Contacts of the helix formed by residues 853 - 876 (chain G) 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 LEU 853 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737G ARG* 3.8 39.5 - - + +
740G GLU* 3.6 41.7 - - + +
741G TYR* 4.2 24.4 - - + +
744G SER* 5.8 1.1 - - - +
849G VAL* 4.0 10.3 - - + -
850G ALA* 3.1 12.9 + - + +
851G GLU 3.1 0.8 - - - -
852G GLU* 1.3 106.6 - - + +
854G LYS* 1.3 65.1 + - - +
855G PRO 3.4 1.8 - - - -
856G PHE* 3.2 21.1 + - + +
857G GLY 3.3 8.1 + - - -
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Residues in contact with LYS 854 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845G ASP* 3.8 16.6 - - + +
846G GLU* 2.8 55.2 + - - +
849G VAL* 3.3 30.1 - - + -
850G ALA 3.4 10.9 + - - +
851G GLU* 3.2 41.3 + - - +
853G LEU* 1.3 77.9 - - - +
855G PRO* 1.3 69.3 - - + +
857G GLY* 3.0 11.7 + - - +
858G LYS* 3.1 12.8 + - - +
861G ARG* 4.6 3.2 + - - +
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Residues in contact with PRO 855 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851G GLU 3.5 13.0 - - - +
852G GLU* 3.9 9.0 - - - +
853G LEU 3.5 3.8 - - - -
854G LYS* 1.3 90.7 - - + +
856G PHE* 1.3 62.0 + - - +
858G LYS* 3.2 8.3 + - + +
859G GLN* 3.0 32.1 + - - +
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Residues in contact with PHE 856 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731G VAL* 4.0 27.1 - - + -
735G GLU* 3.9 29.4 - - + -
737G ARG* 4.0 35.7 - - + +
738G PHE* 4.1 13.7 - + - -
741G TYR* 3.9 33.9 - + + -
853G LEU* 3.2 16.2 + - + +
855G PRO* 1.3 78.4 - - - +
857G GLY* 1.3 61.9 + - - +
859G GLN* 3.3 19.6 + - + +
860G LEU* 3.1 41.8 + - + +
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Residues in contact with GLY 857 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741G TYR* 3.4 28.6 + - - -
845G ASP* 3.5 7.2 - - - -
853G LEU 3.3 4.9 + - - -
854G LYS 3.0 8.1 + - - -
856G PHE* 1.3 80.5 - - - +
858G LYS* 1.3 57.1 + - - +
860G LEU* 3.1 7.4 + - - +
861G ARG* 2.9 37.2 + - - +
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Residues in contact with LYS 858 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838G PRO* 5.9 2.4 - - - +
854G LYS 3.1 11.7 + - - +
855G PRO* 3.2 9.6 + - + +
857G GLY* 1.3 76.0 - - - +
859G GLN* 1.3 58.5 + - + +
861G ARG* 3.3 45.6 + - - +
862G ASP* 2.9 46.6 + - - +
865G VAL* 6.3 1.2 - - - +
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Residues in contact with GLN 859 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737G ARG* 5.1 4.0 + - - -
855G PRO* 3.0 17.2 + - - +
856G PHE* 3.6 29.2 + - + +
857G GLY 3.2 0.2 - - - -
858G LYS* 1.3 75.0 - - + +
860G LEU* 1.3 65.2 + - + +
862G ASP* 3.1 15.6 + - - +
863G LYS* 3.0 35.6 + - - +
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Residues in contact with LEU 860 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731G VAL* 3.8 28.7 - - + -
738G PHE* 4.9 2.0 - - + -
741G TYR* 3.6 31.2 - - + +
786G PHE* 3.8 15.0 - - + -
788G LEU* 4.0 23.6 - - + -
791G TRP* 3.6 12.7 - - + -
792G LEU* 5.2 3.4 - - + -
856G PHE* 3.1 35.0 + - + +
857G GLY 3.1 8.6 + - - +
859G GLN* 1.3 75.2 - - + +
861G ARG* 1.3 57.0 + - - +
863G LYS* 3.3 20.9 + - + +
864G TYR 3.0 22.3 + - - -
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Residues in contact with ARG 861 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741G TYR* 4.0 3.4 + - - -
