Contacts of the helix formed by residues 710 - 733 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708F SER 4.5 4.3 - - - +
709F PRO* 1.3 76.5 - - - +
711F PRO* 1.3 76.8 - - + +
712F GLU* 3.9 24.0 + - - +
713F TRP* 3.1 50.1 + - + +
714F ARG* 3.1 20.1 + - - +
818F GLU* 5.4 5.8 + - - -
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Residues in contact with PRO 711 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709F PRO 4.4 1.6 - - - +
710F LYS* 1.3 88.5 - - + +
712F GLU* 1.3 65.4 + - - +
714F ARG* 3.3 13.3 + - + +
715F LYS* 2.9 29.4 + - - +
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Residues in contact with GLU 712 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710F LYS* 3.9 24.6 + - - +
711F PRO* 1.3 84.9 - - - +
713F TRP* 1.3 75.0 + - + +
715F LYS* 3.8 8.0 - - - +
716F LEU* 3.0 31.5 + - - +
811F VAL* 4.6 12.6 - - + -
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Residues in contact with TRP 713 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707F VAL* 4.6 4.5 - - + -
708F SER 4.4 7.6 - - - -
709F PRO* 4.0 2.5 - - + -
710F LYS* 3.1 56.0 + - + +
712F GLU* 1.3 86.9 - - + +
714F ARG* 1.3 60.9 + - - +
716F LEU* 3.3 2.4 + - - +
717F MET* 2.9 35.8 + - - +
811F VAL* 4.0 13.8 + - + +
814F GLU* 5.2 5.0 + - + -
815F MET* 3.4 41.7 - - + +
818F GLU* 3.8 43.1 - - + -
819F TRP* 3.5 50.7 - + + -
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Residues in contact with ARG 714 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615F TRP* 4.0 32.3 - - + -
618F TYR* 5.2 0.2 - - - -
619F ARG* 4.7 8.5 - - - +
622F GLU* 2.6 42.2 + - - -
709F PRO* 3.9 39.5 + - + +
710F LYS 3.1 12.0 + - - +
711F PRO* 3.3 12.3 + - - +
713F TRP* 1.3 76.6 - - - +
715F LYS* 1.3 58.6 + - - +
717F MET* 3.3 2.6 + - - +
718F ASP* 2.8 39.7 + - - +
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Residues in contact with LYS 715 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711F PRO 2.9 17.3 + - - +
712F GLU* 3.8 8.3 - - - +
714F ARG* 1.3 75.6 - - - +
716F LEU* 1.3 63.4 + - - +
718F ASP* 3.3 10.0 + - + +
719F GLU* 3.1 51.1 + - + +
804F LYS* 5.9 2.0 - - - +
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Residues in contact with LEU 716 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712F GLU 3.0 17.2 + - - +
713F TRP* 3.7 4.3 - - - +
715F LYS* 1.3 74.3 - - - +
717F MET* 1.3 59.4 + - - +
719F GLU* 3.3 17.1 + - + +
720F MET* 2.9 47.5 + - + +
800F PHE* 6.0 0.2 - - + -
801F ALA* 4.1 13.5 - - + -
804F LYS* 4.9 2.2 - - + +
808F ASN* 3.7 37.5 - - + +
811F VAL* 4.0 26.2 - - + -
812F LEU* 3.9 26.7 - - + -
815F MET* 4.5 3.6 - - - -
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Residues in contact with MET 717 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611F LEU* 4.2 23.1 - - + -
615F TRP* 3.4 48.2 - - + -
713F TRP 2.9 21.1 + - - +
714F ARG 3.6 1.1 - - - +
716F LEU* 1.3 75.2 - - - +
718F ASP* 1.3 57.7 + - - +
720F MET* 3.3 22.7 + - + +
721F ALA* 2.9 32.6 + - + +
815F MET* 4.0 3.6 - - + -
819F TRP* 3.9 23.6 - - + -
821F PHE* 4.1 12.1 - - + -
822F PHE* 3.9 23.6 - - - -
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Residues in contact with ASP 718 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615F TRP* 2.7 34.1 + - - +
