Contacts of the helix formed by residues 853 - 876 (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 LEU 853 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B ARG* 3.6 55.0 - - + +
740B GLU* 3.4 34.5 - - + +
741B TYR* 4.3 14.7 - - + +
744B SER* 5.8 1.1 - - - +
849B VAL* 3.9 20.5 - - + +
850B ALA* 3.0 10.5 + - + +
852B GLU* 1.3 89.6 - - + +
854B LYS* 1.3 65.2 + - - +
855B PRO* 3.4 2.5 - - - -
856B PHE* 3.3 24.3 + - + +
857B GLY* 3.2 15.6 + - - -
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Residues in contact with LYS 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B ASP* 3.8 16.3 - - + +
846B GLU* 3.0 38.2 + - - +
849B VAL* 3.3 29.8 - - + -
850B ALA 3.5 11.2 - - - +
851B GLU* 3.3 35.3 + - - +
853B LEU* 1.3 78.9 - - - +
855B PRO* 1.3 67.8 - - + +
857B GLY* 3.1 10.5 + - - +
858B LYS* 3.1 14.0 + - - +
861B ARG* 4.6 3.3 + - - -
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Residues in contact with PRO 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B ARG* 6.3 0.2 - - - +
851B GLU 3.7 9.9 - - - +
852B GLU 4.0 9.2 - - - +
853B LEU 3.5 4.0 - - - -
854B LYS* 1.3 93.2 - - + +
856B PHE* 1.3 61.2 + - - +
858B LYS* 3.3 6.2 + - + +
859B GLN* 3.1 33.3 + - + +
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Residues in contact with PHE 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B VAL* 4.0 28.5 - - + -
735B GLU* 4.0 28.3 - - + -
737B ARG* 4.3 20.9 - - - +
738B PHE* 4.1 14.6 - + - -
741B TYR* 4.0 39.3 - + + -
853B LEU* 3.3 26.3 + - + +
855B PRO* 1.3 78.8 - - - +
857B GLY* 1.3 62.5 + - - +
859B GLN* 3.2 20.9 + - + +
860B LEU* 3.2 33.7 + - + +
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Residues in contact with GLY 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B TYR* 3.4 29.3 + - - -
845B ASP* 3.5 7.6 - - - -
853B LEU 3.2 5.3 + - - -
854B LYS 3.1 8.4 + - - -
856B PHE* 1.3 79.3 - - - +
858B LYS* 1.3 61.3 + - - +
860B LEU* 3.0 16.2 + - - +
861B ARG* 3.0 21.1 + - - +
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Residues in contact with LYS 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B LYS 3.1 11.3 + - - +
855B PRO* 3.3 7.8 + - + +
857B GLY* 1.3 75.5 - - - +
859B GLN* 1.3 58.2 + - + +
861B ARG* 3.5 41.1 - - + +
862B ASP* 2.8 38.6 + - - +
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Residues in contact with GLN 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B PRO* 3.1 19.7 + - + +
856B PHE* 3.5 20.8 - - + +
857B GLY 3.1 0.2 - - - -
858B LYS* 1.3 76.5 - - + +
860B LEU* 1.3 66.0 + - - +
862B ASP* 3.2 16.0 + - - +
863B LYS* 3.0 30.4 + - - +
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Residues in contact with LEU 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B VAL* 3.8 28.5 - - + -
738B PHE* 4.7 1.6 - - + -
741B TYR* 3.7 30.1 - - + +
786B PHE* 3.8 15.3 - - + -
788B LEU* 3.8 26.0 - - + -
791B TRP* 3.6 9.3 - - + -
792B LEU* 4.9 4.9 - - + -
856B PHE* 3.2 32.2 + - + +
857B GLY 3.0 9.2 + - - +
859B GLN* 1.3 77.5 - - + +
861B ARG* 1.3 55.7 + - - +
863B LYS* 3.2 23.9 + - + +
864B TYR* 2.9 22.2 + - - +
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Residues in contact with ARG 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B TYR* 4.0 3.0 + - - -
