Contacts of the helix formed by residues 806 - 824 (chain A) in PDB entry 1WER
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 ALA 806 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A MET* 2.8 27.0 + - - +
805A THR* 1.3 71.7 + - - +
807A THR* 1.3 58.5 + - - +
808A GLN 3.3 2.5 - - - -
809A PHE* 3.2 5.1 + - - +
810A VAL* 2.9 32.2 + - + +
866A LEU* 4.4 8.7 - - + -
867A PRO* 4.5 6.3 - - + -
870A LEU* 4.2 22.2 - - + -
904A LEU* 4.3 19.3 - - + -
915A PHE* 4.7 0.4 - - - -
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Residues in contact with THR 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LYS 3.5 15.9 + - - -
804A ALA 5.1 2.5 + - - -
805A THR 3.4 3.4 - - - -
806A ALA* 1.3 77.4 - - - +
808A GLN* 1.3 61.1 + - + +
810A VAL* 3.2 1.9 + - - +
811A HIS* 2.9 57.4 + - + +
915A PHE* 3.6 21.8 - - + +
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Residues in contact with GLN 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A THR 4.9 8.8 + - - +
806A ALA 3.3 0.6 - - - -
807A THR* 1.3 77.8 - - + +
809A PHE* 1.3 60.1 + - - +
811A HIS* 3.4 5.3 + - + +
812A HIS* 2.9 42.1 + - + +
865A ILE* 3.8 16.8 + - + +
867A PRO* 6.0 2.4 - - - +
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Residues in contact with PHE 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ALA* 3.2 9.9 + - + +
808A GLN* 1.3 78.5 - - - +
810A VAL* 1.3 60.0 + - + +
812A HIS* 3.3 1.1 + - - +
813A ALA* 2.8 41.1 + - + +
859A ILE* 4.1 5.4 - - + -
862A ALA* 3.3 43.7 - - + -
863A SER* 4.4 3.1 - - - -
865A ILE* 3.7 11.3 + - - +
866A LEU* 3.4 46.9 - - + +
867A PRO* 5.1 0.6 - - + +
900A VAL* 4.1 9.9 - - + -
904A LEU* 4.0 20.4 - - + -
905A ILE* 3.7 33.4 - - + -
970A PHE* 4.3 13.5 - + - -
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Residues in contact with VAL 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ALA 2.9 21.2 + - - +
807A THR 3.7 3.6 - - - +
809A PHE* 1.3 78.8 - - + +
811A HIS* 1.3 58.1 + - - +
813A ALA* 4.4 2.9 - - - -
814A LEU* 2.9 52.7 + - + +
815A LYS 4.0 0.2 + - - -
904A LEU* 3.8 38.6 - - + -
905A ILE* 5.6 1.6 - - + -
908A ALA* 4.1 3.6 - - + -
915A PHE* 3.8 40.4 - - + -
917A ILE* 4.2 5.2 - - + -
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Residues in contact with HIS 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A THR* 2.9 38.8 + - + +
808A GLN* 3.8 6.7 - - + +
810A VAL* 1.3 75.2 - - - +
812A HIS* 1.3 70.2 + - + +
815A LYS* 2.9 57.1 + - + +
816A ASP* 4.6 1.4 + - - -
915A PHE* 3.0 32.7 + - + -
916A ASN* 4.7 3.5 + - - +
917A ILE* 3.9 21.1 - - + +
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Residues in contact with HIS 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A GLN* 2.9 40.3 + - + +
809A PHE 3.7 3.8 - - - +
811A HIS* 1.3 76.5 - - + +
813A ALA* 1.3 63.3 + - - +
815A LYS 4.9 0.3 + - - -
816A ASP* 5.5 4.7 + - - +
858A LYS* 4.4 14.4 - - - +
862A ALA* 4.3 14.6 - - + -
865A ILE* 3.7 34.2 - - + +
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Residues in contact with ALA 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A PHE* 2.8 33.0 + - + +
810A VAL* 3.8 4.9 - - - +
812A HIS* 1.3 74.9 - - - +
814A LEU* 1.3 66.1 + - + +
817A SER* 4.8 0.3 + - - -
855A LEU* 3.8 12.6 - - - +
858A LYS* 3.6 32.5 - - - +
859A ILE* 4.0 25.4 - - + +
862A ALA* 4.2 6.5 - - + +
905A ILE* 5.2 1.3 - - + -
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Residues in contact with LEU 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A VAL* 2.9 26.1 + - + +
813A ALA* 1.3 91.7 - - + +
815A LYS* 1.3 65.3 + - - +
816A ASP 3.4 1.8 - - - -
817A SER* 3.3 5.3 + - - -
818A ILE* 3.0 37.1 + - + +
855A LEU* 3.9 20.2 - - + -
859A ILE* 4.1 14.6 - - + -
905A ILE* 4.0 19.3 - - + +
908A ALA* 3.5 32.8 - - + -
909A ILE* 4.0 21.5 - - + +
917A ILE* 4.4 4.3 - - + -
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Residues in contact with LYS 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A VAL 4.0 0.4 + - - -
811A HIS* 2.9 52.0 + - + +
814A LEU* 1.3 78.1 - - - +
816A ASP* 1.3 64.0 + - - +
818A ILE* 3.3 1.0 + - - +
