Contacts of the helix formed by residues 808 - 815 (chain B) in PDB entry 2P0C
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 GLU 808 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A LEU 5.5 2.3 - - - +
803B GLY 4.0 4.9 - - - +
804B VAL* 3.6 15.5 - - + +
805B GLN* 2.7 47.8 + - - +
807B HIS* 1.3 98.6 - - + +
809B MET* 1.3 64.7 + - - +
810B TYR 3.3 2.5 + - - -
811B ASP* 3.4 7.6 + - - +
812B TYR* 3.0 23.7 + - + +
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Residues in contact with MET 809 (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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764B VAL* 3.8 16.8 - - + +
765B LYS* 3.8 25.4 - - + -
772B LEU* 4.7 5.8 - - + -
801B TYR* 3.4 53.2 - - + -
804B VAL* 3.6 22.0 - - - -
805B GLN 3.7 5.6 - - - +
806B ASN* 3.3 19.8 + - - +
807B HIS 3.4 0.4 - - - -
808B GLU* 1.3 77.5 - - - +
810B TYR* 1.3 57.3 + - - +
812B TYR* 3.4 5.9 + - + +
813B LEU* 3.0 52.1 + - + +
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Residues in contact with TYR 810 (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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769B ILE* 3.9 14.1 - - + -
772B LEU* 3.8 35.3 - - + +
773B ALA* 3.4 34.1 - - + +
806B ASN 5.0 0.2 + - - -
807B HIS 4.9 3.6 + - - +
808B GLU 3.4 1.0 - - - -
809B MET* 1.3 77.8 - - - +
811B ASP* 1.3 72.2 + - - +
813B LEU* 3.4 2.6 + - - +
814B LEU* 2.9 62.9 + - + +
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Residues in contact with ASP 811 (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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807B HIS 5.7 0.4 + - - -
808B GLU* 3.4 7.1 + - - +
810B TYR* 1.3 90.2 - - - +
812B TYR* 1.3 65.0 + - - +
814B LEU* 3.9 14.0 - - - +
815B HIS* 3.0 45.8 + - + +
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Residues in contact with TYR 812 (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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801B TYR* 3.6 35.1 - + - -
804B VAL* 3.8 30.4 - - + +
808B GLU* 3.0 21.0 + - + +
809B MET* 3.6 14.8 - - + +
811B ASP* 1.3 78.4 - - - +
813B LEU* 1.3 62.0 + - + +
815B HIS 3.7 1.4 + - - -
817B HIS* 3.3 73.3 + + + +
818B ARG 4.3 8.3 + - - -
820B LYS* 4.3 17.2 + - - -
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Residues in contact with LEU 813 (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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767B ILE 4.4 2.9 - - - +
769B ILE* 3.7 21.2 - - + +
772B LEU* 3.8 25.8 - - + -
784B TRP* 3.8 25.6 - - + -
801B TYR* 3.6 25.4 - - + +
809B MET* 3.0 35.9 + - + +
810B TYR 3.9 1.6 - - - +
812B TYR* 1.3 74.4 - - + +
814B LEU* 1.3 65.3 + - - +
815B HIS 3.3 0.4 - - - -
816B GLY* 3.1 5.7 + - - -
817B HIS 3.5 16.6 - - - +
818B ARG* 3.1 33.9 + - - +
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Residues in contact with LEU 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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769B ILE* 4.6 8.0 - - + +
810B TYR* 2.9 56.0 + - + +
811B ASP* 3.7 17.9 - - - +
812B TYR 3.4 0.4 - - - -
813B LEU* 1.3 77.3 - - - +
815B HIS* 1.3 62.7 - - + +
816B GLY* 3.1 5.8 + - - -
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Residues in contact with HIS 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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811B ASP* 3.0 42.2 + - + +
812B TYR* 5.0 0.2 - - - -
813B LEU 3.3 0.4 - - - -
814B LEU* 1.3 83.4 - - + +
816B GLY* 1.3 58.1 + - - +
817B HIS* 3.4 28.4 + - + +
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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