Contacts of the helix formed by residues 818 - 822 (chain B) in PDB entry 2BKU
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 ILE 818 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773B PHE* 3.9 17.9 - - + -
776B VAL* 4.1 21.5 - - + -
809B ILE* 3.6 31.4 - - + +
810B ALA* 4.4 1.3 - - - -
813B PHE* 3.6 33.4 - - + -
817B SER* 1.3 82.4 - - - +
819B LYS* 1.3 63.9 + - - +
820B GLN* 3.0 14.1 + - - -
821B PHE* 3.1 27.1 + - + -
822B TYR* 3.6 31.0 - - + +
858B GLN* 3.9 5.8 - - - +
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Residues in contact with LYS 819 (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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816B GLY* 3.6 22.6 + - - +
818B ILE* 1.3 76.3 - - - +
820B GLN* 1.3 65.6 + - + +
821B PHE 3.2 0.4 - - - -
822B TYR* 3.2 17.2 + - - +
823B GLY* 3.7 6.9 + - - -
858B GLN* 3.2 48.7 + - - +
859B LEU* 4.2 13.0 - - + +
861B LEU* 3.6 24.3 + - + +
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Residues in contact with GLN 820 (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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816B GLY 5.1 0.9 - - - +
817B SER 3.5 21.6 + - - +
818B ILE* 3.0 3.9 + - - -
819B LYS* 1.3 82.6 + - - +
821B PHE* 1.3 90.8 + - + +
822B TYR 3.7 0.2 + - - -
823B GLY* 3.8 8.0 + - - -
824B GLN* 4.0 11.4 + - - +
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Residues in contact with PHE 821 (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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776B VAL* 3.8 23.8 - - + -
777B GLY* 3.6 33.9 - - - -
780B PHE* 4.0 36.6 - + + -
818B ILE* 3.1 27.4 + - + +
820B GLN* 1.3 102.4 - - + +
822B TYR* 1.3 61.6 + - + +
823B GLY 3.3 2.0 + - - -
824B GLN* 3.5 34.1 + - - +
827B VAL* 3.6 15.2 - - - +
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Residues in contact with TYR 822 (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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780B PHE* 3.6 25.0 - + - -
806B ILE* 2.8 37.9 + - + -
809B ILE* 3.7 10.4 - - - +
810B ALA* 2.9 26.1 + - + -
818B ILE* 3.6 36.6 - - + -
819B LYS* 3.2 4.9 + - - +
821B PHE* 1.3 76.8 - - - +
823B GLY* 1.3 57.3 + - - +
824B GLN 3.4 1.7 + - - -
827B VAL* 4.8 5.1 - - + +
828B ILE* 4.3 4.9 - - - +
854B GLN* 5.9 0.2 - - + -
855B GLN* 3.5 51.1 - - + +
858B GLN* 3.5 35.9 - - + -
859B LEU* 3.7 10.1 - - + +
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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