819A LEU* 2.9 54.7 + - + +
916A ASN 4.6 4.4 + - - -
917A ILE* 4.1 35.8 + - + +
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Residues in contact with ASP 816 (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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811A HIS 4.6 1.5 + - - -
812A HIS 5.5 4.4 + - - +
814A LEU 3.4 0.6 - - - -
815A LYS* 1.3 85.7 - - - +
817A SER* 1.3 62.5 + - - +
819A LEU* 4.1 8.5 - - - +
820A LYS* 3.2 31.5 + - + +
858A LYS* 3.6 31.1 + - + +
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Residues in contact with SER 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A LEU 3.3 9.4 + - - -
816A ASP* 1.3 77.2 - - - +
818A ILE* 1.3 59.5 + - - +
820A LYS* 3.4 6.4 + - - +
821A ILE* 3.1 37.5 + - - +
851A ILE* 5.1 4.0 + - - -
854A GLU* 3.0 24.9 + - - -
855A LEU* 3.6 39.8 - - - +
858A LYS* 4.1 8.1 - - - +
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Residues in contact with ILE 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A LEU* 3.0 37.0 + - + +
815A LYS 3.9 2.5 - - - +
817A SER* 1.3 75.9 - - - +
819A LEU* 1.3 60.1 + - - +
821A ILE* 3.1 10.2 + - + +
822A MET* 2.9 43.6 + - + +
855A LEU* 6.3 0.4 - - + -
908A ALA 4.1 9.0 - - - +
909A ILE* 4.3 13.0 - - + -
912A PRO* 3.9 26.2 - - + -
917A ILE* 3.8 34.8 - - + -
918A ILE* 5.1 2.2 - - + -
930A LEU* 4.4 11.7 - - + -
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Residues in contact with LEU 819 (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 LYS* 2.9 45.4 + - + +
816A ASP* 4.1 9.2 - - - +
818A ILE* 1.3 75.7 - - - +
820A LYS* 1.3 61.8 + - + +
822A MET* 3.5 6.0 + - + +
823A GLU* 3.3 34.5 + - - +
917A ILE* 3.8 15.9 - - + +
918A ILE* 3.8 26.2 - - + -
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Residues in contact with LYS 820 (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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816A ASP* 3.2 23.2 + - + +
817A SER* 3.5 5.6 - - - +
819A LEU* 1.3 74.4 - - + +
821A ILE* 1.3 64.7 + - + +
823A GLU* 3.1 8.4 + - - +
824A SER* 3.0 24.0 + - - -
854A GLU* 3.8 30.0 + - - +
858A LYS* 5.4 3.6 - - - +
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Residues in contact with ILE 821 (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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817A SER* 3.1 24.4 + - - +
818A ILE* 3.1 10.3 + - + +
820A LYS* 1.3 75.5 - - + +
822A MET* 1.3 70.9 + - + +
824A SER* 3.1 23.6 + - - +
851A ILE* 4.2 27.8 - - + -
926A ALA* 3.7 29.8 - - + +
929A THR* 3.8 36.1 - - + -
930A LEU* 4.2 17.0 - - + -
933A VAL* 4.3 10.3 - - + -
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Residues in contact with MET 822 (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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818A ILE* 2.9 27.7 + - + +
819A LEU* 3.6 9.6 - - + +
820A LYS 3.3 0.4 - - - -
821A ILE* 1.3 78.2 - - + +
823A GLU* 1.3 60.9 + - + +
824A SER 4.7 1.3 - - - +
912A PRO* 5.0 0.9 - - + -
918A ILE* 3.5 38.8 - - + -
920A ASP 4.9 0.7 - - - +
922A PRO* 3.8 33.2 - - + -
923A SER* 4.6 11.3 + - - -
926A ALA* 3.8 12.0 - - + +
930A LEU* 3.5 38.1 - - + -
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Residues in contact with GLU 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A LEU* 3.3 22.3 + - - +
820A LYS* 3.1 8.2 + - - +
821A ILE 3.1 0.6 - - - -
822A MET* 1.3 81.7 - - + +
824A SER* 1.3 62.5 + - - +
825A LYS* 3.8 1.9 + - - +
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Residues in contact with SER 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A LYS 3.0 14.7 + - - -
821A ILE* 3.1 17.2 + - - +
822A MET 4.7 1.7 - - - +
823A GLU* 1.3 80.0 - - - +
825A LYS* 1.3 62.4 + - - +
826A GLN* 3.1 27.1 + - - +
847A HIS* 4.1 11.7 + - - -
923A SER* 4.9 5.7 + - - -
925A ILE* 4.4 12.0 - - - +
926A ALA 5.3 0.3 + - - -
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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
------------------------------------------------------------
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