Contacts of the helix formed by residues 807 - 823 (chain G) in PDB entry 1WQ1
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 THR 807 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802G MET 4.2 0.4 + - - -
803G LYS 3.0 22.7 + - - -
804G ALA 4.6 5.1 + - - -
805G THR 3.5 2.0 - - - -
806G ALA* 1.3 75.1 - - - +
808G GLN* 1.3 72.7 + - + +
810G VAL* 3.1 5.0 + - - +
811G HIS* 3.1 31.6 + - + +
915G PHE* 4.0 35.7 - - + +
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Residues in contact with GLN 808 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805G THR 5.1 4.2 + - - +
806G ALA* 4.5 0.2 - - - +
807G THR* 1.3 80.0 - - + +
809G PHE* 1.3 64.4 + - - +
811G HIS* 3.0 10.5 + - - +
812G HIS* 2.9 32.1 + - - +
865G ILE* 5.0 2.7 - - + -
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Residues in contact with PHE 809 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805G THR 5.6 0.2 + - - -
806G ALA* 3.7 15.6 + - + +
808G GLN* 1.3 78.5 - - - +
810G VAL* 1.3 73.1 + - + +
812G HIS* 3.1 3.3 + - - +
813G ALA* 3.0 28.9 + - + +
859G ILE* 5.2 3.6 - - + -
862G ALA* 3.6 36.6 - - + -
863G SER* 5.3 0.2 - - - -
865G ILE* 4.0 24.2 + - + +
866G LEU* 3.6 40.8 - - + -
867G PRO* 5.1 1.8 - - + -
900G VAL* 4.5 8.1 - - + -
904G LEU* 4.4 10.1 - - + -
905G ILE* 3.5 31.0 - - + -
970G PHE* 4.4 20.2 - + - -
974G LEU* 5.9 0.4 - - + -
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Residues in contact with VAL 810 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806G ALA 3.1 16.4 - - - +
807G THR 3.1 8.5 + - - +
809G PHE* 1.3 86.6 - - + +
811G HIS* 1.3 54.6 + - - +
813G ALA* 4.7 2.7 - - - +
814G LEU* 2.8 63.2 + - + +
904G LEU* 4.0 13.0 - - + +
905G ILE* 4.4 5.8 - - + -
908G ALA* 3.8 10.3 - - + -
915G PHE* 3.9 28.0 - - + -
917G ILE* 3.7 18.6 - - + -
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Residues in contact with HIS 811 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807G THR* 3.1 23.9 + - + +
808G GLN* 3.0 12.6 + - - +
810G VAL* 1.3 71.6 - - - +
812G HIS* 1.3 68.0 + - - +
815G LYS* 2.9 56.3 + - + +
816G ASP* 4.6 0.7 + - - +
915G PHE* 3.1 30.9 + - + +
916G ASN 3.3 15.9 + - - -
917G ILE* 3.6 24.4 - - + +
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Residues in contact with HIS 812 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808G GLN* 2.9 17.4 + - - +
809G PHE 3.4 8.5 - - - +
811G HIS* 1.3 79.4 - - - +
813G ALA* 1.3 63.9 + - - +
814G LEU 3.2 0.2 + - - -
815G LYS 4.3 1.0 + - - -
816G ASP* 4.3 13.2 + - - +
858G LYS* 4.8 6.9 - - - +
862G ALA* 5.1 7.0 - - + -
865G ILE* 4.4 34.5 - - + +
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Residues in contact with ALA 813 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809G PHE* 3.0 23.5 + - + +
810G VAL* 4.2 1.1 - - - +
812G HIS* 1.3 79.9 - - - +
814G LEU* 1.3 77.2 + - + +
816G ASP* 5.3 0.3 + - - +
817G SER* 3.4 14.6 + - - -
855G LEU* 4.0 3.6 - - - +
858G LYS* 3.6 27.4 - - - +
859G ILE* 4.1 20.9 - - + -
862G ALA* 4.5 8.5 - - + +
905G ILE* 5.0 0.2 - - + -
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Residues in contact with LEU 814 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810G VAL* 2.8 40.9 + - + +
813G ALA* 1.3 96.3 - - + +
815G LYS* 1.3 64.8 + - - +
816G ASP 3.2 2.5 - - - -
817G SER* 2.9 18.2 + - - -
818G ILE* 3.0 32.6 + - + +
855G LEU* 4.3 15.0 - - + -
859G ILE* 4.3 3.4 - - + -
905G ILE* 3.8 33.9 - - + +
908G ALA* 3.7 18.2 - - + -
909G ILE* 4.0 13.9 - - + -
917G ILE* 4.2 1.3 - - + -
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Residues in contact with LYS 815 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810G VAL 3.7 1.0 + - - -
