Contacts of the helix formed by residues 646 - 669 (chain B) in PDB entry 1GUX
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 646 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A PHE* 5.6 5.8 - - - -
529A TYR* 4.7 2.1 + - - -
530A LYS* 6.1 5.8 - - - -
572A LEU* 3.9 21.9 - - - +
645B THR* 1.3 78.1 + - - +
647B LEU* 1.3 57.4 + - - +
649B LEU* 3.0 9.1 + - - +
650B PHE* 2.7 36.0 + - - +
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Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A LEU* 3.6 30.7 - - + -
572A LEU* 3.5 44.1 - - + +
573A ILE* 3.6 16.6 - - + -
576A SER* 3.6 19.1 - - - +
577A LYS* 6.4 0.2 - - + -
645B THR 4.1 3.3 - - - +
646B SER* 1.3 82.1 + - - +
648B SER* 1.3 56.6 + - - +
650B PHE* 4.1 7.6 - - + -
651B TYR* 2.8 52.4 + - + -
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Residues in contact with SER 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B THR* 2.7 40.4 + - - +
647B LEU* 1.3 75.7 - - - +
649B LEU* 1.3 58.2 + - - +
651B TYR* 3.5 5.5 + - - +
652B LYS* 2.9 44.7 + - - +
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Residues in contact with LEU 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A TYR* 3.2 22.2 - - - +
533A GLU* 6.0 0.2 - - - +
645B THR* 2.8 18.2 + - + +
646B SER* 3.2 8.1 - - - +
648B SER* 1.3 73.9 + - - +
650B PHE* 1.3 66.8 + - - +
652B LYS* 3.1 10.9 + - - +
653B LYS* 3.0 43.2 + - + +
656B ARG* 5.4 2.6 + - - +
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Residues in contact with PHE 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A PHE* 3.7 26.2 - + + -
529A TYR* 3.8 31.0 - + + +
557A ILE 5.2 0.2 - - - -
558A MET* 3.8 24.5 - - + -
562A ALA* 3.9 22.7 - - + -
563A TRP* 3.7 16.2 - + - -
569A LEU* 3.6 34.8 - - + -
646B SER 2.7 14.0 + - - +
647B LEU* 3.5 15.3 - - + +
649B LEU* 1.3 76.1 - - - +
651B TYR* 1.3 62.5 + + - +
653B LYS* 3.2 6.5 + - + +
654B VAL* 2.9 51.5 + - + +
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Residues in contact with TYR 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A TRP* 3.8 17.2 - + - -
573A ILE* 3.7 28.0 - - + +
647B LEU* 2.8 53.1 + - + +
648B SER* 3.9 6.1 - - - +
650B PHE* 1.3 73.9 - + - +
652B LYS* 1.3 61.7 + - + +
654B VAL* 3.6 7.9 - - + +
655B TYR* 2.7 78.3 + + + -
688B LEU* 2.7 37.7 + - + -
689B GLN* 4.2 6.9 + - + -
692B TYR* 3.9 2.3 - - - +
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Residues in contact with LYS 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B SER* 2.9 37.2 + - - +
649B LEU* 3.1 9.6 + - - +
651B TYR* 1.3 77.4 - - + +
653B LYS* 1.3 56.4 + - - +
655B TYR* 3.3 10.7 + - + +
656B ARG* 3.0 44.4 + - - +
784B HIS* 3.8 33.0 + - + +
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Residues in contact with LYS 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A TYR* 3.6 22.4 - - + +
533A GLU* 3.1 33.8 + - - -
554A GLU* 2.9 30.8 + - - +
558A MET* 3.2 27.4 - - + +
649B LEU* 3.0 38.1 + - + +
650B PHE 3.4 7.0 - - - +
652B LYS* 1.3 75.9 - - - +
654B VAL* 1.3 63.3 + - - +
656B ARG* 3.4 21.5 + - - +
657B LEU 3.1 18.4 + - - -
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Residues in contact with VAL 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A MET* 4.1 24.2 - - + +
