Contacts of the helix formed by residues 851 - 875 (chain B) in PDB entry 2XWU
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 VAL 851 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B LEU* 5.9 0.7 - - + -
805B PRO* 4.8 12.8 - - + +
806B ASP* 5.9 0.4 - - - -
808B PHE* 4.4 10.8 - - + -
809B LEU* 3.8 30.3 - - + -
847B ARG* 3.1 29.2 - - + +
849B GLY* 4.4 4.0 + - - -
850B GLU* 1.3 79.7 - - + +
852B GLU* 1.3 66.3 + - - +
853B SER* 3.9 11.9 - - - +
854B VAL* 3.2 30.3 - - + +
855B GLY* 3.2 14.7 + - - -
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Residues in contact with GLU 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B LEU* 4.6 11.4 - - + +
849B GLY* 6.3 0.2 - - - -
850B GLU 4.2 0.6 + - - -
851B VAL* 1.3 73.3 - - - +
853B SER* 1.3 64.0 + - - +
855B GLY* 3.1 4.0 + - - +
856B LYS* 3.0 23.1 + - - +
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Residues in contact with SER 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B PHE 3.6 23.8 - - - -
809B LEU* 4.6 6.8 - - - +
815B VAL* 4.0 16.6 - - - -
851B VAL* 3.3 7.4 - - - +
852B GLU* 1.3 79.2 - - - +
854B VAL* 1.3 62.5 + - - +
856B LYS* 3.4 7.2 + - - +
857B VAL* 3.2 30.2 + - - +
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Residues in contact with VAL 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B LEU* 4.6 5.2 - - + -
808B PHE* 4.3 23.3 - - + -
815B VAL* 4.9 4.5 - - + -
844B LEU* 3.3 53.6 - - + +
847B ARG 4.1 8.7 - - - +
848B CYS* 4.3 1.5 - - - +
851B VAL* 3.2 33.7 + - + -
852B GLU 3.3 0.6 - - - -
853B SER* 1.3 74.1 - - - +
855B GLY* 1.3 61.3 + - - +
857B VAL* 4.0 4.8 - - - +
858B VAL* 3.0 29.2 + - + +
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Residues in contact with GLY 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B ARG 5.0 0.2 + - - -
848B CYS* 4.7 11.4 - - - -
849B GLY* 4.8 8.5 - - - -
851B VAL 3.2 9.7 + - - -
852B GLU* 3.1 7.4 + - - -
854B VAL* 1.3 77.1 - - - +
856B LYS* 1.3 64.6 + - - +
858B VAL* 3.5 2.4 + - - +
859B GLN* 3.0 25.7 + - - +
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Residues in contact with LYS 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B GLU 3.0 12.1 + - - +
853B SER* 3.7 9.2 - - - +
855B GLY* 1.3 76.1 - - - +
857B VAL* 1.3 60.4 + - + +
859B GLN* 3.3 4.5 + - - +
860B GLU* 2.8 51.3 + - - +
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Residues in contact with VAL 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B VAL* 3.3 32.1 - - + +
816B LYS* 4.3 7.9 - - + +
819B PHE* 3.5 45.0 - - + -
844B LEU* 6.4 0.2 - - + -
853B SER 3.2 17.8 + - - +
854B VAL* 4.3 3.8 - - - +
855B GLY 3.3 0.2 - - - -
856B LYS* 1.3 76.2 - - + +
858B VAL* 1.3 60.4 + - + +
860B GLU* 4.4 7.0 - - - +
861B ASP* 2.8 38.5 + - - +
862B GLY 3.6 2.3 + - - -
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Residues in contact with VAL 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B PHE* 4.7 6.3 - - + -
844B LEU* 4.4 12.1 - - + -
845B LEU* 3.9 17.5 - - + -
848B CYS* 3.7 18.2 - - - -
854B VAL* 3.0 27.5 + - + +
855B GLY 4.0 3.1 - - - +
857B VAL* 1.3 77.6 - - + +
859B GLN* 1.3 57.5 + - - +
862B GLY* 2.9 25.7 + - - +
865B LEU* 6.2 0.7 - - + -
892B LEU* 4.9 1.6 - - + -
896B CYS* 4.0 24.9 - - - -
899B LEU* 4.6 5.2 - - + -
903B TRP* 2.9 29.7 - - + -
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Residues in contact with GLN 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B GLY 3.0 18.7 + - - +
