE 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B HIS* 3.1 47.6 - + + -
692B ARG* 3.1 22.1 + - + +
693B TRP 2.9 5.1 + - - +
695B GLY* 1.3 72.3 - - - +
697B VAL* 1.3 59.5 + - + +
699B SER* 3.9 4.4 - - - -
700B GLN* 3.0 48.0 + - + +
703B TRP* 3.7 29.6 - + - -
709B ARG* 3.7 16.8 - - - -
1054B ASP* 5.9 1.3 - - - -
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Residues in contact with VAL 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 5.2 5.6 - - + -
566B HIS* 6.0 1.1 - - + -
693B TRP* 2.8 26.9 + - - +
694B ILE* 3.5 9.4 - - - +
696B PHE* 1.3 76.6 - - + +
698B LEU* 1.3 69.9 + - + +
700B GLN* 2.9 24.2 - - - +
701B LYS* 3.1 13.3 + - + +
1050B ILE* 4.2 20.2 - - + -
1053B ILE* 3.5 35.7 - - + -
1054B ASP* 4.1 28.5 - - + +
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Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B ILE* 2.9 45.9 + - + +
695B GLY 4.0 0.4 - - - +
697B VAL* 1.3 72.4 - - + +
699B SER* 1.3 65.5 + - - +
701B LYS* 2.8 24.1 + - + +
702B LEU* 3.0 11.5 + - - +
713B ALA* 3.3 25.1 - - + -
714B GLY 4.1 16.8 - - - +
715B ARG* 4.3 1.1 - - - +
718B THR* 5.1 3.1 - - - +
1009B LEU* 4.6 18.1 - - + +
1016B PHE* 5.4 7.4 - - + +
1017B VAL* 4.8 20.0 - - + -
1053B ILE* 4.6 19.5 - - + -
----------------------------------------------------------
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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 GLY 2.9 19.8 + - - -
696B PHE* 4.1 2.0 - - - -
698B LEU* 1.3 76.5 - - - +
700B GLN* 1.3 60.1 + - - +
702B LEU* 3.2 9.0 + - - +
703B TRP* 2.9 47.4 + - - -
711B LEU 3.5 14.8 - - - -
712B SER* 3.0 7.6 - - - -
713B ALA* 2.6 30.5 + - - +
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Residues in contact with GLN 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B PHE* 3.0 32.0 + - + +
697B VAL* 2.9 15.1 + - - +
698B LEU 2.8 1.0 + - - -
699B SER* 1.3 73.3 - - - +
701B LYS* 1.3 83.2 + - + +
702B LEU 2.9 3.8 - - - -
703B TRP* 2.8 38.0 + - + +
704B GLU* 3.1 13.5 + - + +
1054B ASP* 3.6 23.1 + - - +
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Residues in contact with LYS 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B VAL* 3.6 16.3 + - + +
698B LEU* 2.8 15.1 + - + +
700B GLN* 1.3 106.8 + - - +
702B LEU* 1.3 56.5 + - - +
704B GLU* 2.7 44.3 + - - +
705B ARG 3.6 2.4 + - - -
1008B PHE* 3.2 31.1 - - + -
1009B LEU* 5.4 3.4 - - + -
1012B ARG* 5.4 13.9 - - - +
1053B ILE* 5.0 6.5 - - + +
1054B ASP* 3.3 34.9 + - - +
----------------------------------------------------------
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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 LEU 3.0 7.2 + - - +
699B SER* 3.4 9.9 - - - +
700B GLN 2.9 1.2 - - - -
701B LYS* 1.3 78.0 - - - +
703B TRP* 1.3 55.7 + - - +
704B GLU 3.3 1.6 - - - -
705B ARG 2.5 23.9 - - - +
706B PHE* 3.8 26.5 - - + -
708B ASN 4.0 0.2 - - - +
711B LEU* 3.2 27.1 - - + +
712B SER 4.0 11.7 - - - +
713B ALA* 3.6 31.0 - - + -
988B TYR* 4.2 3.8 - - - +
1005B VAL* 3.5 24.0 - - + -
1008B PHE* 3.8 4.3 - - + -
1009B LEU* 3.4 32.1 - - + -
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Residues in contact with TRP 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B PHE* 3.7 29.6 - + - -
699B SER* 2.9 21.8 - - - -
700B GLN* 2.8 30.7 + - + +
702B LEU* 1.3 75.8 - - - +
704B GLU* 1.3 60.3 + - - +
705B ARG 3.4 0.2 - - - -
707B ASN* 3.0 28.6 + - - +
708B ASN 2.9 32.1 + - - +
709B ARG* 3.1 68.1 - - + +
710B ASN 3.8 0.6 - - - +
711B LEU* 2.5 37.6 + - + +
712B SER* 5.5 0.4 - - - -
----------------------------------------------------------
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Residues in contact with GLU 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B GLN* 3.1 7.8 + - + +
701B LYS* 2.7 56.7 + - - +
703B TRP* 1.3 77.2 - - - +
705B ARG* 1.3 79.4 + - - +
707B ASN* 3.4 17.3 + - - +
1008B PHE* 4.0 7.1 - - - -
1012B ARG* 4.1 13.7 + - - -
----------------------------------------------------------
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Residues in contact with ARG 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B LYS 3.6 8.7 + - - +
702B LEU 2.5 24.4 - - - +
703B TRP 3.4 0.7 - - - -
704B GLU* 1.3 86.4 - - - +
706B PHE* 1.3 109.5 + - + +
707B ASN 2.6 7.8 + - - -
1008B PHE* 3.4 39.2 - - + +
----------------------------------------------------------
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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