786B PHE* 3.6 20.3 - - + -
838B PRO* 3.6 35.4 - - + -
841B ALA* 4.2 3.7 + - - +
842B GLY* 3.9 18.6 + - - +
845B ASP* 3.1 36.0 + - - +
854B LYS* 4.6 3.0 + - - +
857B GLY 3.0 13.0 + - - +
858B LYS* 3.5 61.4 - - + +
859B GLN 3.2 0.2 - - - -
860B LEU* 1.3 72.6 - - - +
862B ASP* 1.3 66.3 + - - +
864B TYR* 3.2 9.2 + - + +
865B VAL* 3.1 28.9 + - + +
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Residues in contact with ASP 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858B LYS* 2.8 34.0 + - - +
859B GLN* 3.2 19.5 + - - +
861B ARG* 1.3 77.1 - - - +
863B LYS* 1.3 61.2 + - + +
865B VAL* 3.2 13.2 - - + +
866B GLU* 3.0 31.9 + - - +
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Residues in contact with LYS 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B GLU* 2.6 35.4 + - - +
731B VAL* 4.2 15.9 - - - -
791B TRP* 3.8 11.4 - - + -
792B LEU* 4.1 17.5 - - + -
859B GLN* 3.0 19.0 + - - +
860B LEU* 3.2 17.9 + - + +
862B ASP* 1.3 74.8 - - + +
864B TYR* 1.3 55.9 + - - +
866B GLU* 3.2 21.0 + - - +
867B THR* 2.6 40.4 + - - +
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Residues in contact with TYR 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B ARG 4.7 4.0 - - - -
786B PHE* 3.5 31.0 - + + -
787B HIS* 5.4 1.6 - - + -
791B TRP* 3.6 34.0 - + + -
833B PHE* 3.4 37.2 + + - -
836B GLY* 3.5 27.6 + - - -
837B ASP 4.6 0.2 - - - -
838B PRO* 3.4 33.1 - - + +
860B LEU 2.9 12.9 + - - +
861B ARG* 3.4 14.1 - - - +
862B ASP 3.2 0.2 - - - -
863B LYS* 1.3 77.2 - - - +
865B VAL* 1.3 68.7 + - + +
867B THR* 3.6 1.7 - - - -
868B GLN* 3.0 35.5 + - - +
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Residues in contact with VAL 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B PRO* 4.6 12.8 - - + -
861B ARG* 3.1 13.2 + - + +
862B ASP* 3.2 18.2 - - + +
864B TYR* 1.3 89.6 - - + +
866B GLU* 1.3 67.6 + - + +
868B GLN* 3.9 8.5 + - - +
869B GLN* 3.0 32.0 + - + +
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Residues in contact with GLU 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B GLU* 5.4 1.4 - - - +
795B GLY* 4.7 15.1 - - - -
796B ALA* 4.8 2.9 + - - -
799B LYS* 5.2 9.0 - - - +
862B ASP* 3.0 22.0 + - - +
863B LYS* 3.2 35.2 + - - +
865B VAL* 1.3 76.8 - - + +
867B THR* 1.3 73.3 + - - +
869B GLN* 4.6 7.2 - - - -
870B LEU* 3.0 36.7 + - + +
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Residues in contact with THR 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B TRP* 3.9 17.0 - - + +
794B VAL* 3.9 20.4 - - + -
795B GLY* 3.4 37.2 + - - +
798B PHE* 4.9 1.4 - - + -
829B LEU* 6.0 0.2 - - + -
833B PHE* 4.0 20.6 - - + -
863B LYS* 2.6 24.7 + - - +
864B TYR 3.6 3.8 - - - -
866B GLU* 1.3 79.2 - - - +
868B GLN* 1.3 62.1 + - - +
870B LEU* 3.3 2.9 + - - +
871B LEU* 2.9 22.7 + - + +
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Residues in contact with GLN 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B PHE* 3.6 44.6 - - + +
864B TYR* 3.0 32.2 + - + +
865B VAL* 3.9 9.2 + - - +
867B THR* 1.3 76.7 - - - +
869B GLN* 1.3 64.9 + - - +
871B LEU* 3.3 4.2 + - + +
872B LEU* 3.0 43.6 + - + +
880B ILE* 3.5 32.4 - - + +
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Residues in contact with GLN 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B VAL* 3.0 22.2 + - - +