563A TRP* 4.4 12.3 - - + -
650B PHE* 2.9 50.3 + - + +
651B TYR* 3.1 12.3 + - + +
653B LYS* 1.3 77.0 - - - +
655B TYR* 1.3 59.1 + - + +
657B LEU* 3.2 4.5 + - - +
658B ALA* 2.9 26.7 + - - +
688B LEU* 4.3 12.6 - - + -
700B LEU* 4.1 29.8 - - + +
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Residues in contact with TYR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B TYR* 2.7 60.4 + + + +
652B LYS* 3.7 10.1 - - + +
654B VAL* 1.3 72.3 - - + +
656B ARG* 1.3 57.1 + - - +
658B ALA* 4.2 1.8 - - - -
659B TYR* 2.8 33.6 + - - +
681B TRP* 3.5 26.4 - + + -
685B GLN* 3.1 36.1 + - + -
688B LEU* 3.9 25.8 - - + -
689B GLN* 3.6 15.6 + - - +
783B PRO* 4.0 13.9 - - + -
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Residues in contact with ARG 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B LEU* 5.9 2.0 - - - +
652B LYS* 3.0 30.9 + - - +
653B LYS* 3.7 21.3 - - - +
654B VAL 3.3 0.2 - - - -
655B TYR* 1.3 76.2 - - - +
657B LEU* 1.3 62.0 + - - +
659B TYR* 3.9 1.4 - - - +
660B LEU* 3.0 35.1 + - + +
783B PRO* 4.5 9.6 - - + -
784B HIS* 3.0 60.2 + - + +
785B ILE* 3.2 33.0 - - - +
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Residues in contact with LEU 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A HIS* 4.1 39.5 - - + +
558A MET* 3.7 25.8 - - + -
559A GLU* 4.6 0.7 - - + -
653B LYS 3.1 12.9 + - - +
654B VAL 3.5 7.6 - - - +
656B ARG* 1.3 77.5 - - - +
658B ALA* 1.3 63.1 + - - +
660B LEU* 3.3 12.0 + - + +
661B ARG* 3.1 79.4 + - + +
700B LEU* 4.2 11.4 - - + -
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Residues in contact with ALA 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B VAL 2.9 17.8 + - - +
655B TYR* 3.6 5.8 - - - +
657B LEU* 1.3 77.8 - - - +
659B TYR* 1.3 56.8 + - - +
661B ARG* 3.3 7.3 + - - +
662B LEU* 2.9 28.1 + - - +
681B TRP* 4.0 8.3 - - + -
684B PHE* 3.5 36.7 - - + -
688B LEU* 4.5 2.5 - - + -
700B LEU* 4.0 16.5 - - + +
704B MET* 5.7 0.4 - - - -
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Residues in contact with TYR 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B TYR 2.8 11.9 + - - +
656B ARG 4.0 1.8 - - - +
658B ALA* 1.3 71.4 - - - +
660B LEU* 1.3 71.3 + - + +
662B LEU* 3.1 9.3 + - + +
663B ASN* 2.8 46.1 + - + +
677B GLU* 2.4 41.5 + - + -
681B TRP* 3.8 24.8 - + + -
782B ILE* 3.7 36.4 - - + +
783B PRO* 3.3 43.1 - - + -
785B ILE 5.5 2.9 - - - -
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Residues in contact with LEU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656B ARG* 3.0 28.6 + - + +
657B LEU* 3.7 11.0 - - + +
659B TYR* 1.3 85.6 - - + +
661B ARG* 1.3 64.6 + - + +
663B ASN* 3.5 7.6 + - + +
664B THR* 3.2 25.9 + - - -
785B ILE 4.4 23.1 - - - +
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Residues in contact with ARG 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ARG* 3.5 15.8 - - - +
555A HIS* 4.2 4.8 + - - +
559A GLU* 2.8 40.3 + - - +
657B LEU* 3.1 50.9 + - + +
658B ALA* 3.8 3.8 - - - +
660B LEU* 1.3 74.1 - - + +
662B LEU* 1.3 65.7 + - - +
664B THR* 3.3 8.0 + - - -
665B LEU* 3.2 26.2 + - - +
700B LEU* 4.5 2.6 - - - +
701B ASP* 2.9 32.3 + - - -
704B MET* 3.6 16.8 - - - -
