Contacts of the helix formed by residues 853 - 876 (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 LEU 853 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737F ARG* 3.9 47.6 - - + +
740F GLU* 3.4 39.5 - - + +
741F TYR* 4.1 24.5 - - + +
744F SER* 5.2 3.1 - - - +
849F VAL* 3.6 22.2 - - + +
850F ALA* 2.9 14.5 + - + +
852F GLU* 1.3 83.0 - - + +
854F LYS* 1.3 64.0 + - - +
855F PRO* 3.5 2.0 - - - -
856F PHE* 3.4 14.9 + - + +
857F GLY 3.4 13.9 + - - -
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Residues in contact with LYS 854 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845F ASP* 3.9 16.3 - - + +
846F GLU* 3.1 36.6 + - + +
849F VAL* 3.3 29.4 - - + +
850F ALA 3.3 11.7 - - - +
851F GLU* 3.3 39.6 + - - +
853F LEU* 1.3 75.6 - - - +
855F PRO* 1.3 71.4 - - + +
857F GLY* 3.1 3.2 + - - +
858F LYS* 3.1 20.5 + - - +
861F ARG* 4.6 3.4 + - - +
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Residues in contact with PRO 855 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851F GLU 3.6 11.0 - - - +
852F GLU 4.0 8.5 - - - +
853F LEU 3.6 2.9 - - - -
854F LYS* 1.3 94.3 - - + +
856F PHE* 1.3 60.4 + - - +
858F LYS* 3.3 8.4 + - + +
859F GLN* 3.1 34.2 + - - +
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Residues in contact with PHE 856 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731F VAL* 4.0 18.8 - - + -
735F GLU* 4.0 26.0 - - + -
737F ARG* 4.3 29.6 - - + +
738F PHE* 4.0 30.1 - + - -
741F TYR* 3.9 29.6 - + + -
852F GLU 5.5 0.4 + - - -
853F LEU* 3.4 16.7 + - + +
854F LYS 3.2 0.4 - - - -
855F PRO* 1.3 79.7 - - - +
857F GLY* 1.3 60.5 + - - +
859F GLN* 3.2 21.8 + - + +
860F LEU* 3.2 40.8 + - + +
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Residues in contact with GLY 857 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741F TYR* 3.5 27.9 + - - -
786F PHE* 5.1 0.2 - - - -
845F ASP* 3.6 9.9 - - - -
853F LEU 3.4 4.8 + - - -
854F LYS 3.1 4.8 + - - -
856F PHE* 1.3 78.1 - - - +
858F LYS* 1.3 64.4 + - - +
860F LEU* 3.0 7.9 + - - +
861F ARG* 2.9 32.0 + - - +
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Residues in contact with LYS 858 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854F LYS 3.1 13.1 + - - +
855F PRO* 3.3 11.4 + - + +
857F GLY* 1.3 74.0 - - - +
859F GLN* 1.3 58.3 + - - +
861F ARG* 3.4 37.4 + - + +
862F ASP* 2.9 47.4 + - - +
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Residues in contact with GLN 859 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855F PRO* 3.1 19.9 + - - +
856F PHE* 3.5 22.8 - - + +
857F GLY 3.1 0.4 - - - -
858F LYS* 1.3 75.9 - - + +
860F LEU* 1.3 65.1 + - + +
862F ASP* 3.2 14.0 + - - +
863F LYS* 3.0 32.9 + - - +
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Residues in contact with LEU 860 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731F VAL* 3.7 26.5 - - + -
738F PHE* 4.8 8.7 - - + -
741F TYR* 3.7 31.2 - - + +
786F PHE* 3.8 21.8 - - + -
788F LEU* 4.6 17.0 - - + -
791F TRP* 3.6 8.0 - - + -
792F LEU* 4.7 1.1 - - + -
856F PHE* 3.2 32.3 + - + +
857F GLY* 3.0 7.1 + - - +
859F GLN* 1.3 77.7 - - + +
861F ARG* 1.3 56.2 + - - +
863F LYS* 3.1 24.6 + - + +
864F TYR 2.9 21.7 + - - -
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Residues in contact with ARG 861 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741F TYR* 4.2 3.0 + - - -