856B LYS* 3.7 5.2 - - - +
858B VAL* 1.3 81.5 - - - +
860B GLU* 1.3 63.9 + - + +
899B LEU* 4.1 21.6 - - + +
903B TRP* 3.8 12.1 + - - -
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Residues in contact with GLU 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B LYS* 3.9 19.0 + - - +
856B LYS* 2.8 38.9 + - - +
857B VAL* 4.0 3.8 - - - +
859B GLN* 1.3 77.3 - - + +
861B ASP* 1.3 74.1 + - - +
863B ARG* 5.2 2.3 + - - +
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Residues in contact with ASP 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B LYS* 3.0 42.3 + - - +
819B PHE* 3.5 24.3 - - + -
820B GLN* 5.7 4.3 - - - +
857B VAL* 2.8 22.1 + - - +
860B GLU* 1.3 82.9 - - - +
862B GLY* 1.3 64.7 + - - +
863B ARG* 3.2 3.6 - - - -
864B MET* 3.0 41.2 - - + +
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Residues in contact with GLY 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B PHE* 4.1 13.0 - - - -
857B VAL 3.6 2.0 + - - -
858B VAL* 2.9 26.6 + - - -
860B GLU 3.7 1.2 - - - -
861B ASP* 1.3 77.7 - - - +
863B ARG* 1.3 62.5 + - - +
865B LEU* 3.0 15.8 + - - +
866B LEU* 3.0 10.6 + - - +
892B LEU* 6.0 0.2 - - - +
903B TRP* 3.3 19.8 - - - -
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Residues in contact with ARG 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B GLU 5.2 1.7 + - - +
861B ASP* 3.2 2.3 + - - -
862B GLY* 1.3 74.7 - - - +
864B MET* 1.3 58.0 + - - +
866B LEU* 3.2 5.1 + - - +
867B ILE* 2.9 43.7 + - + +
903B TRP* 3.6 38.0 - - + +
906B GLU* 6.1 0.9 - - - +
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Residues in contact with MET 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B PHE* 5.1 1.6 - - + -
820B GLN* 3.8 29.8 - - - +
823B VAL* 3.9 20.4 - - + +
861B ASP* 3.0 31.1 + - + +
863B ARG* 1.3 81.8 - - - +
865B LEU* 1.3 58.2 + - - +
867B ILE* 3.6 10.6 + - - +
868B ALA* 3.2 22.2 + - - +
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Residues in contact with LEU 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B PHE* 3.7 23.7 - - + -
823B VAL* 4.2 9.2 - - + +
826B LEU* 3.9 12.1 - - + -
841B PHE* 3.5 55.4 - - + -
845B LEU* 4.9 6.5 - - + -
858B VAL* 6.2 0.4 - - + -
861B ASP 3.6 1.0 + - - -
862B GLY* 3.0 10.6 + - - +
864B MET* 1.3 77.5 - - - +
866B LEU* 1.3 66.5 - - - +
868B ALA* 3.1 5.5 + - - +
869B VAL* 3.0 31.0 + - + +
888B ILE* 4.2 19.5 - - + -
892B LEU* 4.5 19.5 - - + -
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Residues in contact with LEU 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B GLY 3.0 8.8 + - - +
863B ARG* 3.6 9.4 - - - +
865B LEU* 1.3 80.8 - - - +
867B ILE* 1.3 58.8 + - + +
869B VAL* 3.1 7.5 + - + +
870B LEU* 2.9 38.9 + - + +
889B LEU* 3.8 27.8 - - + -
892B LEU* 4.1 11.2 - - + +
900B LEU* 3.9 18.2 - - + -
903B TRP* 3.7 34.8 - - + +
904B ILE* 3.8 20.0 - - + +
907B ALA* 4.3 12.8 - - + -
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Residues in contact with ILE 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B ARG* 2.9 31.7 + - + +
864B MET* 3.8 9.6 - - - +
866B LEU* 1.3 77.2 - - + +
868B ALA* 1.3 57.3 + - - +
870B LEU* 3.3 8.1 + - - +
871B GLU* 2.9 46.8 + - - +
907B ALA* 4.6 19.3 - - + -
913B PHE* 3.8 19.7 - - + -
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Residues in contact with ALA 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823B VAL* 3.9 25.6 - - + +
