Contacts of the helix formed by residues 850 - 856 (chain j) in PDB entry 5JPQ
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 ASP 850 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844j TYR* 5.4 1.1 - - - +
848j LEU 3.3 4.3 + - - +
849j LEU* 1.4 79.6 - - - +
851j TYR* 1.3 68.5 + - - +
852j HIS* 3.5 4.9 - - + +
853j VAL* 3.4 22.5 + - + +
854j VAL* 3.4 7.6 + - - +
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Residues in contact with TYR 851 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844j TYR* 6.2 1.3 - - - -
849j LEU 3.9 0.2 + - - -
850j ASP* 1.3 71.0 - - - +
852j HIS* 1.3 55.5 + - - +
854j VAL* 3.0 6.3 + - - +
855j LEU* 2.6 44.1 + - + +
879j LEU* 5.5 12.6 - - + -
912j PHE* 6.3 2.7 - - + -
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Residues in contact with HIS 852 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749j GLN* 4.0 26.7 - - + -
850j ASP* 3.5 3.5 - - + +
851j TYR* 1.3 77.7 - - - +
853j VAL* 1.3 64.4 + - - +
855j LEU* 3.2 14.0 + - - -
856j ASP* 3.4 16.1 + - - +
859j PRO* 5.4 0.2 - - - +
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Residues in contact with VAL 853 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620j GLN 4.9 13.0 - - - +
621j GLN* 4.9 17.8 - - + +
849j LEU* 5.1 5.4 - - + -
850j ASP* 3.4 22.3 + - + +
852j HIS* 1.3 80.7 - - - +
854j VAL* 1.3 59.8 + - + +
859j PRO* 4.4 7.1 - - - +
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Residues in contact with VAL 854 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840j ARG* 5.2 11.4 - - + +
841j LEU* 5.8 2.5 - - - -
844j TYR* 4.7 17.5 - - + -
849j LEU* 6.1 2.2 - - + -
850j ASP 3.4 6.8 + - - +
851j TYR* 3.0 6.9 + - - +
853j VAL* 1.3 78.8 - - - +
855j LEU* 1.3 56.9 + - - +
859j PRO* 3.0 17.6 - - - +
860j THR* 3.1 8.8 + - - +
861j ILE* 2.9 34.7 + - + +
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Residues in contact with LEU 855 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851j TYR* 2.6 33.3 + - + +
852j HIS* 3.2 3.7 + - - -
854j VAL* 1.3 71.7 - - - +
856j ASP* 1.4 73.5 + - - +
857j LEU 3.5 2.4 - - - +
858j MET* 3.4 3.5 + - - -
859j PRO 3.1 15.7 - - - -
861j ILE* 3.5 13.9 - - + +
862j ALA* 4.0 5.7 + - - +
878j GLY 5.2 8.1 - - - +
879j LEU* 5.5 6.1 - - + -
888j GLY* 6.2 1.6 - - - -
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Residues in contact with ASP 856 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785j ARG* 5.2 1.6 - - + +
788j SER* 3.5 26.5 - - - +
789j LEU* 3.8 10.1 - - + +
792j TYR* 4.0 14.4 - - + -
852j HIS* 3.4 15.1 + - - +
855j LEU* 1.4 87.0 - - - +
857j LEU* 1.3 64.6 + - - +
859j PRO* 4.3 6.2 - - + +
888j GLY* 4.9 8.3 - - - +
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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