Contacts of the strand formed by residues 812 - 815 (chain B) in PDB entry 2EYQ
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 VAL 812 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802B ILE* 4.3 16.6 - - + +
805B GLU* 3.6 25.1 - - + -
806B ILE* 5.4 0.9 - - + -
810B GLY 4.8 0.4 - - - +
811B GLN* 1.3 85.6 - - - +
813B TYR* 1.3 78.3 + - - +
814B TYR* 5.1 0.7 - - + -
857B PHE* 5.5 0.4 - - - -
863B ASN 2.9 12.5 + - - +
864B VAL* 3.3 21.0 - - + +
865B LEU* 2.9 28.8 + - - +
880B ALA* 4.5 1.8 - - - +
882B THR* 3.5 16.2 - - + +
884B ILE* 3.6 25.1 - - + -
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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
----------------------------------------------------------
812B VAL* 1.3 83.9 - - - +
814B TYR* 1.3 60.3 + - - +
815B LEU 4.2 0.9 - - - +
857B PHE* 6.3 0.4 - + - -
865B LEU* 3.8 23.1 - - + +
867B CYS* 4.6 6.3 - - - -
873B THR* 4.1 27.3 + - + +
875B ILE 3.3 16.4 + - - -
876B ASP* 4.1 2.1 - - - -
877B ILE* 3.3 44.3 + - + +
880B ALA* 3.5 32.5 - - + -
882B THR 3.0 12.8 + - - -
883B ILE* 3.5 17.6 - - + -
884B ILE 3.1 20.3 + - - -
902B ARG* 4.1 22.8 + - + -
903B VAL* 4.3 10.5 - - + -
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Residues in contact with TYR 814 (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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793B TYR* 3.9 17.8 + - - -
798B VAL* 4.2 14.8 - - + +
802B ILE* 5.3 2.0 - - + -
812B VAL* 5.1 0.7 - - + -
813B TYR* 1.3 75.5 - - - +
815B LEU* 1.3 65.3 + - - +
816B TYR* 3.7 5.1 + - + -
825B ALA* 5.9 4.3 - - + -
829B LEU* 3.8 32.6 - - + +
864B VAL* 4.5 11.2 - - + -
865B LEU 3.0 13.2 + - - +
866B VAL* 3.4 20.8 - - + +
867B CYS* 2.8 25.8 + - - +
884B ILE* 3.4 46.2 - - + -
886B GLU* 2.6 42.3 + - + +
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Residues in contact with LEU 815 (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* 4.2 0.8 - - - +
814B TYR* 1.3 76.4 - - - +
816B TYR* 1.3 65.4 + - - +
867B CYS* 3.6 17.5 - - + +
868B THR 3.8 5.2 - - - +
869B THR* 3.5 30.5 - - - +
870B ILE* 4.3 6.3 - - - -
873B THR* 4.0 12.3 - - - +
883B ILE* 5.4 2.4 - - + +
884B ILE 2.9 8.0 + - - +
885B ILE* 3.7 25.6 - - + -
886B GLU* 2.9 27.5 + - - +
891B PHE* 3.9 23.3 - - + -
899B LEU* 3.6 28.9 - - + -
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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