786F PHE* 3.7 20.3 - - + -
838F PRO* 3.7 34.1 - - + -
841F ALA* 4.3 2.7 + - - +
842F GLY* 3.8 20.3 + - - +
845F ASP* 3.0 36.6 + - - +
854F LYS* 4.6 3.2 + - - +
857F GLY 2.9 16.9 + - - +
858F LYS* 3.7 54.6 - - + +
860F LEU* 1.3 72.5 - - - +
862F ASP* 1.3 67.2 + - - +
864F TYR* 3.1 8.8 + - + +
865F VAL* 3.0 30.3 + - + +
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Residues in contact with ASP 862 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858F LYS* 2.9 35.0 + - - +
859F GLN* 3.2 17.8 + - - +
861F ARG* 1.3 76.3 - - - +
863F LYS* 1.3 57.4 + - + +
865F VAL* 3.3 13.4 - - + +
866F GLU* 2.9 31.2 + - - +
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Residues in contact with LYS 863 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727F GLU* 2.7 32.8 + - - +
731F VAL* 4.2 19.3 - - - +
791F TRP* 3.8 10.8 - - + -
792F LEU* 4.0 17.0 - - + -
859F GLN* 3.0 21.9 + - - +
860F LEU* 3.1 19.3 + - + +
862F ASP* 1.3 75.3 - - + +
864F TYR* 1.3 54.8 + - - +
866F GLU* 3.8 9.9 - - - +
867F THR* 2.6 40.2 + - - +
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Residues in contact with TYR 864 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785F ARG 4.6 3.4 - - - -
786F PHE* 3.4 35.0 - + + -
787F HIS* 5.5 1.6 - + + -
791F TRP* 3.5 38.5 - + + -
833F PHE* 3.6 29.2 + + - -
836F GLY* 3.4 30.0 + - - -
837F ASP 3.6 0.6 + - - -
838F PRO* 3.4 33.5 - - + +
860F LEU 2.9 9.1 + - - +
861F ARG* 3.1 13.9 + - - +
863F LYS* 1.3 76.1 - - - +
865F VAL* 1.3 68.0 + - - +
867F THR* 3.7 1.7 - - - -
868F GLN* 3.0 40.5 + - - +
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Residues in contact with VAL 865 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838F PRO* 4.7 12.6 - - + -
861F ARG* 3.0 16.1 + - + +
862F ASP* 3.3 18.2 - - - +
864F TYR* 1.3 87.0 - - + +
866F GLU* 1.3 67.1 + - + +
868F GLN* 4.6 1.3 - - - -
869F GLN* 2.6 39.3 + - - +
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Residues in contact with GLU 866 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795F GLY* 5.1 6.9 - - - -
799F LYS* 3.2 33.8 + - - +
862F ASP 2.9 18.5 + - - +
863F LYS* 3.8 9.7 - - - +
865F VAL* 1.3 78.3 - - + +
867F THR* 1.3 66.0 + - - +
869F GLN* 3.4 4.3 + - + +
870F LEU* 3.2 33.7 + - + +
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Residues in contact with THR 867 (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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791F TRP* 3.9 17.5 - - + +
793F GLY 5.7 0.2 + - - -
794F VAL* 3.9 20.2 - - + -
795F GLY* 3.4 37.4 + - - +
798F PHE* 5.0 0.7 - - + -
829F LEU* 6.2 0.2 - - + -
833F PHE* 4.0 19.7 - - + -
863F LYS* 2.6 25.9 + - - +
864F TYR 3.7 3.6 - - - -
866F GLU* 1.3 77.2 - - - +
868F GLN* 1.3 63.0 + - - +
870F LEU* 3.4 3.3 + - - +
871F LEU* 3.0 23.4 + - + +
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Residues in contact with GLN 868 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833F PHE* 3.6 37.3 - - + +
864F TYR* 3.0 39.9 + - - +
865F VAL* 4.6 1.1 - - - -
867F THR* 1.3 76.0 - - - +
869F GLN* 1.3 85.0 + - - +
871F LEU* 3.3 4.2 + - + +
872F LEU* 3.0 38.9 + - + +
880F ILE* 3.4 34.2 - - + +
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Residues in contact with GLN 869 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865F VAL* 2.6 37.0 + - + +
