Contacts of the helix formed by residues 844 - 854 (chain A) in PDB entry 5OQN
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 LYS 844 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781A ASP* 2.3 52.2 + - - +
785A SER* 6.2 0.7 - - - -
842A ILE* 4.0 2.2 - - + +
843A GLU* 1.3 91.1 + - + +
845A LYS* 1.3 68.6 + - - +
846A GLU* 4.3 14.4 - - + +
847A ILE* 3.9 22.9 - - + +
848A LYS* 3.1 22.8 + - - +
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Residues in contact with LYS 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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843A GLU 3.8 4.2 + - - +
844A LYS* 1.3 69.9 - - - +
846A GLU* 1.3 66.6 + - - +
848A LYS* 2.9 12.7 + - - +
849A LYS* 2.8 24.4 + - - +
884A ASN* 5.5 8.1 - - - +
886A ASP* 4.4 28.8 + - - +
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Residues in contact with GLU 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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780A TRP* 4.2 24.6 - - + -
784A GLN* 6.1 0.7 - - - +
844A LYS* 4.3 16.6 - - + +
845A LYS* 1.3 74.8 - - - +
847A ILE* 1.3 65.5 + - + +
849A LYS* 3.0 18.8 + - - +
850A MET* 2.8 41.6 + - + +
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Residues in contact with ILE 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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777A CYS* 3.7 49.1 - - - +
780A TRP* 4.0 28.0 - - + -
781A ASP* 4.0 16.2 - - + +
799A PRO* 4.5 4.3 - - + -
842A ILE* 3.8 20.2 - - + -
844A LYS* 3.5 26.9 + - + +
845A LYS 3.2 0.4 - - - -
846A GLU* 1.3 78.2 - - + +
848A LYS* 1.3 64.4 + - - +
850A MET* 2.9 18.6 + - - +
851A ILE* 2.9 25.4 + - + +
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Residues in contact with LYS 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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839A TYR* 3.3 53.2 + - + +
840A ALA* 4.9 4.0 + - - +
842A ILE* 2.9 43.5 + - + -
843A GLU* 3.9 10.1 + - - +
844A LYS 3.1 13.2 + - - +
845A LYS* 2.9 11.1 + - - +
847A ILE* 1.3 77.0 - - - +
849A LYS* 1.3 63.5 + - - +
851A ILE* 3.3 4.8 + - - +
852A ILE* 3.0 29.6 + - - +
883A ASP* 5.1 7.9 + - - +
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Residues in contact with LYS 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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845A LYS* 2.8 15.5 + - - +
846A GLU* 3.3 17.4 - - + +
848A LYS* 1.3 73.2 - - - +
850A MET* 1.3 56.9 + - + +
852A ILE 3.0 1.0 + - - -
853A THR* 2.7 50.4 + - + +
886A ASP* 3.5 23.0 - - - +
888A VAL* 4.0 20.5 - - + +
889A SER* 3.3 24.7 - - - +
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Residues in contact with MET 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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780A TRP* 3.7 28.0 - - + -
798A LYS* 4.6 13.5 - - + -
799A PRO* 3.8 24.9 - - - -
800A ASN* 3.7 33.9 - - + +
803A PHE* 4.5 0.3 - - - -
846A GLU* 2.8 33.1 + - + +
847A ILE* 2.9 16.1 + - - +
849A LYS* 1.3 75.1 - - + +
851A ILE* 1.3 63.8 + - + +
853A THR* 2.9 18.7 + - - -
854A ASN* 2.9 17.5 - - - +
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Residues in contact with ILE 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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773A LEU* 4.0 22.2 - - + -
777A CYS* 4.2 13.2 - - - -
799A PRO* 4.3 14.8 - - + +
803A PHE* 3.1 46.2 - - + -
832A LEU* 6.2 0.4 - - + -
835A VAL* 4.5 12.8 - - + -
836A LEU* 6.2 3.1 - - + -
839A TYR* 4.7 11.0 - - + -
842A ILE* 5.7 8.1 - - + -
847A ILE* 2.9 36.5 + - + +
848A LYS* 3.7 9.2 - - - +
850A MET* 1.3 78.6 - - + +
852A ILE* 1.3 73.2 + - + +
853A THR 3.4 0.2 + - - -
854A ASN 3.4 1.7 + - - -
855A ILE* 3.1 7.5 - - + +
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Residues in contact with ILE 852 (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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836A LEU* 5.3 10.3 - - + -
839A TYR* 3.9 35.9 - - + +
848A LYS 3.0 18.8 + - - +
849A LYS 3.0 2.0 + - - +
851A ILE* 1.3 82.0 - - + +
853A THR* 1.3 65.4 + - - +
855A ILE* 3.0 46.3 - - + +
879A ILE* 5.4 1.3 - - + -
885A LEU* 5.4 2.5 - - + -
889A SER* 3.4 42.0 - - - +
892A ALA* 4.4 3.6 - - + +
893A LEU* 4.2 18.8 - - + +
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Residues in contact with THR 853 (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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800A ASN* 5.0 0.9 - - - +
849A LYS* 2.7 34.9 + - + +
850A MET* 2.9 22.0 + - - -
852A ILE* 1.3 72.9 - - - +
854A ASN* 1.3 68.4 + - - +
855A ILE 3.8 0.5 + - - -
856A ASN* 4.7 6.1 + - - +
888A VAL* 3.7 30.5 - - + -
889A SER* 4.4 3.8 - - - +
892A ALA* 4.5 16.0 - - + +
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Residues in contact with ASN 854 (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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800A ASN* 3.3 22.1 - - - +
803A PHE* 3.8 19.6 - - + -
804A GLN* 3.8 35.6 + - + +
807A LEU* 3.7 13.2 - - - +
850A MET 2.9 18.7 - - - +
851A ILE 3.4 1.4 + - - -
852A ILE 3.1 1.0 - - - -
853A THR* 1.3 86.1 + - - +
855A ILE* 1.3 59.2 + - - +
856A ASN 3.1 7.0 + - - -
857A ALA* 3.5 13.8 + - + +
2D A 4.3 11.9 + - - -
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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