Contacts of the helix formed by residues 890 - 907 (chain B) in PDB entry 5V87
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 ARG 890 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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850B PHE* 3.3 54.1 - - - +
880B TYR* 4.7 4.0 - - - -
885B LEU* 3.7 6.1 - - + +
888B LYS* 3.6 15.1 + - + +
889B PHE* 1.3 85.0 - - - +
891B LEU* 1.3 61.0 + - - +
892B ASP* 3.4 20.4 + - - +
893B ILE* 3.3 18.2 + - + +
894B PHE* 2.8 29.1 + - - +
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Residues in contact with LEU 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889B PHE* 3.9 21.8 - - + -
890B ARG* 1.3 71.7 - - - +
892B ASP* 1.3 68.6 + - + +
894B PHE* 3.1 4.0 + - + +
895B LYS* 2.9 57.6 + - + +
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Residues in contact with ASP 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850B PHE* 6.0 0.2 - - - -
890B ARG* 3.8 21.7 + - - +
891B LEU* 1.3 86.2 + - + +
893B ILE* 1.3 83.7 + - - +
895B LYS* 3.4 9.5 + - + +
896B ASP* 3.1 26.4 + - - +
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Residues in contact with ILE 893 (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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850B PHE* 3.5 26.0 - - + -
852B LYS* 6.3 1.1 - - + -
855B TYR* 3.5 25.6 - - + -
880B TYR* 3.7 18.8 - - + +
881B TYR* 3.6 25.8 - - + -
885B LEU* 3.9 13.2 - - + -
890B ARG* 3.3 25.7 + - + +
891B LEU 3.3 0.6 - - - -
892B ASP* 1.3 96.4 + - - +
894B PHE* 1.3 61.0 + - - +
896B ASP* 3.2 6.1 + - - +
897B PHE* 2.8 25.8 + - - +
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Residues in contact with PHE 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B LEU* 3.8 11.1 - - + +
889B PHE* 3.5 26.9 - + + -
890B ARG 2.8 17.5 + - - +
891B LEU* 3.1 5.8 + - + +
893B ILE* 1.3 75.2 - - - +
895B LYS* 1.3 63.4 + - + +
897B PHE* 3.1 13.5 + + - +
898B GLN* 3.0 50.6 + - - +
916B PHE* 3.7 31.4 - + - -
919B PHE* 3.3 34.5 - + - -
920B LEU* 4.9 0.4 - - + -
928B LEU* 3.9 25.1 - - + -
929B ASP 4.0 11.9 - - - -
930B ILE* 4.5 4.5 - - + -
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Residues in contact with LYS 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B LEU* 2.9 49.4 + - + +
892B ASP* 3.6 10.3 - - - +
894B PHE* 1.3 77.5 - - + +
896B ASP* 1.3 63.4 + - - +
898B GLN* 3.3 18.2 + - - +
899B GLU* 3.0 23.1 + - - +
929B ASP* 5.5 4.6 + - - +
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Residues in contact with ASP 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B TYR* 2.6 38.3 + - - +
856B GLU* 4.9 1.7 - - - +
859B LYS* 3.3 24.3 + - + +
881B TYR* 3.5 6.3 - - - +
892B ASP 3.1 14.6 + - - +
893B ILE* 3.2 9.3 + - - +
895B LYS* 1.3 75.2 - - - +
897B PHE* 1.3 59.4 + - - +
899B GLU* 3.1 13.9 + - - +
900B GLU* 2.8 35.9 + - + +
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Residues in contact with PHE 897 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B PHE* 3.8 16.2 - + - -
881B TYR* 3.4 51.3 - + + -
882B SER* 4.1 4.9 - - - -
885B LEU* 3.8 13.2 - - + -
893B ILE 2.8 14.6 + - - +
894B PHE* 3.2 17.5 - + + +
896B ASP* 1.3 74.7 - - - +
898B GLN* 1.3 61.2 + - - +
900B GLU* 3.9 0.5 - - - +
901B THR* 2.7 44.6 + - - -
912B GLY 4.5 0.2 - - - -
915B LYS* 3.7 7.2 - - + -
916B PHE* 3.4 43.7 - + + -
919B PHE* 3.7 23.8 - + + -
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Residues in contact with GLN 898 (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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894B PHE* 3.0 48.4 + - + +
895B LYS* 3.7 16.5 - - - +
896B ASP 3.2 0.2 - - - -
897B PHE* 1.3 74.4 - - - +
899B GLU* 1.3 63.5 + - - +
901B THR* 3.3 1.7 + - - -
902B VAL* 3.0 30.7 + - - +
916B PHE* 3.6 22.4 - - + -
929B ASP 3.4 13.5 + - - +
930B ILE* 4.4 1.8 - - - -
931B ASP* 3.1 36.5 + - + +
934B LEU* 3.7 15.9 - - + +
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Residues in contact with GLU 899 (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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859B LYS* 5.0 4.0 + - - -