619F ARG* 4.3 9.7 + - - -
714F ARG* 2.8 25.9 + - - +
715F LYS* 3.5 9.6 - - + +
717F MET* 1.3 77.9 - - - +
719F GLU* 1.3 63.9 + - + +
721F ALA* 3.4 9.2 + - - +
722F VAL* 3.5 12.1 + - - +
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Residues in contact with GLU 719 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715F LYS* 3.1 46.6 + - + +
716F LEU* 3.8 13.3 - - + +
718F ASP* 1.3 75.2 - - + +
720F MET* 1.3 67.5 + - + +
722F VAL* 3.2 26.0 - - + +
723F VAL* 3.6 7.8 + - - +
800F PHE* 3.9 18.2 - - + -
804F LYS* 3.2 39.8 + - - +
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Residues in contact with MET 720 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611F LEU* 4.4 10.1 - - + -
716F LEU* 2.9 25.3 + - + +
717F MET* 3.8 30.7 - - + +
719F GLU* 1.3 75.5 - - - +
721F ALA* 1.3 63.1 + - - +
723F VAL* 3.4 10.3 + - - +
724F ALA* 2.9 27.0 + - - +
797F ALA* 3.6 25.6 - - + +
798F PHE* 3.9 27.1 - - + -
800F PHE* 5.0 3.4 - - + -
801F ALA* 4.0 20.9 - - + -
812F LEU* 3.7 23.1 - - + -
815F MET* 4.6 0.9 - - + -
822F PHE* 4.4 8.1 - - + -
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Residues in contact with ALA 721 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611F LEU* 5.5 2.7 - - - +
612F SER* 3.1 24.9 + - - +
615F TRP* 4.2 17.7 - - + -
717F MET* 2.9 17.7 + - + +
718F ASP* 3.6 7.0 - - - +
719F GLU 3.2 0.2 - - - -
720F MET* 1.3 77.4 - - - +
722F VAL* 1.3 61.6 + - - +
724F ALA* 4.5 0.9 - - - -
725F THR* 3.0 30.0 + - - -
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Residues in contact with VAL 722 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718F ASP 3.5 6.7 + - - +
719F GLU* 3.2 17.9 + - + +
721F ALA* 1.3 80.1 - - - +
723F VAL* 1.3 72.2 + - + +
725F THR* 3.7 4.5 - - - -
726F GLU* 3.0 28.4 + - + +
800F PHE* 6.1 0.9 - - + -
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Residues in contact with VAL 723 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719F GLU 3.9 7.6 - - - +
720F MET* 3.4 12.6 - - - +
722F VAL* 1.3 88.5 - - + +
724F ALA* 1.3 67.9 + - - +
726F GLU* 3.7 6.5 - - - +
727F GLU* 3.0 26.3 + - - +
796F ALA* 4.3 5.6 - - + +
797F ALA* 3.5 24.9 - - - +
800F PHE* 4.0 37.7 - - + -
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Residues in contact with ALA 724 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608F ALA 4.5 1.6 - - - +
609F GLY* 5.9 1.1 - - - -
611F LEU* 4.6 13.0 - - + +
612F SER* 3.6 14.1 - - - +
720F MET 2.9 19.0 + - - +
721F ALA* 4.5 0.7 - - - -
723F VAL* 1.3 78.0 - - - +
725F THR* 1.3 62.6 + - - +
727F GLU* 5.0 0.2 - - - -
728F TYR* 2.9 25.6 + - - +
793F GLY* 3.4 34.4 - - - +
797F ALA* 3.9 6.1 - - + -
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Residues in contact with THR 725 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568F LEU* 4.2 7.7 - - + +
608F ALA* 3.4 30.7 + - + +
612F SER* 2.7 27.7 + - - -
721F ALA 3.0 14.5 + - - -
722F VAL* 3.7 5.4 - - - -
724F ALA* 1.3 76.6 - - - +
726F GLU* 1.3 60.2 + - - +
728F TYR* 3.7 0.7 - - - +
729F ARG* 2.9 46.8 + - - +
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Residues in contact with GLU 726 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722F VAL* 3.0 18.3 + - + +