786G PHE* 3.7 19.7 - - + -
838G PRO* 3.7 34.8 - - + -
841G ALA* 4.2 4.1 + - - +
842G GLY* 3.8 17.3 + - - +
845G ASP* 2.9 41.4 + - - +
846G GLU* 5.6 2.8 + - - -
854G LYS* 4.6 4.2 + - - +
857G GLY 2.9 15.5 + - - +
858G LYS* 3.3 57.1 - - - +
859G GLN 3.2 0.2 - - - -
860G LEU* 1.3 74.1 - - - +
862G ASP* 1.3 66.4 + - - +
864G TYR* 3.3 8.9 + - + +
865G VAL* 3.1 29.1 + - + +
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Residues in contact with ASP 862 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858G LYS* 2.9 36.6 + - - +
859G GLN* 3.1 19.0 + - - +
861G ARG* 1.3 77.8 - - - +
863G LYS* 1.3 57.9 + - + +
865G VAL* 3.2 13.5 - - + +
866G GLU* 2.9 28.9 + - - +
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Residues in contact with LYS 863 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727G GLU* 2.5 35.8 + - - +
731G VAL* 4.4 13.7 - - - -
791G TRP* 3.8 10.8 - - + -
792G LEU* 4.5 10.8 - - + -
859G GLN* 3.0 20.6 + - - +
860G LEU* 3.3 23.5 + - + +
862G ASP* 1.3 72.7 - - + +
864G TYR* 1.3 56.9 + - - +
866G GLU* 3.6 19.8 + - - +
867G THR* 2.6 40.8 + - - +
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Residues in contact with TYR 864 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785G ARG 4.7 4.0 - - - -
786G PHE* 3.6 31.4 - + + -
787G HIS* 5.5 0.9 - + - -
791G TRP* 3.6 36.2 - + + -
833G PHE* 3.5 30.0 + + - -
836G GLY* 3.4 30.6 + - - -
838G PRO* 3.5 33.8 - - + +
860G LEU 3.0 13.4 + - - +
861G ARG* 3.3 13.7 - - - +
863G LYS* 1.3 76.8 - - - +
865G VAL* 1.3 66.1 + - + +
867G THR* 3.6 2.4 - - - -
868G GLN* 2.9 45.3 + - - +
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Residues in contact with VAL 865 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838G PRO* 4.8 12.1 - - + -
858G LYS* 6.3 1.3 - - - +
861G ARG* 3.1 16.0 + - + +
862G ASP* 3.2 17.7 - - - +
864G TYR* 1.3 87.7 - - + +
866G GLU* 1.3 68.3 + - + +
868G GLN* 3.9 6.3 - - - +
869G GLN* 3.0 26.2 + - - +
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Residues in contact with GLU 866 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727G GLU* 5.3 1.9 - - - +
795G GLY* 4.2 20.8 - - - +
796G ALA* 4.3 2.7 + - - -
799G LYS* 4.7 14.1 - - + +
862G ASP 2.9 18.1 + - - +
863G LYS* 3.6 24.4 + - - +
865G VAL* 1.3 80.0 - - + +
867G THR* 1.3 62.6 + - - +
869G GLN* 3.5 11.1 + - - +
870G LEU* 3.2 41.9 + - + +
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Residues in contact with THR 867 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791G TRP* 3.8 19.2 - - + +
794G VAL* 3.9 18.8 - - + -
795G GLY* 3.4 37.8 + - - +
798G PHE* 5.0 1.1 - - + -
829G LEU* 6.0 0.4 - - + -
833G PHE* 3.9 20.6 - - + -
863G LYS* 2.6 27.1 + - - +
864G TYR 3.6 3.6 - - - -
866G GLU* 1.3 74.7 + - - +
868G GLN* 1.3 62.3 + - - +
870G LEU* 3.2 4.4 + - - +
871G LEU* 2.9 24.5 + - + +
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Residues in contact with GLN 868 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833G PHE* 3.6 48.5 - - + +
838G PRO* 5.8 0.2 - - - +
864G TYR* 2.9 33.0 + - + +
865G VAL* 3.9 6.5 - - - +
867G THR* 1.3 77.0 - - - +
869G GLN* 1.3 64.7 + - - +
871G LEU* 3.3 3.5 + - + +
872G LEU* 3.1 41.7 + - + +
879G ASP* 5.7 1.8 + - - -
880G ILE* 4.3 16.5 - - + +
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Residues in contact with GLN 869 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865G VAL 3.0 16.8 + - - +
