Contacts of the helix formed by residues 650 - 677 (chain B) in PDB entry 5QSY
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 ILE 650 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B LEU* 4.1 22.9 - - + +
604B TYR* 3.6 31.0 - - + +
605B SER* 4.3 8.5 + - - +
610B GLU* 4.9 3.8 - - + -
613B LEU* 3.4 29.8 - - + -
643B LEU* 4.4 11.4 - - + +
645B SER* 4.6 1.3 - - - +
648B TYR* 2.8 38.7 + - + +
649B THR* 1.3 73.2 - - - +
651B GLN* 1.3 58.8 + - - +
653B ARG* 2.7 45.0 + - - +
654B VAL* 3.2 11.3 + - + +
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Residues in contact with GLN 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B LEU 4.6 2.0 - - - -
644B CYS* 4.5 10.1 - - + -
645B SER* 4.6 2.0 - - - +
646B GLU* 3.3 56.8 + - + +
647B GLU 5.2 1.0 - - - +
648B TYR 2.7 19.5 + - - +
649B THR 3.3 0.2 - - - -
650B ILE* 1.3 73.1 - - - +
652B ASN* 1.3 66.5 + - - +
654B VAL* 3.2 12.5 + - - +
655B ASP* 2.7 48.2 + - - +
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Residues in contact with ASN 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TYR* 4.0 12.2 - - + -
649A THR* 6.0 2.2 - - - +
649B THR 3.9 9.7 + - - +
650B ILE 3.2 0.4 + - - -
651B GLN* 1.3 81.2 - - - +
653B ARG* 1.3 62.5 + - - +
655B ASP* 3.4 14.5 + - - +
656B ILE* 3.2 43.1 + - - +
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Residues in contact with ARG 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TYR* 3.6 62.9 + - + +
651A GLN* 5.0 1.6 + - - -
610B GLU* 3.3 39.5 - - - +
613B LEU* 4.4 18.2 - - + +
614B ASP* 2.9 38.7 + - - +
617B LEU* 4.0 6.7 - - + +
649B THR* 4.2 10.7 + - - +
650B ILE* 2.7 36.2 + - - +
652B ASN* 1.3 71.7 - - - +
654B VAL* 1.3 62.7 + - - +
656B ILE* 3.8 3.4 + - - +
657B ALA* 3.6 18.2 + - - +
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Residues in contact with VAL 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LEU* 4.6 12.1 - - + -
617B LEU* 4.2 12.5 - - + +
640B TYR* 3.7 22.2 - - + -
643B LEU* 3.6 41.5 - - + +
644B CYS* 3.4 26.9 - - - +
650B ILE* 3.2 16.7 + - + +
651B GLN* 3.5 7.2 - - - +
653B ARG* 1.3 73.2 - - - +
655B ASP* 1.4 55.2 + - - +
657B ALA* 2.9 6.2 + - - +
658B ARG* 2.8 32.8 + - - +
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Residues in contact with ASP 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B CYS* 3.7 11.3 - - - +
651B GLN* 2.7 40.4 + - - +
652B ASN* 3.4 14.1 + - - +
654B VAL* 1.4 76.9 - - - +
656B ILE* 1.3 59.3 + - + +
658B ARG* 2.9 37.3 + - - +
659B SER* 2.9 36.0 + - - +
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Residues in contact with ILE 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TYR* 3.8 25.8 - - + +
649A THR 6.2 0.4 - - - +
652A ASN* 4.1 26.9 - - + +
652B ASN* 3.2 34.0 + - - +
653B ARG 4.1 4.5 - - - +
654B VAL 3.1 1.0 + - - -
655B ASP* 1.3 77.4 - - + +
657B ALA* 1.3 58.9 + - - +
659B SER* 3.7 5.0 + - - -
660B GLN* 2.9 33.4 + - + +
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Residues in contact with ALA 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B LEU* 4.1 20.0 - - + -
621B LYS* 5.4 4.2 - - + +
640B TYR* 3.8 14.3 + - - +
653B ARG 3.6 9.7 + - - +
654B VAL 2.9 7.6 + - - +
656B ILE* 1.3 76.2 - - - +
658B ARG* 1.3 66.3 + - - +
660B GLN* 3.4 10.5 + - + +
661B LEU* 3.0 23.9 + - - +
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Residues in contact with ARG 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B TYR* 3.9 26.5 + - + -
644B CYS* 3.6 27.2 - - - +
654B VAL 2.8 17.0 + - - +
655B ASP* 2.9 35.1 + - - +
657B ALA* 1.3 66.8 - - - +
659B SER* 1.3 70.3 + - - +
661B LEU* 2.8 17.3 + - + +
662B ILE* 3.0 28.6 + - + +
701B PHE* 5.7 4.0 - - + -
705B HIS* 3.4 42.8 + - - +
707B LEU* 6.1 1.1 - - - -
710B TRP* 6.3 0.7 - - + -
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Residues in contact with SER 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B ASP* 2.9 20.1 + - - +
