Contacts of the strand formed by residues 818 - 821 (chain B) in PDB entry 4X52
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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787B TYR* 3.7 22.9 - - + +
801B ASN* 6.0 0.4 - - - +
802B PHE* 3.7 30.1 - - + +
803B ASP 4.2 2.9 - - - +
804B SER* 3.7 27.6 - - - +
806B LEU 6.0 2.0 - - - +
817B GLY* 1.3 71.0 - - - -
819B TYR* 1.3 61.8 + - - +
820B PHE* 3.4 37.0 - - + -
877B PHE 3.2 6.4 - - - +
878B VAL* 3.3 1.4 - - - -
879B ILE* 2.8 47.9 + - + +
880B PHE 5.8 0.9 - - - -
881B GLN 5.2 0.9 - - - +
882B LYS* 4.8 18.2 - - + +
885B VAL* 5.2 2.5 - - + -
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Residues in contact with TYR 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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786B PHE 4.2 2.1 - - - +
787B TYR* 3.3 26.7 - - + -
808B GLU* 3.8 34.8 - - + +
810B ASN* 4.4 11.7 - - + -
812B ASN* 3.1 20.3 - - - -
814B TYR* 2.8 45.4 + + - -
815B GLY 2.8 30.7 + - - -
817B GLY 3.3 16.4 - - - -
818B ILE* 1.3 74.9 - - - +
820B PHE* 1.3 60.9 + - - +
821B ALA 4.2 0.6 + - - -
827B SER* 5.1 2.4 + - - -
876B VAL* 3.8 22.9 - - + -
877B PHE 3.5 3.1 - - - -
878B VAL* 3.7 17.3 - - + -
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Residues in contact with PHE 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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785B LEU* 3.7 25.1 - - + -
786B PHE 3.3 5.4 - - - -
787B TYR* 3.9 20.4 - + + -
802B PHE* 3.6 30.1 - + + -
818B ILE* 3.4 39.0 - - + -
819B TYR* 1.3 72.5 - - - +
821B ALA* 1.3 61.5 + - - +
843B ALA* 3.8 12.3 - - + -
845B VAL* 3.9 11.9 - - + -
876B VAL* 3.4 3.6 - - - +
877B PHE* 2.8 40.2 + - + +
879B ILE* 3.8 16.6 - - + -
885B VAL* 3.5 36.6 - - + -
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Residues in contact with ALA 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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785B LEU* 3.6 7.1 - - - +
786B PHE* 2.9 31.4 + - + +
819B TYR 4.2 0.8 + - - -
820B PHE* 1.3 72.8 - - - +
822B LYS* 1.3 63.2 + - - +
823B ASP 3.4 20.2 - - - +
826B TYR* 3.8 16.8 - - + -
827B SER* 3.7 27.5 + - - +
875B SER 3.4 7.0 - - - +
876B VAL* 4.4 1.8 - - + +
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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