Contacts of the helix formed by residues 809 - 828 (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 THR 809 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B GLU* 5.6 1.8 - - - +
802B LEU* 3.7 4.2 - - - +
807B GLY 3.6 8.8 + - - +
808B PHE* 1.3 87.7 - - - +
810B GLN* 1.3 64.8 + - - +
811B HIS* 4.0 5.7 + - - +
812B VAL* 3.1 31.4 + - + +
813B TYR* 3.1 21.5 + - - +
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Residues in contact with GLN 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B PHE* 3.7 25.8 - - + -
809B THR* 1.3 73.5 - - - +
811B HIS* 1.3 58.2 + - - +
813B TYR* 3.8 14.7 - - - -
814B HIS* 2.8 46.8 + - + +
854B MET* 5.4 1.8 - - - +
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Residues in contact with HIS 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B THR* 3.2 6.1 - - - +
810B GLN* 1.3 78.9 - - - +
812B VAL* 1.3 76.5 + - + +
814B HIS* 3.9 4.4 - - - +
815B LYS* 3.1 53.5 + - + +
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Residues in contact with VAL 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B PRO* 4.6 13.5 - - + -
801B GLU* 4.0 28.7 - - - +
802B LEU* 3.8 24.2 - - + -
809B THR* 3.1 21.5 + - + +
811B HIS* 1.3 89.0 - - + +
813B TYR* 1.3 58.8 + - - +
815B LYS* 3.5 7.9 + - - +
816B TYR* 2.9 26.9 + - - +
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Residues in contact with TYR 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B LEU* 3.7 15.4 - - + +
808B PHE* 3.6 25.1 - + + -
809B THR 3.1 11.2 + - - +
810B GLN* 3.8 17.5 - - - +
812B VAL* 1.3 75.2 - - - +
814B HIS* 1.3 59.9 + - - +
816B TYR* 3.1 4.6 + + - +
817B ARG* 2.7 66.4 + - + +
838B LEU* 4.3 8.3 - - + -
841B PHE* 3.6 34.8 - + - -
842B TRP* 3.0 25.7 + - - -
854B MET* 3.5 29.9 - - + +
857B GLU* 4.4 1.6 + - - -
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Residues in contact with HIS 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B GLN* 2.8 34.8 + - + +
811B HIS* 3.9 5.6 - - - +
813B TYR* 1.3 78.4 - - - +
815B LYS* 1.3 62.5 + - - +
817B ARG* 4.0 18.2 + - - +
818B ARG* 3.0 57.0 + - + +
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Residues in contact with LYS 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B HIS* 3.1 45.4 + - + +
812B VAL* 3.9 6.9 - - - +
814B HIS* 1.3 77.1 - - + +
816B TYR* 1.3 63.3 + - - +
818B ARG* 3.3 32.7 + - - +
819B ARG* 3.1 23.0 + - - +
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Residues in contact with TYR 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B HIS* 3.4 24.2 - + - -
798B PRO* 3.9 28.0 - - + -
799B SER* 3.6 16.7 - - - -
802B LEU* 3.8 16.8 - - + -
812B VAL 2.9 19.9 + - - +
813B TYR* 3.6 6.7 - + - +
815B LYS* 1.3 77.6 - - - +
817B ARG* 1.3 64.1 + - - +
819B ARG* 3.3 7.3 + - + +
820B CYS* 3.1 47.1 + - - -
834B GLU* 4.3 2.7 - - - -
837B THR* 2.7 40.8 + - - -
838B LEU* 3.1 21.6 + - + -
841B PHE* 4.4 8.5 - + + -
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Residues in contact with ARG 817 (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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813B TYR* 2.7 56.9 + - + +
814B HIS* 4.0 18.5 + - - +
816B TYR* 1.3 75.5 - - - +
818B ARG* 1.3 68.7 + - - +
820B CYS* 3.1 3.3 + - - +
821B LEU* 2.9 45.9 + - + +
838B LEU* 4.5 18.2 - - + -
857B GLU* 2.7 39.6 + - - +
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Residues in contact with ARG 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B HIS* 3.0 58.2 + - + +
815B LYS* 3.3 34.1 + - - +
817B ARG* 1.3 85.5 - - - +
819B ARG* 1.3 58.7 + - - +
821B LEU* 3.3 5.5 + - - +
822B ASN* 2.9 54.5 + - - +
