Contacts of the helix formed by residues 710 - 733 (chain B) in PDB entry 6V3O
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 LYS 710 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B VAL* 6.2 1.3 - - + -
708B SER 4.7 3.1 - - - +
709B PRO* 1.3 77.0 - - - +
711B PRO* 1.3 76.9 - - + +
712B GLU* 3.4 27.1 + - - +
713B TRP* 3.2 50.8 + - + +
714B ARG* 3.1 20.7 + - - +
814B GLU* 6.2 0.2 - - - -
818B GLU* 5.1 4.5 - - - -
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Residues in contact with PRO 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B PRO 4.4 1.3 - - - +
710B LYS* 1.3 89.8 - - + +
712B GLU* 1.3 65.2 + - - +
714B ARG* 3.2 14.2 + - + +
715B LYS* 2.9 29.0 + - - +
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Residues in contact with GLU 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B LYS* 3.4 29.8 + - + -
711B PRO* 1.3 86.8 - - - +
713B TRP* 1.3 78.9 + - + +
715B LYS* 3.9 18.3 - - - +
716B LEU* 3.0 27.4 + - - +
811B VAL* 4.4 13.1 - - + +
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Residues in contact with TRP 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B VAL* 5.1 10.3 - - + -
708B SER 4.6 3.8 - - - -
709B PRO* 3.8 6.3 - - + -
710B LYS* 3.2 55.2 + - + +
711B PRO 3.2 0.6 - - - -
712B GLU* 1.3 80.5 - - + +
714B ARG* 1.3 67.3 + - - +
716B LEU* 3.3 2.8 + - - +
717B MET* 2.9 28.9 + - - +
811B VAL* 3.9 21.3 + - + +
814B GLU* 4.6 4.6 + - + +
815B MET* 3.3 40.1 - - + +
818B GLU* 3.8 43.5 - - + -
819B TRP* 3.6 51.4 - + + -
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Residues in contact with ARG 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B TRP* 4.0 33.9 - - + -
618B TYR* 5.3 0.2 - - - -
619B ARG* 4.4 7.1 - - - +
622B GLU* 2.7 41.2 + - - -
709B PRO* 4.0 37.4 + - + +
710B LYS 3.1 12.3 + - - +
711B PRO* 3.2 11.9 + - - +
713B TRP* 1.3 76.7 - - - +
715B LYS* 1.3 56.9 + - - +
717B MET* 3.0 3.5 + - - +
718B ASP* 2.8 39.3 + - - +
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Residues in contact with LYS 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B PRO 2.9 17.2 + - - +
712B GLU* 3.9 18.8 - - - +
714B ARG* 1.3 74.2 - - - +
716B LEU* 1.3 80.2 + - - +
718B ASP* 3.3 10.0 + - - +
719B GLU* 3.1 60.6 + - + +
804B LYS* 4.8 6.9 - - - +
808B ASN* 5.2 6.2 + - - +
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Residues in contact with LEU 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B GLU 3.0 18.3 + - - +
713B TRP* 3.8 4.3 - - - +
715B LYS* 1.3 87.2 - - - +
717B MET* 1.3 61.0 + - - +
719B GLU* 3.4 10.8 + - + +
720B MET* 2.9 40.9 + - + +
800B PHE* 5.8 1.1 - - + -
801B ALA* 4.1 12.8 - - + -
804B LYS* 5.6 0.7 - - + -
808B ASN* 4.0 27.4 - - + +
811B VAL* 3.4 34.5 - - + -
812B LEU* 3.5 25.8 - - + -
815B MET* 4.7 6.1 - - + -
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Residues in contact with MET 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B LEU* 4.4 21.1 - - + -
615B TRP* 3.4 48.8 - - + -
713B TRP 2.9 18.9 + - - +
714B ARG 3.0 3.8 + - - +
716B LEU* 1.3 76.4 - - - +
718B ASP* 1.3 61.6 + - - +
720B MET* 3.3 10.5 + - + +
721B ALA* 2.9 25.5 + - - +
815B MET* 4.0 7.0 - - + -
819B TRP* 3.8 23.3 - - + -
821B PHE* 3.7 18.4 - - + -
822B PHE* 3.9 29.6 - - + -
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Residues in contact with ASP 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B TRP* 2.8 23.5 + - - +
619B ARG* 3.1 21.2 + - - -