731B LEU* 4.2 16.2 - - + +
733B HIS* 3.4 26.6 + - + +
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Residues in contact with LEU 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B ALA 2.9 14.5 + - - +
659B TYR* 3.1 16.8 + - + +
661B ARG* 1.3 75.9 - - - +
663B ASN* 1.3 57.0 + - - +
665B LEU* 3.2 3.9 + - - -
666B CYS* 2.9 44.4 + - - -
677B GLU* 3.7 34.5 - - + +
680B ILE* 3.7 17.7 - - + -
681B TRP* 3.8 27.4 - - + +
684B PHE* 4.3 11.7 - - + -
704B MET* 3.5 11.6 - - + -
708B MET* 3.8 15.3 - - + -
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Residues in contact with ASN 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659B TYR* 2.8 39.2 + - + +
660B LEU* 3.7 9.3 - - + +
662B LEU* 1.3 72.7 - - - +
664B THR* 1.3 60.0 + - - +
667B GLU* 2.9 61.2 + - - +
677B GLU* 2.8 35.3 + - - +
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Residues in contact with THR 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B LEU 3.2 15.6 + - - -
661B ARG* 3.6 9.9 - - - -
662B LEU 3.2 0.2 - - - -
663B ASN* 1.3 77.4 + - - +
665B LEU* 1.3 65.5 + - - +
667B GLU* 3.6 4.0 + - - +
668B ARG* 3.3 46.6 + - - +
731B LEU* 3.8 14.8 - - + -
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Residues in contact with LEU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B ARG 3.2 8.3 + - - +
662B LEU 3.7 4.9 - - - +
664B THR* 1.3 78.4 - - - +
666B CYS* 1.3 52.9 + - - +
668B ARG* 3.1 8.5 + - - +
669B LEU* 2.8 39.3 + - + +
704B MET* 3.3 34.1 - - + -
705B MET* 4.6 7.0 - - + -
708B MET* 3.5 32.5 - - + -
724B ILE* 4.6 3.4 - - + +
727B ALA* 3.9 16.4 - - + +
728B TYR* 3.8 38.1 - - + +
731B LEU* 4.1 13.7 - - + -
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Residues in contact with CYS 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B LEU* 2.9 40.8 + - - +
665B LEU* 1.3 72.9 - - - +
667B GLU* 1.3 63.3 + - + +
668B ARG 3.0 1.8 - - - -
670B LEU* 2.8 51.9 + - + +
677B GLU* 3.7 35.9 - - + +
680B ILE* 3.9 18.2 - - - -
708B MET* 4.5 4.3 - - - -
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Residues in contact with GLU 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B ASN* 2.9 54.5 + - - +
664B THR* 4.2 4.5 - - - +
666B CYS* 1.3 72.5 - - - +
668B ARG* 1.3 58.3 + - - +
670B LEU 5.4 0.2 - - - -
671B SER* 3.9 18.9 + - - +
677B GLU* 4.7 2.0 - - - +
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Residues in contact with ARG 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664B THR* 3.3 39.9 + - - +
665B LEU* 3.1 7.6 + - - +
666B CYS 3.0 0.6 - - - -
667B GLU* 1.3 81.1 - - - +
669B LEU* 1.3 65.7 + - + +
671B SER* 3.6 10.4 + - - -
727B ALA* 2.5 52.5 + - - +
730B ASP* 3.6 26.6 + - - +
731B LEU* 3.8 10.8 - - - +
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Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B LEU* 2.8 21.5 + - + +
668B ARG* 1.3 87.8 - - + +
670B LEU* 1.3 68.7 + - + +
671B SER* 3.4 5.1 + - - -
672B GLU* 3.4 10.9 - - - +
708B MET* 4.3 14.4 - - + -
719B LEU* 4.1 15.3 - - + +
723B ILE* 3.8 21.1 - - + +
724B ILE* 3.8 25.4 - - + +
727B ALA* 3.5 35.7 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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