866F GLU* 3.9 5.4 - - + +
867F THR 3.3 0.2 - - - -
868F GLN* 1.3 100.0 + - - +
870F LEU* 1.3 63.1 - - + +
872F LEU* 3.4 13.0 + - - +
873F GLN* 3.0 38.4 + - + +
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Residues in contact with LEU 870 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795F GLY* 3.7 26.7 - - - +
798F PHE* 4.1 24.2 - - + -
799F LYS* 3.5 43.5 - - + +
802F ILE* 4.9 11.2 - - + -
809F PHE* 6.6 0.2 - - + -
866F GLU* 3.2 23.9 + - + +
867F THR 3.9 2.9 - - - +
869F GLN* 1.3 77.9 - - + +
871F LEU* 1.3 63.6 + - - +
873F GLN* 3.1 13.0 + - + +
874F ILE* 3.0 28.0 + - + +
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Residues in contact with LEU 871 (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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794F VAL* 5.9 0.4 - - + -
798F PHE* 4.1 14.8 - - + -
826F LEU* 3.6 47.8 - - + +
829F LEU* 4.1 7.0 - - + -
830F GLU* 3.8 28.5 - - + +
833F PHE* 3.6 34.1 - - + -
867F THR* 3.0 18.2 + - + +
868F GLN* 3.3 4.9 + - + +
870F LEU* 1.3 77.0 - - - +
872F LEU* 1.3 69.2 + - + +
874F ILE* 3.3 3.8 + - - +
875F ALA* 3.0 25.8 + - + +
880F ILE* 6.4 0.2 - - + -
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Residues in contact with LEU 872 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830F GLU* 4.0 25.6 - - + +
868F GLN* 3.0 36.0 + - + +
869F GLN* 3.7 22.7 - - - +
871F LEU* 1.3 80.1 - - + +
873F GLN* 1.3 68.2 + - - +
875F ALA* 3.3 4.1 + - + +
876F GLY 3.0 18.7 + - - -
877F HIS* 3.1 26.2 + - + +
878F LYS 4.1 17.7 - - - +
879F ASP* 4.2 9.4 - - - +
880F ILE* 4.0 23.1 - - + +
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Residues in contact with GLN 873 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809F PHE* 3.9 30.8 - - + -
813F LYS* 4.0 5.7 - - - +
869F GLN* 3.0 32.8 + - + +
870F LEU* 3.1 14.1 + - + +
872F LEU* 1.3 84.4 - - - +
874F ILE* 1.3 62.5 + - - +
876F GLY* 3.3 12.3 + - - +
877F HIS 4.9 3.8 + - - -
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Residues in contact with ILE 874 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798F PHE* 3.5 49.6 - - + -
802F ILE* 5.3 2.0 - - + -
809F PHE* 4.3 12.1 - - + -
812F LEU* 3.7 46.7 - - + +
813F LYS* 3.5 25.9 - - - +
816F TYR* 4.0 7.4 - - + +
822F PHE* 4.1 6.3 - - + -
826F LEU* 4.0 20.2 - - + -
870F LEU* 3.0 16.8 + - + +
871F LEU* 3.3 5.1 + - - +
872F LEU 3.3 0.2 - - - -
873F GLN* 1.3 76.0 - - - +
875F ALA* 1.3 60.9 + - - +
876F GLY 3.4 0.5 + - - -
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Residues in contact with ALA 875 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816F TYR* 3.3 50.3 - - + +
817F ASN* 5.2 1.9 + - - -
830F GLU* 4.7 4.5 - - - +
871F LEU* 3.0 21.3 + - + +
872F LEU* 3.3 4.7 + - - +
874F ILE* 1.3 76.4 - - - +
876F GLY* 1.3 62.2 + - - +
877F HIS* 3.4 25.4 - - + +
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Residues in contact with GLY 876 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813F LYS* 5.6 4.7 - - - -
872F LEU 3.0 5.1 + - - -
873F GLN* 3.3 8.3 + - - -
874F ILE 3.2 4.6 + - - -
875F ALA* 1.3 78.9 - - - +
877F HIS* 1.3 64.4 + - - +
878F LYS* 4.3 4.9 + - - +
882F GLU* 3.9 7.1 - - - +
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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