714B ARG* 2.8 25.9 + - - +
715B LYS* 3.5 12.0 - - - +
716B LEU 3.3 0.2 - - - -
717B MET* 1.3 74.9 - - - +
719B GLU* 1.3 63.6 + - + +
721B ALA* 3.4 10.1 + - - +
722B VAL* 3.5 18.0 + - - +
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Residues in contact with GLU 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B LYS* 3.1 43.2 + - + +
716B LEU* 4.0 9.4 - - + +
718B ASP* 1.3 75.1 - - + +
720B MET* 1.3 67.1 + - - +
722B VAL* 3.2 26.1 - - + +
723B VAL* 3.4 9.2 + - - +
800B PHE* 3.9 16.5 - - + -
804B LYS* 3.4 41.0 + - - +
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Residues in contact with MET 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B LEU* 4.4 11.4 - - + -
716B LEU* 2.9 31.3 + - + +
717B MET* 3.8 18.6 - - + +
719B GLU* 1.3 76.5 - - - +
721B ALA* 1.3 57.9 + - - +
723B VAL* 3.2 5.0 + - - +
724B ALA* 2.9 31.1 + - - +
797B ALA* 3.5 33.8 - - + +
798B PHE* 3.3 39.7 - - + -
800B PHE* 5.0 2.7 - - + -
801B ALA* 3.7 21.5 - - + -
812B LEU* 3.8 24.5 - - + -
822B PHE* 5.1 3.1 - - - -
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Residues in contact with ALA 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B LEU* 5.6 2.5 - - - -
612B SER* 2.8 42.8 + - - +
615B TRP* 4.3 14.6 - - + -
619B ARG* 5.8 1.8 - - - +
717B MET* 2.9 17.4 + - + +
718B ASP* 3.6 7.0 - - - +
719B GLU 3.2 0.2 - - - -
720B MET* 1.3 76.4 - - - +
722B VAL* 1.3 59.2 + - + +
724B ALA* 3.3 1.0 + - - -
725B THR* 2.9 20.4 + - - -
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Residues in contact with VAL 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B ASP 3.5 15.0 - - - +
719B GLU* 3.2 16.6 - - + +
721B ALA* 1.3 76.5 - - + +
723B VAL* 1.3 74.1 + - + +
725B THR* 3.5 5.4 + - - -
726B GLU* 3.0 27.0 + - - +
800B PHE* 6.0 1.1 - - + -
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Residues in contact with VAL 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B GLU 3.4 14.1 - - - +
720B MET 3.2 7.6 + - - +
722B VAL* 1.3 84.1 - - + +
724B ALA* 1.3 58.2 + - - +
726B GLU* 3.4 9.9 + - - +
727B GLU* 3.0 27.5 + - - +
796B ALA* 3.7 36.1 - - + +
797B ALA* 4.3 3.6 - - - -
800B PHE* 3.6 38.6 - - + -
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Residues in contact with ALA 724 (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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608B ALA 4.7 2.2 - - - +
609B GLY* 6.0 2.0 - - - -
611B LEU* 4.4 15.0 - - + +
612B SER* 3.6 14.1 - - - +
720B MET 2.9 16.4 + - - +
723B VAL* 1.3 74.7 - - - +
725B THR* 1.3 60.5 + - - +
727B GLU* 3.3 1.9 + - - +
728B TYR* 2.9 31.5 + - - +
793B GLY* 3.3 33.7 + - - +
797B ALA* 4.1 6.0 - - + +
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Residues in contact with THR 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU* 4.3 6.2 - - + +
608B ALA* 3.5 30.7 + - + +
612B SER* 2.9 25.7 + - - -
721B ALA 2.9 12.5 + - - -
722B VAL* 3.9 5.2 - - - -
724B ALA* 1.3 76.8 - - - +
726B GLU* 1.3 63.1 + - - +
728B TYR* 3.3 1.1 + - - +
729B ARG* 2.9 47.1 + - + +
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Residues in contact with GLU 726 (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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722B VAL* 3.0 19.6 + - - +
723B VAL* 3.9 8.9 - - - +
725B THR* 1.3 77.5 - - - +
727B GLU* 1.3 58.2 + - - +
729B ARG* 4.0 3.0 - - - +
730B SER* 3.0 33.1 + - - -