656B ILE* 3.9 5.6 - - - -
658B ARG* 1.3 75.4 + - - +
660B GLN* 1.3 64.7 + - - +
661B LEU 3.1 0.2 + - - -
662B ILE* 3.8 1.7 - - - +
663B ASP* 2.8 39.4 + - - +
710B TRP* 4.2 22.8 - - - -
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Residues in contact with GLN 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LYS* 4.9 11.0 - - + -
656B ILE* 2.9 24.0 + - + +
657B ALA* 3.5 10.8 - - - +
658B ARG 3.1 0.4 - - - -
659B SER* 1.3 76.9 - - - +
661B LEU* 1.3 62.5 + - - +
663B ASP* 3.5 7.5 - - - +
664B GLU* 3.2 39.6 + - - +
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Residues in contact with LEU 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LYS* 3.9 32.5 - - + +
624B VAL* 4.0 16.8 - - + -
625B GLU* 4.5 4.9 - - - +
640B TYR* 3.8 31.2 - - + +
657B ALA 3.0 11.7 + - - +
658B ARG* 2.8 10.6 + - + +
660B GLN* 1.3 74.9 - - - +
662B ILE* 1.3 62.3 + - + +
664B GLU* 2.9 26.1 + - + +
665B PHE* 3.0 54.9 + - + -
701B PHE* 4.4 11.2 - - + -
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Residues in contact with ILE 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B ARG* 3.0 29.5 + - + +
659B SER* 3.8 3.6 - - - +
661B LEU* 1.3 72.9 - - + +
663B ASP* 1.3 58.3 + - - +
665B PHE* 3.0 21.1 + - + +
666B VAL* 2.8 42.1 + - + +
698B LEU* 4.5 6.5 - - + -
701B PHE* 4.4 24.5 - - + -
707B LEU* 3.9 31.9 - - + -
710B TRP* 3.4 40.6 - - + +
----------------------------------------------------------
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Residues in contact with ASP 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B SER* 2.8 36.4 + - - +
660B GLN* 3.5 10.0 - - - +
662B ILE* 1.3 70.8 - - - +
664B GLU* 1.3 58.3 + - + +
666B VAL* 3.9 2.2 - - - +
667B ASP* 3.1 36.1 + - - +
709B LYS* 4.8 7.1 + - - -
710B TRP* 3.7 28.8 + - - +
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Residues in contact with GLU 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LYS* 2.7 37.1 + - - +
625B GLU* 4.5 3.9 - - - +
660B GLN* 3.2 31.8 + - - +
661B LEU* 2.9 12.9 + - + +
663B ASP* 1.3 75.3 - - + +
665B PHE* 1.3 67.8 + - + +
667B ASP* 3.6 5.4 + - - +
668B ARG* 3.1 24.9 + - - +
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Residues in contact with PHE 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B VAL* 3.6 19.5 - - + -
625B GLU* 4.4 15.5 - - + -
661B LEU* 3.0 61.0 + - + -
662B ILE* 3.0 19.5 + - + +
664B GLU* 1.3 76.0 - - + +
666B VAL* 1.3 57.0 + - - +
668B ARG* 3.3 7.4 + - + +
669B PHE* 2.6 36.9 + - - +
694B THR* 4.4 8.5 - - + +
697B ARG* 3.6 43.3 - - + -
698B LEU* 3.8 20.0 - - + -
701B PHE* 4.8 6.1 - + - -
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Residues in contact with VAL 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B ILE* 2.8 25.3 + - + +
663B ASP* 3.9 3.1 - - - +
665B PHE* 1.3 73.3 - - - +
667B ASP* 1.3 63.6 + - - +
669B PHE* 3.5 6.7 - - - +
670B ASN* 2.8 57.4 + - - +
698B LEU* 3.7 19.7 - - + -
710B TRP* 3.6 42.6 - - + -
711B ASP 5.7 2.0 - - - +
712B LEU* 4.1 11.9 - - + -
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Residues in contact with ASP 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B ASP* 3.1 22.2 + - - +
664B GLU* 4.0 5.6 - - - +
665B PHE 3.3 0.2 - - - -
666B VAL* 1.3 81.7 - - - +
668B ARG* 1.3 59.3 + - - +
670B ASN* 4.0 5.3 + - - +
671B HIS* 3.0 49.6 + - + +
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Residues in contact with ARG 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B GLU 3.1 16.0 + - - +
665B PHE* 3.8 6.7 - - - +
667B ASP* 1.3 79.6 - - - +
669B PHE* 1.3 52.4 + - - +
671B HIS* 4.0 5.6 - - - +
672B SER* 2.4 41.8 + - - +
689B TYR* 5.1 4.8 - - - -
690B ASN* 2.8 40.3 + - - +
693B SER* 4.3 8.5 + - - -
694B THR* 3.5 20.1 - - + +
697B ARG* 4.6 8.3 - - - +
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Residues in contact with PHE 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B PHE 2.6 22.5 + - - +
