Contacts of the helix formed by residues 840 - 851 (chain A) in PDB entry 2P8Q
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 ARG 840 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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795A GLU* 2.6 30.5 + - - -
798A LEU* 3.4 18.2 + - - +
799A SER* 3.1 40.8 + - - +
802A ASP* 3.1 26.9 - - - +
836A LEU* 2.8 30.7 + - - +
837A VAL 3.1 12.7 + - - +
839A ALA* 1.3 91.0 + - - +
841A PRO* 1.3 68.1 - - - +
842A MET 3.1 2.0 - - - -
843A ILE* 2.9 34.5 + - + +
844A HIS* 3.9 2.2 + - - -
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Residues in contact with PRO 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A GLU 4.8 3.1 - - - +
839A ALA 3.7 8.3 - - - +
840A ARG* 1.3 85.3 - - - +
842A MET* 1.3 69.7 + - + +
843A ILE 3.2 0.2 - - - -
844A HIS* 3.2 28.7 + - + +
845A GLU* 3.3 19.9 + - - +
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Residues in contact with MET 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A ASP* 3.3 23.6 - - - +
805A ALA* 3.3 25.9 - - + +
806A GLY* 3.3 35.2 - - - +
808A GLU* 5.8 2.7 - - - +
840A ARG 3.0 1.0 + - - -
841A PRO* 1.3 82.5 - - + +
843A ILE* 1.3 59.7 + - - +
845A GLU* 3.3 30.1 + - + +
846A LEU 3.0 22.3 + - - -
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Residues in contact with ILE 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798A LEU* 4.4 23.3 - - + +
801A ILE* 4.5 8.3 - - + -
802A ASP* 4.3 16.6 - - - +
805A ALA* 4.7 1.6 - - - -
822A ILE* 4.4 20.9 - - + -
836A LEU 4.7 0.2 - - - +
837A VAL* 4.0 34.8 - - + +
840A ARG* 2.9 41.2 + - + +
842A MET* 1.3 74.4 - - - +
844A HIS* 1.3 66.7 + - - +
846A LEU* 3.1 17.5 + - + +
847A LEU* 3.1 26.0 + - + +
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Residues in contact with HIS 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A LEU* 6.4 0.4 - - + -
837A VAL* 4.3 16.1 - - + +
838A GLU* 3.7 41.1 + - + +
840A ARG 4.2 3.4 - - - -
841A PRO* 3.2 28.7 + - + +
843A ILE* 1.3 79.0 - - - +
845A GLU* 1.3 62.4 + - + +
847A LEU* 3.3 14.8 + - - +
848A THR* 3.2 25.1 + - - -
851A ARG* 4.9 0.9 + - - -
869A LEU* 5.6 3.7 - - + +
873A LYS* 5.9 1.8 - - - -
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Residues in contact with GLU 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A PRO* 3.3 13.9 + - - +
842A MET* 3.6 34.2 - - + +
843A ILE 3.2 0.2 - - - -
844A HIS* 1.3 81.7 - - + +
846A LEU* 1.3 61.9 + - - +
848A THR* 3.5 8.7 + - - -
849A GLU* 3.2 23.8 + - - +
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Residues in contact with LEU 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801A ILE* 4.0 22.0 - - + +
804A ILE* 5.0 5.6 - - + -
805A ALA* 4.0 17.7 - - + +
810A HIS* 4.4 15.9 - - + +
815A VAL* 3.3 42.1 - - + +
818A ALA* 3.9 26.5 - - + -
819A ALA* 5.9 1.1 - - + +
822A ILE* 6.3 0.4 - - + -
842A MET 3.0 13.2 + - - +
843A ILE* 3.1 10.7 + - + +
845A GLU* 1.3 77.2 - - - +
847A LEU* 1.3 65.2 + - + +
849A GLU* 3.4 8.5 + - - +
850A GLY 3.2 14.9 + - - -
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Residues in contact with LEU 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A VAL* 5.7 0.7 - - - -
819A ALA* 3.9 22.9 - - + -
822A ILE* 5.0 7.0 - - + -
843A ILE* 3.1 23.3 + - + +
844A HIS* 3.3 12.8 + - - +
846A LEU* 1.3 78.6 - - + +
848A THR* 1.3 66.3 + - - +
850A GLY* 2.9 3.7 + - - +
851A ARG* 2.9 24.6 + - - +
862A ALA* 3.5 13.8 - - - +
865A ALA* 3.8 24.9 - - + -
866A THR* 3.9 22.0 - - + +
869A LEU* 4.0 27.8 - - + -
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Residues in contact with THR 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844A HIS 3.2 12.3 + - - -
845A GLU* 3.8 10.1 - - - -
847A LEU* 1.3 77.9 - - - +
849A GLU* 1.3 56.7 + - - +
851A ARG* 2.8 60.6 + - + +
852A ARG* 3.4 27.0 - - - +
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Residues in contact with GLU 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A HIS* 2.9 40.3 + - - +
812A ASP* 5.4 6.2 - - - +
815A VAL* 3.5 17.1 - - + +
845A GLU 3.2 11.2 + - - +
846A LEU* 3.5 11.5 - - - +
848A THR* 1.3 79.5 - - - +
850A GLY* 1.3 57.8 + - - +
852A ARG* 3.3 42.0 + - - +
854A LYS 4.9 0.5 - - - +
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Residues in contact with GLY 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812A ASP* 6.1 0.9 - - - -
815A VAL* 4.0 17.5 - - - -
846A LEU 3.2 5.7 + - - -
847A LEU 2.9 8.6 + - - -
849A GLU* 1.3 74.2 - - - +
851A ARG* 1.3 57.6 + - - +
852A ARG 2.9 14.9 + - - +
854A LYS 5.2 0.4 - - - -
858A ALA* 3.5 7.5 - - - +
859A LYS* 2.9 28.4 + - - +
862A ALA* 3.4 15.3 - - - -
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Residues in contact with ARG 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844A HIS 4.9 0.8 + - - -
847A LEU* 2.9 9.4 + - - +
848A THR* 2.8 50.4 + - + +
850A GLY* 1.3 75.2 - - - +
852A ARG* 1.3 60.4 + - + +
853A SER 4.3 0.4 + - - -
859A LYS* 4.4 12.8 - - - +
862A ALA* 4.2 2.0 - - - +
863A THR* 4.2 25.8 - - - +
866A THR* 3.7 35.1 + - - +
870A ARG* 5.4 1.6 - - - +
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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