826B LEU* 4.6 11.5 - - + +
827B LYS* 6.4 2.7 - - + -
864B MET 3.2 11.2 + - - +
865B LEU* 3.1 9.5 + - - +
867B ILE* 1.3 78.9 - - - +
869B VAL* 1.3 57.2 + - - +
871B GLU* 3.2 17.1 + - - +
872B ALA* 3.1 26.9 + - - +
885B PHE* 4.9 2.5 - - - -
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Residues in contact with VAL 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B LEU* 4.6 2.9 - - + -
865B LEU* 3.0 20.5 + - + +
866B LEU* 3.4 12.3 - - + +
868B ALA* 1.3 74.3 - - - +
870B LEU* 1.3 65.2 + - + +
872B ALA* 3.3 3.1 + - - +
873B ILE* 3.1 31.3 + - + +
885B PHE* 4.0 24.9 - - + +
888B ILE* 4.0 35.0 - - + -
889B LEU* 4.0 32.1 - - + -
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Residues in contact with LEU 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B LEU* 2.9 34.8 + - + +
867B ILE* 3.3 4.7 + - - +
869B VAL* 1.3 76.1 - - + +
871B GLU* 1.3 60.6 + - - +
873B ILE* 3.7 10.9 - - + +
874B GLY 2.7 24.9 + - - -
889B LEU* 5.5 4.3 - - + -
904B ILE* 5.4 2.5 - - + +
907B ALA* 3.9 27.6 - - + -
908B LEU* 4.2 21.8 - - + -
913B PHE* 4.3 9.4 - - + -
914B PRO* 3.3 27.3 - - + +
926B PHE* 4.2 26.0 - - + -
930B ILE* 5.8 0.2 - - + -
947B PHE* 5.0 2.2 - - + -
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Residues in contact with GLU 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B ILE* 2.9 33.5 + - - +
868B ALA* 3.5 17.2 - - - +
869B VAL 3.2 0.2 - - - -
870B LEU* 1.3 76.8 - - - +
872B ALA* 1.3 60.3 + - - +
874B GLY* 3.5 2.6 + - - +
875B GLY 3.3 5.9 + - - -
876B GLN* 3.0 61.6 + - - +
913B PHE* 3.7 26.1 - - + -
914B PRO* 5.0 2.9 - - - -
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Residues in contact with ALA 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B LEU 5.6 0.9 - - - +
868B ALA 3.1 10.0 + - - +
869B VAL 3.5 8.1 - - - +
871B GLU* 1.3 78.5 - - - +
873B ILE* 1.3 61.5 + - - +
875B GLY 3.1 9.4 + - - -
876B GLN* 4.3 2.0 - - - -
877B ALA* 3.3 30.6 + - + +
882B MET* 4.3 2.3 - - - +
885B PHE* 3.4 40.8 - - + -
952B ARG* 3.4 8.3 + - - -
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Residues in contact with ILE 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B VAL* 3.1 25.6 + - + +
870B LEU* 4.0 9.0 - - + +
872B ALA* 1.3 71.0 - - - +
874B GLY* 1.3 66.2 + - - +
875B GLY* 3.0 2.3 + - - -
882B MET* 3.1 25.4 - - + -
885B PHE* 4.3 12.8 - - + +
889B LEU* 3.9 25.8 - - + -
926B PHE* 4.8 4.3 - - + -
944B VAL* 3.6 24.2 - - + -
947B PHE* 3.5 31.0 - - + -
948B THR* 2.7 31.3 + - - +
951B CYS* 4.0 1.0 - - - +
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Residues in contact with GLY 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B LEU 2.7 21.7 + - - -
871B GLU 3.5 3.8 + - - -
872B ALA 3.2 0.4 - - - -
873B ILE* 1.3 73.1 - - - +
875B GLY* 1.3 56.0 + - - +
914B PRO* 3.8 18.9 - - - +
915B SER* 4.3 4.5 + - - -
947B PHE* 5.3 0.2 - - - -
951B CYS* 3.1 39.7 - - - +
952B ARG* 4.3 1.0 - - - +
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Residues in contact with GLY 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B GLU 3.3 0.2 + - - -
872B ALA 3.1 0.4 + - - -
873B ILE 3.0 4.0 - - - -
874B GLY* 1.3 82.7 - - - +
876B GLN* 1.3 60.1 + - - +
877B ALA 3.1 11.2 + - - +
952B ARG* 3.2 36.3 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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