666B VAL 3.5 2.7 - - - +
668B ARG* 1.3 68.8 - - - +
670B ASN* 1.3 69.9 + - - +
672B SER* 3.1 4.0 + - - -
673B VAL* 2.9 53.2 + - + +
691B VAL* 4.3 4.9 - - + -
694B THR* 3.6 22.3 - - - -
695B LEU* 3.9 38.6 - - + -
698B LEU* 3.4 23.3 - - + -
712B LEU* 3.9 21.1 - - + -
715B ASN* 3.6 27.6 - - + -
716B CYS* 4.4 6.1 - - - -
719B LEU* 4.2 13.9 - - + -
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Residues in contact with ASN 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B VAL* 2.8 45.9 + - - +
667B ASP* 4.1 7.9 + - - +
669B PHE* 1.3 76.4 - - - +
671B HIS* 1.3 70.2 + - + +
673B VAL* 3.2 3.8 + - - +
674B GLU* 3.0 28.9 + - + +
711B ASP 5.4 1.2 - - - +
712B LEU* 5.2 2.3 - - - +
715B ASN* 2.5 35.4 + - - +
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Residues in contact with HIS 671 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B ASP* 3.0 38.2 + - + +
668B ARG* 4.0 6.1 - - + +
670B ASN* 1.3 79.6 - - + +
672B SER* 1.3 57.3 + - - +
674B GLU* 3.1 8.8 + - + +
675B ASP* 2.9 39.8 + - - +
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Residues in contact with SER 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ARG* 2.4 32.1 + - - +
669B PHE 3.1 5.8 + - - -
671B HIS* 1.3 76.6 - - - +
673B VAL* 1.3 55.1 + - - +
675B ASP* 3.6 8.7 + - - +
676B LEU* 3.1 21.5 + - - +
687B ASP* 5.0 2.1 - - - +
690B ASN* 3.5 25.6 + - - +
691B VAL* 3.3 37.6 - - - +
694B THR* 3.7 3.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B PHE* 2.9 54.9 + - + +
670B ASN 3.7 4.9 - - - +
671B HIS 3.2 0.2 - - - -
672B SER* 1.3 74.7 - - - +
674B GLU* 1.3 66.3 + - - +
676B LEU* 3.7 1.8 - - - +
677B LEU* 3.2 36.1 + - + +
691B VAL* 4.3 8.5 - - + -
715B ASN* 3.4 26.0 - - - +
718B ARG* 4.5 6.3 - - + +
719B LEU* 4.0 27.6 - - + -
----------------------------------------------------------
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Residues in contact with GLU 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B ASN* 3.0 20.5 + - + +
671B HIS* 3.1 11.6 + - + +
673B VAL* 1.3 78.7 - - - +
675B ASP* 1.3 64.8 + - - +
676B LEU 3.4 0.7 + - - -
677B LEU* 3.6 8.5 + - - +
678B GLN* 3.4 20.1 + - - +
718B ARG* 3.2 36.4 + - - +
----------------------------------------------------------
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Residues in contact with ASP 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B HIS* 2.9 23.0 + - - +
672B SER* 3.9 7.7 - - - +
674B GLU* 1.3 79.6 - - - +
676B LEU* 1.3 60.5 + - - +
678B GLN* 3.6 20.2 - - - +
679B GLU 4.7 0.9 + - - -
687B ASP* 4.3 24.0 - - + +
690B ASN* 5.8 2.7 + - - +
1001B K0J 4.9 12.3 + - + +
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Residues in contact with LEU 676 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B SER 3.1 17.6 + - - +
673B VAL 3.7 4.9 - - - +
674B GLU 3.2 0.4 - - - -
675B ASP* 1.3 74.9 - - - +
677B LEU* 1.3 62.0 + - + +
678B GLN 2.8 12.0 + - - -
679B GLU 3.7 13.2 + - - -
684B ASP 5.0 0.7 - - - +
687B ASP* 3.7 27.2 - - + +
688B ILE* 3.8 29.4 - - + +
691B VAL* 3.6 20.0 - - + -
719B LEU* 3.8 23.1 - - + -
729B MET* 3.9 23.1 - - + -
730B PRO* 6.3 0.2 - - + -
733B ILE* 4.8 2.2 - - + -
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Residues in contact with LEU 677 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B VAL* 3.2 23.2 + - + +
674B GLU* 3.6 5.3 + - - +
676B LEU* 1.3 80.8 - - + +
678B GLN* 1.3 74.5 + - - +
718B ARG* 3.7 42.0 - - + +
719B LEU* 4.7 2.2 - - + -
722B THR* 3.6 42.6 - - + +
729B MET* 4.3 13.7 - - + -
----------------------------------------------------------
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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
------------------------------------------------------------
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