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Residues in contact with GLU 727 (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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723B VAL 3.0 18.3 + - - +
724B ALA 3.8 2.9 - - - +
725B THR 3.2 0.2 - - - -
726B GLU* 1.3 75.1 - - - +
728B TYR* 1.3 66.5 + - - +
730B SER* 3.2 26.0 + - - -
731B VAL* 3.5 8.3 + - - +
792B LEU* 4.6 4.3 - - + +
793B GLY* 3.9 17.9 - - - +
796B ALA* 3.7 28.8 + - + +
863B LYS* 2.6 42.6 + - - +
866B GLU* 5.4 1.9 - - - +
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Residues in contact with TYR 728 (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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605B GLY 3.6 5.8 - - - -
606B LYS* 2.8 38.2 + - - +
607B ASP 3.7 9.4 - - - -
608B ALA* 3.9 7.4 - - - -
609B GLY* 3.4 36.1 - - - +
724B ALA 2.9 18.3 + - - +
725B THR 3.8 3.1 - - - +
727B GLU* 1.3 79.7 - - - +
729B ARG* 1.3 62.8 + - + +
731B VAL* 3.3 1.4 + - - +
732B VAL* 2.9 57.4 + - + +
733B VAL* 5.4 1.8 - - + -
777B TRP* 3.5 22.5 + + - -
788B LEU* 5.4 0.2 - - + -
789B PRO* 4.8 13.0 - - + -
792B LEU* 3.8 35.6 - - + +
793B GLY* 4.5 0.2 - - - -
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Residues in contact with ARG 729 (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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607B ASP* 4.0 17.5 - - - +
608B ALA* 4.9 0.9 - - - -
725B THR* 2.9 35.5 + - + +
726B GLU* 4.5 3.5 - - - +
728B TYR* 1.3 84.9 - - + +
730B SER* 1.3 59.5 + - - +
733B VAL* 3.0 42.6 + - + +
734B LYS* 2.8 37.7 + - + +
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Residues in contact with SER 730 (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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726B GLU* 3.0 22.4 + - - -
727B GLU* 3.2 17.3 + - - -
728B TYR 3.3 0.4 - - - -
729B ARG* 1.3 77.5 - - - +
731B VAL* 1.3 68.1 + - - +
734B LYS* 3.9 13.4 - - - +
735B GLU* 3.6 20.1 + - - +
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Residues in contact with VAL 731 (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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727B GLU* 3.5 8.3 + - - +
728B TYR 3.3 5.8 + - - +
729B ARG 3.2 0.2 - - - -
730B SER* 1.3 91.0 + - - +
732B VAL* 1.3 64.5 + - - +
733B VAL 3.5 0.2 - - - -
735B GLU* 3.5 11.4 - - - +
738B PHE* 3.3 37.6 - - + +
788B LEU* 5.4 0.4 - - + -
792B LEU* 4.2 16.2 - - + -
856B PHE* 4.0 11.9 - - + -
860B LEU* 3.8 25.6 - - + -
863B LYS* 4.2 25.4 - - - -
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Residues in contact with VAL 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B LYS 5.3 0.7 - - - +
728B TYR* 2.9 49.8 + - + +
731B VAL* 1.3 77.7 - - - +
733B VAL* 1.3 72.4 + - + +
735B GLU 4.9 0.7 - - - +
738B PHE* 3.7 36.3 - - + +
739B VAL* 5.7 1.0 - - - +
769B ILE* 4.2 35.9 + - + +
777B TRP* 4.2 7.2 - - + -
788B LEU* 4.5 1.1 - - + -
792B LEU* 3.9 15.7 - - + -
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Residues in contact with VAL 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ASP 5.4 3.6 - - - +
728B TYR* 5.4 0.9 - - + -
729B ARG* 3.0 48.8 + - + +
732B VAL* 1.3 93.3 - - + +
734B LYS* 1.3 68.5 + - + +
735B GLU 3.3 6.4 + - - +
769B ILE* 6.2 0.9 - - + -
770B THR* 5.6 13.5 - - + -
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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) + - + + + + + -
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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