Contacts of the helix formed by residues 871 - 888 (chain B) in PDB entry 5V4R
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 871 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ARG* 3.7 27.8 - - - +
875A GLU* 4.7 5.7 + - - -
908A GLY 5.2 0.2 + - - -
909A GLN* 3.0 23.0 + - - +
866B ALA* 4.5 9.3 + - - +
869B GLY* 3.9 12.1 - - - +
870B TYR* 1.3 73.9 - - - +
872B TYR* 1.3 59.6 + - - +
873B GLY 3.4 2.2 - - - -
874B LEU* 3.1 31.7 + - - +
875B GLU* 2.8 51.1 + - - +
878B PHE* 4.9 1.6 - - - -
904B ASP* 2.9 36.8 + - - -
907B ALA* 6.2 1.0 - - - +
909B GLN* 3.7 28.2 - - - +
911B TYR* 4.2 14.8 - - - +
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Residues in contact with TYR 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A GLY 5.4 5.5 + - - +
909A GLN* 4.2 2.6 + - - -
910A LEU* 3.5 45.2 - - + +
914A GLU* 3.2 36.4 + - - +
940A LYS* 5.5 1.5 + - - -
941A PHE* 5.4 3.6 - - - -
836B ASN* 3.3 48.0 - - + +
839B PHE* 4.3 2.7 - - + -
840B ARG* 3.5 26.6 - - + +
870B TYR* 3.5 2.0 - - + +
871B ARG* 1.3 77.0 - - - +
873B GLY* 1.3 59.5 + - - +
875B GLU* 3.2 15.1 + - - +
876B CYS* 2.8 45.7 + - - -
879B ARG* 3.6 10.8 + - - -
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Residues in contact with GLY 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B PHE* 3.5 40.8 - - - -
858B PHE* 3.7 2.4 - - - -
862B ALA* 3.4 18.9 - - - +
865B ASP* 5.1 2.8 + - - +
870B TYR 4.8 2.0 + - - -
871B ARG 3.4 0.6 - - - -
872B TYR* 1.3 76.9 - - - +
874B LEU* 1.3 57.8 + - - +
876B CYS* 3.3 4.5 + - - +
877B LEU* 2.9 22.0 + - - +
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Residues in contact with LEU 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B ALA* 3.7 11.1 + - + +
863B LEU* 4.0 22.0 - - + -
866B ALA* 3.8 24.0 - - + -
870B TYR 5.2 0.2 + - - -
871B ARG* 3.1 36.3 + - - +
873B GLY* 1.3 72.8 - - - +
875B GLU* 1.3 61.0 + - - +
877B LEU* 3.1 24.5 + - + +
878B PHE* 2.9 57.3 + - + -
900B GLU* 5.2 2.9 - - + +
904B ASP* 3.8 13.9 - - + +
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Residues in contact with GLU 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ARG* 5.1 1.4 + - - -
875A GLU* 3.9 14.2 - - - +
909A GLN* 5.1 1.3 - - - +
910A LEU 5.3 0.3 + - - -
911A TYR* 3.8 38.6 + - - +
914A GLU* 4.9 0.3 - - - +
871B ARG* 2.8 43.7 + - + +
872B TYR* 3.5 24.3 + - - +
874B LEU* 1.3 76.2 - - - +
876B CYS* 1.3 62.2 + - - +
878B PHE 3.3 0.9 + - - -
879B ARG* 3.0 47.0 + - - +
911B TYR* 3.8 28.4 - - + -
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Residues in contact with CYS 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B PHE* 3.7 29.6 - - + +
840B ARG* 3.9 4.5 - - - -
843B SER* 2.8 28.2 + - - -
858B PHE* 3.6 4.9 - - + -
872B TYR* 2.8 56.9 + - - +
873B GLY 3.4 9.6 - - - +
875B GLU* 1.3 72.5 - - - +
877B LEU* 1.3 57.1 + - - +
879B ARG* 3.4 12.6 + - - +
880B TYR* 3.0 15.1 + - - +
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Residues in contact with LEU 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B TYR* 4.2 11.4 - - + -
858B PHE* 3.4 35.4 - - + -
859B LYS* 4.0 26.9 - - + +
862B ALA* 4.5 4.3 - - + -
863B LEU* 5.4 0.7 - - + -
873B GLY 2.9 14.9 + - - +
874B LEU* 3.1 29.1 + - + +
876B CYS* 1.3 76.9 - - - +
878B PHE* 1.3 57.0 + - + +
880B TYR* 3.2 6.0 + - + +
881B TYR* 2.9 65.3 + - + +
900B GLU* 4.6 5.6 - - + -
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Residues in contact with PHE 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B ARG* 4.9 1.8 - - - -
874B LEU* 2.9 49.9 + - + +
875B GLU 3.9 3.4 - - - +
877B LEU* 1.3 78.0 - - - +
879B ARG* 1.3 57.6 + - - +
881B TYR* 3.4 9.3 + + - +
882B SER* 3.0 29.1 + - - -
897B PHE* 3.7 19.5 - + - -
900B GLU* 3.5 34.5 - - + -
901B THR* 3.6 25.6 - - - -
904B ASP* 3.7 15.9 - - + -
911B TYR* 4.1 9.4 - + + -
912B GLY* 3.7 28.3 - - - -
915B LYS* 4.0 20.1 - - + +
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Residues in contact with ARG 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A TYR* 5.1 4.4 - - - -
914A GLU* 3.6 18.0 + - - -
1001A MGT 4.0 13.1 + - - -
