Contacts of the helix formed by residues 893 - 901 (chain B) in PDB entry 5B2R
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 893 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A A 4.1 9.4 - - - -
9A G 3.9 29.6 - - - +
853B ASP* 2.7 39.1 + - - +
887B LEU* 3.8 2.9 - - - -
890B LYS 5.8 1.6 - - - +
892B ILE* 1.3 80.2 - - - +
894B GLN* 1.3 60.7 + - - +
895B ARG* 3.5 4.8 + - - +
896B LYS* 3.1 15.4 + - - +
897B PHE* 2.9 27.4 + - - +
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Residues in contact with GLN 894 (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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7A U 3.8 23.5 + - + +
8A A 3.7 34.7 + - - +
887B LEU* 3.6 29.2 - - + +
893B THR* 1.3 72.9 - - - +
895B ARG* 1.3 58.1 + - - +
897B PHE* 3.2 12.2 + - - +
898B ASP* 2.7 68.8 + - - +
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Residues in contact with ARG 895 (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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8A A 4.6 3.3 + - - +
847B LEU* 3.7 23.6 - - - +
849B ASP* 3.3 24.4 + - - -
853B ASP* 4.0 23.5 + - - +
854B ASN* 5.1 2.0 - - - +
893B THR* 3.2 8.8 + - - +
894B GLN* 1.3 78.0 - - - +
896B LYS* 1.3 63.9 + - - +
898B ASP* 3.4 7.7 + - - +
899B ASN* 3.1 47.2 + - - +
916B PHE* 5.7 2.8 - - - -
919B ARG* 5.1 8.1 - - - +
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Residues in contact with LYS 896 (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 LEU* 4.3 7.1 - - - +
816B LEU* 5.5 2.4 - - - +
817B GLN* 5.5 2.4 + - - +
822B MET* 4.7 1.5 - - - +
841B ILE* 3.6 17.6 - - + +
852B ILE* 2.9 37.4 + - + +
853B ASP* 3.5 24.9 - - - +
855B LYS 2.9 23.2 + - - -
856B VAL* 3.9 9.6 - - - +
891B LEU 5.0 2.6 + - - -
892B ILE* 3.7 31.7 - - + +
893B THR* 3.1 21.7 + - - +
895B ARG* 1.3 80.1 - - - +
897B PHE* 1.3 62.1 + - - +
899B ASN* 3.4 4.4 + - - +
900B LEU* 3.0 34.1 + - + +
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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
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880B LYS* 4.0 7.2 - - + -
883B TRP* 3.9 28.9 - + + -
884B ARG* 3.5 59.7 - - - -
887B LEU* 3.9 18.6 - - + -
892B ILE* 3.8 10.9 - - + +
893B THR 2.9 13.4 + - - +
894B GLN* 3.5 14.8 - - - +
896B LYS* 1.3 77.6 - - - +
898B ASP* 1.3 73.7 + - - +
900B LEU* 3.2 6.0 + - - +
901B THR* 2.8 51.6 + - + +
904B GLU* 5.9 1.3 - - - -
905B ARG* 6.0 0.2 - - - -
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Residues in contact with ASP 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 GLN* 2.7 52.5 + - - +
895B ARG* 3.9 7.1 - - - +
897B PHE* 1.3 83.1 - - - +
899B ASN* 1.3 66.9 + - - +
901B THR* 3.4 5.4 + - - -
902B LYS* 3.1 11.4 + - - +
905B ARG* 2.8 35.6 + - - +
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Residues in contact with ASN 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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841B ILE* 3.5 17.1 - - + +
842B VAL* 4.1 22.9 - - + +
853B ASP 4.9 3.0 + - - -
854B ASN* 4.6 4.9 + - - -
870B VAL* 3.1 27.5 - - - +
895B ARG* 3.1 52.3 + - - +
896B LYS* 3.9 5.1 - - - +
898B ASP* 1.3 78.1 - - - +
900B LEU* 1.3 64.4 + - - +
901B THR 3.4 0.2 + - - -
902B LYS* 3.5 15.7 + - - +
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Residues in contact with LEU 900 (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 MET* 3.7 24.9 - - + -
823B TYR* 4.2 14.8 - - + -
841B ILE* 3.6 32.1 - - + -
856B VAL* 4.3 6.1 - - + -
870B VAL* 4.5 0.3 - - - +
871B PRO* 4.3 11.1 - - + +
876B VAL* 3.2 19.2 - - - +
883B TRP* 3.3 42.9 - - + -
892B ILE* 4.3 10.8 - - + -
896B LYS* 3.0 37.5 + - + +
897B PHE* 3.6 4.7 - - - +
899B ASN* 1.3 77.8 - - - +
901B THR* 1.3 56.8 + - - +
902B LYS 3.3 1.4 + - - -
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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
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876B VAL* 3.9 16.2 - - + -
880B LYS* 4.7 4.9 - - + -
883B TRP* 3.6 25.4 - - + -
897B PHE* 2.8 46.9 + - + +
898B ASP* 3.4 3.9 + - - -
900B LEU* 1.3 74.5 - - - +
902B LYS* 1.3 63.5 + - - +
903B ALA 3.1 3.9 + - - -
904B GLU* 3.1 36.7 + - - +
905B ARG* 3.3 18.5 + - - -
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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
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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