811G HIS* 2.9 47.5 + - + +
813G ALA 4.0 0.2 - - - -
814G LEU* 1.3 75.6 - - - +
816G ASP* 1.3 67.5 + - - +
818G ILE* 4.0 1.2 - - - +
819G LEU* 3.1 46.1 + - + +
916G ASN 4.9 1.6 + - - -
917G ILE* 3.4 39.4 + - + +
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Residues in contact with ASP 816 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811G HIS 5.4 0.4 - - - +
812G HIS 4.3 11.9 + - - +
813G ALA 5.9 0.4 - - - +
814G LEU 3.0 0.6 + - - -
815G LYS* 1.3 83.8 - - - +
817G SER* 1.3 65.4 + - - +
819G LEU* 3.6 7.4 + - - +
820G LYS* 3.2 26.6 + - - +
854G GLU* 5.6 0.9 - - - -
858G LYS* 3.6 33.1 - - + +
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Residues in contact with SER 817 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813G ALA 3.4 16.6 + - - -
814G LEU 2.9 8.5 + - - -
816G ASP* 1.3 76.3 + - - +
818G ILE* 1.3 60.8 + - - +
820G LYS* 3.6 5.6 + - - +
821G ILE* 3.0 35.6 + - - +
851G ILE* 5.0 5.1 - - - +
854G GLU* 5.0 10.1 - - - -
855G LEU* 3.5 37.6 - - - +
858G LYS* 4.4 8.5 - - - +
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Residues in contact with ILE 818 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814G LEU* 3.0 41.8 + - + +
815G LYS 4.0 2.9 - - - +
817G SER* 1.3 77.4 - - - +
819G LEU* 1.3 65.3 + - - +
821G ILE* 3.0 21.1 + - + +
822G MET* 3.0 27.7 + - + +
855G LEU* 6.2 0.9 - - + -
908G ALA 3.8 15.5 - - - +
909G ILE* 4.4 9.0 - - + -
912G PRO* 4.1 24.5 - - + -
917G ILE* 3.8 28.3 - - + -
918G ILE* 4.9 3.8 - - + -
930G LEU* 4.9 9.9 - - + -
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Residues in contact with LEU 819 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815G LYS* 3.1 50.9 + - + +
816G ASP* 4.0 6.5 - - - +
818G ILE* 1.3 76.6 - - - +
820G LYS* 1.3 62.8 + - - +
822G MET* 3.3 6.6 + - + +
823G GLU* 2.9 45.2 + - - +
917G ILE* 5.1 6.1 - - + +
918G ILE* 3.6 27.8 - - + -
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Residues in contact with LYS 820 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816G ASP 3.2 17.2 + - - +
817G SER* 3.8 6.5 - - - +
818G ILE 3.2 0.2 - - - -
819G LEU* 1.3 78.5 - - - +
821G ILE* 1.3 62.3 + - + +
823G GLU* 3.5 5.9 + - - +
824G SER* 3.3 24.1 + - - -
847G HIS* 6.0 6.1 - - - -
851G ILE* 5.8 7.6 - - - -
854G GLU* 3.8 25.8 - - - +
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Residues in contact with ILE 821 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817G SER* 3.0 26.0 - - - +
818G ILE* 3.0 14.1 + - + +
820G LYS* 1.3 76.4 - - + +
822G MET* 1.3 64.7 + - + +
824G SER* 3.3 19.8 + - - +
851G ILE* 3.8 36.3 - - + -
855G LEU* 6.2 1.3 - - + -
909G ILE* 6.1 0.9 - - + -
926G ALA* 4.3 13.9 - - + +
929G THR* 4.0 26.0 - - + -
930G LEU* 4.2 23.3 - - + -
933G VAL* 4.4 19.3 - - + -
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Residues in contact with MET 822 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818G ILE* 3.0 25.6 + - + +
819G LEU* 3.5 9.0 - - + +
821G ILE* 1.3 80.3 - - - +
823G GLU* 1.3 63.2 + - + +
824G SER 3.1 10.9 + - - +
912G PRO* 4.6 4.3 - - + -
918G ILE* 4.0 33.7 - - + -
920G ASP* 4.9 2.5 - - - +
921G SER 5.5 0.2 - - - -
922G PRO* 4.1 30.5 - - + -
923G SER* 4.8 5.2 + - - -
926G ALA* 4.3 14.2 - - + +
930G LEU* 3.8 39.7 - - + -
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Residues in contact with GLU 823 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819G LEU* 2.9 42.0 + - - +
820G LYS* 4.0 5.4 - - - +
822G MET* 1.3 82.1 - - + +
824G SER* 1.3 60.2 + - - +
825G LYS* 4.0 6.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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