866B GLU* 3.9 7.7 - - - +
868B GLN* 1.3 78.1 - - - +
870B LEU* 1.3 68.0 + - + +
872B LEU* 3.5 10.5 + - + +
873B GLN* 3.1 31.8 + - + +
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Residues in contact with LEU 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B GLY* 4.7 4.0 - - - +
798B PHE* 4.2 17.9 - - + -
799B LYS* 4.0 36.6 - - + +
802B ILE* 4.9 9.2 - - + -
866B GLU* 3.0 31.7 + - + +
867B THR* 4.1 2.7 - - - +
868B GLN 3.3 0.4 - - - -
869B GLN* 1.3 89.0 - - + +
871B LEU* 1.3 66.6 + - - +
873B GLN* 3.2 13.6 + - + +
874B ILE* 2.9 29.0 + - + +
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Residues in contact with LEU 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B VAL* 5.9 0.7 - - + -
798B PHE* 4.1 15.3 - - + -
816B TYR* 5.9 0.2 - - + -
826B LEU* 3.6 45.1 - - + +
829B LEU* 4.1 7.0 - - + -
830B GLU* 3.8 30.1 - - + +
833B PHE* 3.5 34.3 - - + -
867B THR* 2.9 18.8 + - + +
868B GLN* 3.3 4.7 + - + +
870B LEU* 1.3 76.7 - - - +
872B LEU* 1.3 68.5 + - + +
874B ILE* 3.3 3.3 + - - +
875B ALA* 3.0 25.2 + - + +
880B ILE* 6.3 0.2 - - + -
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Residues in contact with LEU 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B GLU* 4.1 17.9 - - + +
868B GLN* 3.0 33.7 + - + +
869B GLN* 3.7 9.4 - - + +
871B LEU* 1.3 80.2 - - + +
873B GLN* 1.3 57.9 + - + +
875B ALA* 3.3 3.7 + - - +
876B GLY 2.9 24.4 + - - -
877B HIS* 3.1 25.5 + - + +
878B LYS 4.0 18.6 - - - +
879B ASP* 4.3 13.2 - - - +
880B ILE* 4.0 35.2 - - + +
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Residues in contact with GLN 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B PHE* 3.9 31.7 - - + -
813B LYS* 4.2 5.0 - - - +
869B GLN* 3.1 20.7 + - + +
870B LEU* 3.2 15.9 + - + +
872B LEU* 1.3 78.1 - - + +
874B ILE* 1.3 63.3 + - + +
876B GLY* 3.1 13.2 + - - -
877B HIS 5.1 0.9 - - - -
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Residues in contact with ILE 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B PHE* 3.7 44.4 - - + -
802B ILE* 5.1 2.9 - - + -
809B PHE* 4.2 20.2 - - + -
812B LEU* 3.8 51.6 - - + +
813B LYS* 3.5 20.8 - - - +
816B TYR* 4.0 9.5 - - + +
817B ASN* 5.2 0.9 + - - -
822B PHE* 4.2 14.1 - - + -
826B LEU* 4.5 7.4 - - + -
870B LEU* 2.9 14.7 + - + +
871B LEU* 3.9 4.9 - - - +
873B GLN* 1.3 76.4 - - - +
875B ALA* 1.3 61.7 + - - +
876B GLY 3.4 0.5 + - - -
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Residues in contact with ALA 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B TYR* 3.5 47.5 - - + +
817B ASN* 5.1 4.0 + - - +
830B GLU* 4.6 5.4 - - - +
871B LEU* 3.0 19.5 + - + +
872B LEU* 3.9 4.5 - - - +
874B ILE* 1.3 76.7 - - - +
876B GLY* 1.3 62.2 + - - +
877B HIS* 3.6 27.1 + - - +
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Residues in contact with GLY 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B LYS* 5.5 5.8 - - - -
872B LEU 2.9 6.7 + - - -
873B GLN* 3.1 12.4 + - - -
874B ILE 3.2 0.8 + - - -
875B ALA* 1.3 79.6 - - - +
877B HIS* 1.3 63.7 + - - +
878B LYS* 4.2 2.3 + - - +
882B GLU* 4.0 6.6 - - - +
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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