843B SER* 4.1 2.0 + - - +
844B PHE* 6.3 0.8 - - - -
847B ARG* 3.9 15.2 - - - +
872B TYR* 3.6 18.6 + - - -
875B GLU* 3.0 27.9 + - - +
876B CYS* 3.6 35.5 - - - +
877B LEU 3.3 0.2 - - - -
878B PHE* 1.3 72.8 - - - +
880B TYR* 1.3 65.7 + - - +
883B TYR* 3.0 45.9 + - + +
911B TYR* 2.7 43.1 + - - +
915B LYS* 3.7 13.2 - - - +
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Residues in contact with TYR 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B SER* 3.7 27.9 + - - +
846B LEU* 3.4 42.7 + - + -
847B ARG* 4.0 11.4 - - + +
850B PHE* 3.1 30.0 - + - +
855B TYR* 3.9 18.2 - + - -
858B PHE* 4.1 8.5 - + + -
876B CYS 3.0 14.6 + - - +
877B LEU* 3.4 16.6 - - + +
879B ARG* 1.3 76.5 - - - +
881B TYR* 1.3 80.8 + + - +
884B GLY* 2.7 38.1 + - - -
885B LEU* 3.9 1.5 + - + -
890B ARG* 5.5 1.0 - - - -
893B ILE* 3.9 12.8 - - + +
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Residues in contact with TYR 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B TYR* 2.7 38.0 + + - -
859B LYS* 3.6 15.4 - - - +
877B LEU* 2.9 41.5 + - + +
878B PHE* 3.6 10.5 - + - +
880B TYR* 1.3 86.0 - + - +
882B SER* 1.3 63.4 + - - +
885B LEU* 3.0 33.7 + - + +
893B ILE* 3.7 28.3 - - + -
896B ASP* 3.6 4.5 - - - +
897B PHE* 3.4 56.9 - + + -
900B GLU* 3.9 13.0 - - + +
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Residues in contact with SER 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A MGT 2.9 38.4 + - - -
878B PHE 3.0 17.6 + - - -
879B ARG 4.1 1.8 - - - -
881B TYR* 1.3 78.2 - - - +
883B TYR* 1.3 63.9 + - - +
886B GLU* 3.4 14.4 + - - +
897B PHE* 4.1 8.5 - - - -
915B LYS* 3.1 38.9 + - - +
918B ALA* 4.0 2.1 - - - +
919B PHE* 3.6 11.4 + - - -
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Residues in contact with TYR 883 (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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1001A MGT 3.2 80.4 + + - -
847B ARG* 3.5 30.1 - - - +
879B ARG* 3.0 47.9 + - + +
882B SER* 1.3 75.9 - - - +
884B GLY* 1.3 65.5 + - - +
886B GLU* 3.5 6.6 + - - +
887B LYS* 3.3 29.6 + - - +
915B LYS* 4.7 4.0 - - + -
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Residues in contact with GLY 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B ARG* 3.9 29.6 - - - +
880B TYR* 2.7 28.3 + - - -
883B TYR* 1.3 71.9 - - - +
885B LEU* 1.3 58.0 + - - +
887B LYS* 3.4 4.0 + - - +
888B LYS* 2.9 30.5 + - - +
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Residues in contact with LEU 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B TYR* 3.9 1.5 + - + -
881B TYR* 3.0 24.4 + - - +
884B GLY* 1.3 72.3 - - - +
886B GLU* 1.3 66.3 + - - +
888B LYS 2.9 20.6 - - - +
889B PHE* 3.4 16.2 + - + +
890B ARG* 3.5 40.6 - - + +
893B ILE* 4.1 22.4 - - + +
894B PHE* 3.8 24.2 - - + +
897B PHE* 3.6 28.9 - - + -
919B PHE* 3.5 16.5 - - + -
923B SER* 5.4 0.3 + - - -
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Residues in contact with GLU 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A MGT 2.7 37.6 + - - +
882B SER 3.4 15.1 + - - +
883B TYR* 3.5 9.7 + - - +
884B GLY 3.2 0.4 - - - -
885B LEU* 1.3 81.9 - - - +
887B LYS* 1.3 81.3 + - + +
888B LYS 4.9 0.2 - - - -
889B PHE* 5.8 0.2 - - - +
919B PHE* 3.5 14.6 - - + -
922B TYR* 3.8 35.8 - - - +
923B SER* 4.3 6.0 + - - -
924B LYS* 4.7 16.4 + - + +
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Residues in contact with LYS 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A MGT 6.1 0.2 - - - -
847B ARG* 5.4 6.7 - - + +
848B ASP* 5.9 4.5 - - - +
883B TYR* 3.3 16.7 + - + +
884B GLY* 3.9 4.7 - - - +
886B GLU* 1.3 104.2 - - + +
888B LYS* 1.3 77.4 + - + +
924B LYS* 5.6 2.8 + - - -
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Residues in contact with LYS 888 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B ARG 4.4 15.0 - - - +
848B ASP* 6.0 3.8 - - - +
884B GLY 2.9 19.0 + - - +
885B LEU* 2.9 13.9 - - - +
887B LYS* 1.3 91.9 - - + +
889B PHE* 1.3 62.1 + - - +
890B ARG* 3.9 8.4 + - + +
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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