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Residues in contact with ARG 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B LYS 3.1 17.2 + - - +
816B TYR* 3.7 7.2 - - + +
817B ARG 3.2 0.2 - - - -
818B ARG* 1.3 77.4 - - - +
820B CYS* 1.3 63.8 + - - +
822B ASN* 3.5 8.7 + - - +
823B GLU* 3.1 32.8 + - - +
834B GLU* 3.8 33.0 + - + +
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Residues in contact with CYS 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B TYR* 3.1 46.6 + - - -
817B ARG 3.6 6.7 - - - +
819B ARG* 1.3 79.0 - - - +
821B LEU* 1.3 58.0 + - - +
823B GLU* 3.4 4.0 + - - +
824B ARG* 3.0 26.2 + - - +
832B SER* 4.4 2.6 + - - -
834B GLU* 3.3 42.4 - - - +
835B MET* 4.2 8.3 - - - +
838B LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B ARG* 2.9 62.2 + - + +
818B ARG* 3.9 4.7 - - - +
820B CYS* 1.3 72.6 - - - +
822B ASN* 1.3 68.1 + - - +
824B ARG* 3.2 12.0 + - - +
825B LYS* 2.9 23.7 + - - +
835B MET* 4.1 13.7 - - + -
838B LEU* 4.7 4.3 - - + -
857B GLU* 3.7 7.4 - - - +
861B LEU* 3.7 30.1 - - + -
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Residues in contact with ASN 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818B ARG* 2.9 41.5 + - - +
819B ARG* 3.7 8.5 - - + +
821B LEU* 1.3 78.8 - - - +
823B GLU* 1.3 58.1 + - - +
825B LYS* 3.2 7.3 + - - +
826B ARG* 2.8 30.4 + - - +
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Residues in contact with GLU 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B ARG* 3.1 30.1 + - - +
820B CYS* 3.7 3.8 - - - +
822B ASN* 1.3 73.3 - - - +
824B ARG* 1.3 60.5 + - - +
826B ARG* 3.9 23.3 + - - +
827B LEU* 2.8 57.6 + - + +
832B SER* 2.5 30.1 + - - +
833B GLN* 3.8 1.7 + - - +
834B GLU* 3.4 31.1 + - - +
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Residues in contact with ARG 824 (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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820B CYS 3.0 13.8 + - - +
821B LEU* 3.2 21.1 + - - +
823B GLU* 1.3 77.4 - - - +
825B LYS* 1.3 56.2 + - - +
828B GLY* 2.7 47.4 + - - +
829B ILE* 3.5 23.8 - - + +
830B GLY 4.8 1.4 - - - +
832B SER* 4.2 6.3 - - - -
835B MET* 3.8 33.4 - - + +
839B PHE* 4.5 3.8 - - - -
861B LEU* 3.7 23.3 + - - +
864B GLU* 3.1 31.5 + - - +
865B ASP* 2.7 36.5 + - - -
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Residues in contact with LYS 825 (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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821B LEU 2.9 13.5 + - - +
822B ASN* 3.6 9.2 - - - +
824B ARG* 1.3 78.4 - - - +
826B ARG* 1.3 62.4 + - - +
828B GLY* 4.2 2.8 + - - -
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Residues in contact with ARG 826 (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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822B ASN 2.8 16.3 + - - +
823B GLU* 3.9 33.5 + - - +
825B LYS* 1.3 81.3 - - - +
827B LEU* 1.3 84.3 + - + +
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Residues in contact with LEU 827 (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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823B GLU* 2.8 48.2 + - + +
826B ARG* 1.3 105.8 - - + +
828B GLY* 1.3 57.6 + - - +
831B GLN* 3.4 46.1 - - + +
832B SER* 4.4 0.2 - - - -
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Residues in contact with GLY 828 (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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824B ARG* 2.7 32.5 + - - +
825B LYS 4.2 3.1 + - - -
826B ARG 3.6 1.0 - - - -
827B LEU* 1.3 75.2 - - - +
829B ILE* 1.3 68.8 + - - -
830B GLY 3.3 0.5 + - - -
831B GLN* 3.1 17.0 + - - +
832B SER* 4.3 3.3 + - - -
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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