866G GLU* 4.0 15.3 + - - +
867G THR 3.3 0.2 - - - -
868G GLN* 1.3 78.2 - - - +
870G LEU* 1.3 77.8 + - - +
872G LEU* 3.4 9.1 + - - +
873G GLN* 2.8 52.0 + - + +
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Residues in contact with LEU 870 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795G GLY* 3.6 26.2 - - - +
798G PHE* 4.0 25.8 - - + -
799G LYS* 4.2 17.3 - - + +
802G ILE* 4.7 14.6 - - + -
809G PHE* 5.9 3.4 - - + -
866G GLU* 3.2 34.3 + - + +
867G THR 3.8 3.1 - - - +
869G GLN* 1.3 93.7 - - - +
871G LEU* 1.3 66.5 + - - +
873G GLN* 3.2 9.8 + - + +
874G ILE* 3.0 28.8 + - + +
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Residues in contact with LEU 871 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798G PHE* 4.1 14.5 - - + -
816G TYR* 6.1 0.2 - - + -
826G LEU* 3.6 27.2 - - + +
829G LEU* 3.5 36.1 - - + -
830G GLU* 4.0 39.0 - - + +
833G PHE* 4.0 16.6 - - + -
867G THR* 2.9 17.9 + - + +
868G GLN* 3.3 6.3 + - + +
870G LEU* 1.3 75.4 - - - +
872G LEU* 1.3 71.0 + - + +
874G ILE* 3.1 5.1 + - - +
875G ALA* 2.9 24.5 + - + +
880G ILE* 5.1 2.0 - - + -
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Residues in contact with LEU 872 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830G GLU* 4.0 14.8 - - - +
868G GLN* 3.1 38.3 + - + +
869G GLN* 3.7 7.6 - - - +
870G LEU 3.3 0.2 - - - -
871G LEU* 1.3 82.2 - - + +
873G GLN* 1.3 57.8 + - + +
875G ALA* 3.3 3.4 + - - +
876G GLY* 2.9 24.1 + - - -
877G HIS* 3.0 27.3 + - + +
878G LYS 4.2 17.0 - - - +
879G ASP* 4.2 13.0 - - - +
880G ILE* 3.7 36.6 - - + +
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Residues in contact with GLN 873 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809G PHE* 3.8 36.4 - - + -
813G LYS* 3.9 6.6 + - - -
869G GLN* 2.8 39.3 + - + +
870G LEU* 3.2 13.3 + - + +
872G LEU* 1.3 78.2 - - + +
874G ILE* 1.3 63.1 + - - +
876G GLY* 3.3 11.6 + - - -
877G HIS 5.1 0.7 - - - -
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Residues in contact with ILE 874 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798G PHE* 3.5 46.7 - - + -
802G ILE* 5.3 1.8 - - + -
809G PHE* 4.7 12.8 - - + -
812G LEU* 3.7 50.7 - - + +
813G LYS* 3.4 25.9 + - - +
816G TYR* 4.1 11.8 - - + +
817G ASN* 5.4 0.5 - - - +
822G PHE* 4.2 15.3 - - + -
826G LEU* 5.0 4.3 - - + -
870G LEU* 3.0 14.0 + - + +
871G LEU* 3.1 7.8 + - - +
873G GLN* 1.3 75.7 - - - +
875G ALA* 1.3 61.4 + - - +
876G GLY 3.4 0.7 + - - -
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Residues in contact with ALA 875 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813G LYS* 4.6 1.3 + - - -
816G TYR* 3.4 48.5 - - + +
817G ASN* 5.2 3.1 + - - -
826G LEU* 6.1 0.2 - - + -
830G GLU* 4.5 4.3 - - - +
871G LEU* 2.9 19.6 + - + +
872G LEU* 3.8 4.9 - - - +
873G GLN 3.3 0.2 - - - -
874G ILE* 1.3 78.1 - - - +
876G GLY* 1.3 60.2 + - - +
877G HIS* 3.6 25.6 + - - +
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Residues in contact with GLY 876 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813G LYS* 3.6 20.4 - - - -
872G LEU 2.9 5.8 + - - -
873G GLN* 3.3 4.4 + - - -
874G ILE 3.2 4.6 + - - -
875G ALA* 1.3 79.1 - - - +
877G HIS* 1.3 63.0 + - - +
878G LYS 4.1 0.7 + - - -
882G GLU* 4.1 5.7 - - - +
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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