723F VAL* 3.7 8.9 - - - +
724F ALA 3.2 0.4 - - - -
725F THR* 1.3 78.4 - - - +
727F GLU* 1.3 61.3 + - - +
729F ARG* 3.8 10.5 - - - +
730F SER* 2.9 33.9 + - - -
734F LYS* 5.7 5.4 + - - +
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Residues in contact with GLU 727 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723F VAL 3.0 16.3 + - - +
724F ALA 4.1 1.1 - - - +
726F GLU* 1.3 77.8 + - - +
728F TYR* 1.3 67.9 + - - +
730F SER* 3.0 26.2 + - - +
731F VAL* 3.3 9.2 + - + +
792F LEU* 4.6 4.3 - - - +
793F GLY* 3.4 20.4 + - - -
795F GLY 5.1 0.2 + - - -
796F ALA* 2.6 39.5 + - + +
863F LYS* 2.7 42.6 + - - +
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Residues in contact with TYR 728 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605F GLY 3.7 5.8 - - - -
606F LYS* 2.8 38.4 + - - +
607F ASP 3.8 7.2 - - - -
608F ALA* 3.8 6.3 - - - +
609F GLY* 3.5 35.9 - - - +
724F ALA 2.9 18.1 + - - +
725F THR 3.7 3.1 - - - +
727F GLU* 1.3 79.1 - - - +
729F ARG* 1.3 62.5 + - + +
731F VAL* 3.3 1.2 + - - +
732F VAL* 3.0 53.3 + - + +
733F VAL* 5.4 1.8 - - + -
777F TRP* 3.5 22.8 + + - -
788F LEU* 6.3 0.7 - - + -
789F PRO* 4.9 11.9 - - + -
792F LEU* 3.7 38.8 - - + +
793F GLY* 4.6 1.6 - - - -
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Residues in contact with ARG 729 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607F ASP 4.1 20.0 - - - +
608F ALA* 5.2 0.7 - - - +
725F THR* 2.9 37.6 + - + +
726F GLU* 4.1 8.9 - - - +
728F TYR* 1.3 79.9 - - + +
730F SER* 1.3 60.7 + - - +
733F VAL* 3.1 37.0 + - + +
734F LYS* 2.9 53.4 + - + +
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Residues in contact with SER 730 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726F GLU* 2.9 28.2 + - - -
727F GLU* 3.0 16.6 + - - +
729F ARG* 1.3 78.6 - - - +
731F VAL* 1.3 67.3 + - - +
734F LYS* 3.8 15.0 - - - +
735F GLU* 3.6 20.6 + - - +
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Residues in contact with VAL 731 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727F GLU* 3.3 16.2 + - + +
728F TYR 4.0 2.2 - - - +
729F ARG 3.2 0.2 - - - -
730F SER* 1.3 85.5 + - - +
732F VAL* 1.3 62.9 + - - +
735F GLU* 3.4 21.2 - - - +
738F PHE* 3.5 21.6 - - + +
788F LEU* 5.6 0.4 - - + -
792F LEU* 4.1 17.3 - - + -
856F PHE* 4.0 18.4 - - + -
860F LEU* 3.7 25.6 - - + -
863F LYS* 4.2 25.4 - - + +
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Residues in contact with VAL 732 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606F LYS 5.4 0.9 - - - +
728F TYR* 3.0 43.6 + - + +
731F VAL* 1.3 78.4 - - - +
733F VAL* 1.3 70.7 + - + +
735F GLU 4.6 1.0 - - - +
738F PHE* 3.7 37.7 - - + +
739F VAL* 5.7 1.6 - - - +
769F ILE* 4.0 38.6 + - + +
777F TRP* 4.2 9.2 - - + -
788F LEU* 5.3 2.0 - - + -
792F LEU* 4.2 13.9 - - + -
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Residues in contact with VAL 733 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607F ASP 5.4 3.8 - - - +
728F TYR* 5.4 2.0 - - + -
729F ARG* 3.1 47.0 + - + +
732F VAL* 1.3 90.9 - - + +
734F LYS* 1.3 68.3 + - + +
735F GLU 3.3 7.2 + - - +
769F ILE* 6.1 1.6 - - + -
770F THR* 5.4 14.4 - - + -
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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