895B LYS 3.0 17.1 + - - +
896B ASP* 3.1 17.2 + - - +
898B GLN* 1.3 77.5 - - - +
900B GLU* 1.3 77.2 + - - +
902B VAL* 3.4 6.6 + - - +
903B LYS* 3.2 35.3 + - + +
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Residues in contact with GLU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859B LYS* 4.1 13.8 + - + +
863B LEU* 3.6 24.5 - - - +
874B LEU* 5.2 2.5 - - + +
877B LEU* 4.6 8.1 - - + -
878B PHE* 3.5 19.2 - - + -
881B TYR* 3.8 22.4 - - + +
896B ASP 2.8 23.6 + - - +
897B PHE 4.1 0.9 - - - +
899B GLU* 1.3 85.2 - - - +
901B THR* 1.3 60.5 + - - +
903B LYS* 2.9 37.2 + - - +
904B ASP* 2.9 29.1 + - - +
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Residues in contact with THR 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B PHE* 3.6 10.0 - - - -
897B PHE* 2.7 42.5 + - - -
898B GLN 3.7 4.3 - - - -
900B GLU* 1.3 75.0 - - - +
902B VAL* 1.3 66.3 + - - +
904B ASP* 3.2 1.3 + - - +
905B TYR* 2.9 23.4 + - - +
912B GLY 3.8 1.6 - - - +
913B LEU* 3.6 37.0 + - + +
916B PHE* 3.7 10.8 - - + +
934B LEU* 3.7 21.5 - - + -
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Residues in contact with VAL 902 (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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898B GLN 3.0 22.1 + - - +
899B GLU* 3.7 7.2 - - - +
900B GLU 3.4 0.2 - - - -
901B THR* 1.3 75.2 - - - +
903B LYS* 1.3 60.7 + - + +
905B TYR* 3.4 1.7 + - - +
906B GLU* 2.9 60.3 + - + +
931B ASP* 4.5 12.1 - - - +
933B LYS* 3.7 17.5 - - - +
934B LEU* 3.9 34.8 - - + +
937B TYR* 4.2 9.2 - - + -
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Residues in contact with LYS 903 (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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863B LEU* 3.8 21.7 - - - +
899B GLU* 3.2 28.0 + - + +
900B GLU* 2.9 39.8 + - - +
902B VAL* 1.3 81.4 - - + +
904B ASP* 1.3 56.9 + - - +
906B GLU* 3.3 8.4 + - - +
907B ALA* 2.9 30.9 + - - +
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Residues in contact with ASP 904 (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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871B ARG* 2.8 33.9 + - - -
874B LEU* 3.8 8.0 - - + +
878B PHE* 3.7 16.6 - - + -
900B GLU 2.9 18.9 + - - +
901B THR* 3.6 4.7 - - - +
903B LYS* 1.3 74.8 - - - +
905B TYR* 1.3 62.5 + - - +
907B ALA* 3.2 14.3 + - - +
908B GLY 3.4 0.3 + - - -
909B GLN* 3.1 37.9 + - - +
911B TYR 3.7 1.6 + - - -
912B GLY* 2.8 27.8 + - - -
913B LEU 4.4 0.7 + - - +
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Residues in contact with TYR 905 (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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833A GLN* 3.4 37.7 + - - +
901B THR 2.9 17.4 + - - +
902B VAL 3.8 2.7 - - - +
904B ASP* 1.3 77.7 - - - +
906B GLU* 1.3 58.3 + - - +
908B GLY* 3.0 18.9 + - - -
909B GLN 3.4 8.8 + - - +
910B LEU* 3.7 20.2 - - + -
913B LEU* 3.5 41.0 - - + +
937B TYR* 3.3 59.4 + + + +
940B LYS* 6.0 1.6 - - - +
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Residues in contact with GLU 906 (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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902B VAL* 2.9 32.5 + - - +
903B LYS* 3.9 7.3 - - - +
905B TYR* 1.3 78.0 - - + +
907B ALA* 1.3 58.4 + - - +
908B GLY* 3.2 1.9 + - - -
933B LYS* 2.8 25.2 + - - +
937B TYR* 2.7 33.0 + - + +
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Residues in contact with ALA 907 (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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870A TYR* 3.7 13.6 - - - -
871B ARG* 6.1 0.9 - - - +
903B LYS 2.9 17.4 + - - +
904B ASP* 3.5 10.5 - - - +
905B TYR 3.1 0.4 - - - -
906B GLU* 1.3 76.6 - - - +
908B GLY* 1.3 58.1 + - - +
909B GLN* 3.5 14.9 + - + +
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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
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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