Contacts of the helix formed by residues 855 - 877 (chain B) in PDB entry 3N57
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 PRO 855 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853B GLU 4.0 2.0 - - - +
854B LYS* 1.3 97.8 - - + +
856B PRO* 1.4 74.5 - - + +
857B HIS* 3.6 35.9 - - + +
858B TYR* 3.1 21.2 + - + +
859B LEU* 3.2 10.7 + - - +
963B MET* 4.1 17.0 - - - -
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Residues in contact with PRO 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B SER* 3.9 15.3 - - - -
790B GLY 4.3 7.6 - - - +
791B ILE* 3.5 5.6 - - + +
855B PRO* 1.4 82.7 - - + +
857B HIS* 1.3 66.9 + - - +
859B LEU* 3.1 14.2 + - + +
860B GLU* 3.0 25.6 + - - +
957B HIS* 3.3 36.3 - - + +
958B VAL 4.3 1.3 - - - +
959B LEU* 3.7 24.5 - - + -
963B MET* 3.8 17.5 - - + -
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Residues in contact with HIS 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B PRO* 3.6 30.8 - - + +
856B PRO* 1.3 79.4 - - - +
858B TYR* 1.3 78.3 + + + +
860B GLU* 3.4 16.6 - - - +
861B SER* 3.4 9.5 + - - -
957B HIS* 4.0 12.6 + - + +
986B LEU* 5.9 0.2 - - - +
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Residues in contact with TYR 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B GLU* 4.7 0.5 + - - -
829B LEU* 4.1 13.0 - - + +
854B LYS* 3.4 37.2 + - + -
855B PRO* 3.1 25.0 + - + +
857B HIS* 1.3 87.1 - + + +
859B LEU* 1.3 69.2 + - + +
861B SER* 3.2 28.2 + - - -
862B ARG* 3.2 43.6 + - + +
980B LEU* 3.9 18.4 - - + +
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Residues in contact with LEU 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B SER* 4.2 7.6 - - - +
791B ILE* 4.0 32.3 - - + -
829B LEU* 4.0 20.4 - - + -
850B ILE* 4.4 22.1 - - + +
852B SER* 3.5 30.3 - - - +
854B LYS* 3.8 27.4 - - + +
855B PRO 3.2 9.0 + - - +
856B PRO* 3.1 15.2 + - + +
858B TYR* 1.3 75.9 - - + +
860B GLU* 1.3 66.5 + - - +
862B ARG* 3.1 7.0 + - - +
863B VAL* 3.1 28.5 + - - +
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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
----------------------------------------------------------
776B TRP* 3.5 14.0 - - + -
791B ILE* 3.6 8.0 - - + +
793B ILE* 3.7 13.6 - - - +
856B PRO 3.0 13.0 + - - +
857B HIS* 3.4 10.8 - - - +
859B LEU* 1.3 76.3 - - - +
861B SER* 1.3 62.3 + - - +
862B ARG 3.3 0.2 + - - -
863B VAL* 3.3 2.4 + - - +
864B GLU* 3.0 29.6 + - - +
953B LYS* 2.5 33.4 + - - -
955B SER* 2.4 26.6 + - - -
957B HIS* 2.7 33.9 + - + +
986B LEU* 4.8 9.2 - - + -
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Residues in contact with SER 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B HIS 3.4 7.9 + - - -
858B TYR* 3.2 22.0 + - - -
860B GLU* 1.3 80.3 - - - +
862B ARG* 1.3 64.7 + - - +
864B GLU* 3.4 7.6 + - - +
865B ALA 2.9 22.3 + - - -
983B ALA* 3.4 27.0 - - - +
984B PRO 5.7 1.8 - - - -
986B LEU* 4.7 10.3 - - - -
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Residues in contact with ARG 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B LEU* 3.9 5.5 - - + +
827B GLU* 2.8 54.2 + - - +
829B LEU* 4.0 19.7 - - + -
858B TYR* 3.4 48.4 + - + +
859B LEU 3.1 8.1 + - - +
861B SER* 1.3 83.2 + - - +
863B VAL* 1.3 60.4 + - - +
865B ALA* 3.1 27.2 + - - +
866B PHE* 3.0 26.3 + - - +
980B LEU* 3.5 25.5 - - - +
981B SER* 2.5 33.1 + - - -
983B ALA* 4.0 10.5 - - - +
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Residues in contact with VAL 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B ILE* 4.0 21.3 - - + -
795B TYR* 4.1 11.4 - - - +
823B LEU* 4.2 10.3 - - + -
848B PHE* 3.8 44.9 - - + -
850B ILE* 3.8 25.1 - - + -
859B LEU 3.1 15.6 + - - +
860B GLU 3.8 4.3 - - - +
862B ARG* 1.3 73.0 - - - +
864B GLU* 1.3 60.1 + - - +
866B PHE* 3.1 8.6 + - - +
867B LEU* 3.0 29.8 + - + +
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Residues in contact with GLU 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B ILE* 5.8 0.2 - - - +
795B TYR* 2.7 27.0 + - - -
860B GLU 3.0 21.0 + - - +
861B SER* 3.5 8.1 - - - +
863B VAL* 1.3 75.8 - - + +
865B ALA* 1.3 63.8 + - - +
867B LEU* 3.3 18.5 + - - +
868B ILE* 3.4 16.8 + - - +
946B VAL* 4.4 10.0 - - - +
951B ARG* 2.7 34.7 + - - -
953B LYS* 3.1 11.9 + - - +
984B PRO* 3.8 18.7 - - + +
986B LEU* 3.9 23.3 - - + -
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Residues in contact with ALA 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B SER 2.9 15.3 + - - +
862B ARG* 3.1 37.9 - - - +
864B GLU* 1.3 75.4 - - - +
866B PHE* 1.3 60.8 + - - +
868B ILE* 3.5 5.6 + - - +
869B THR* 3.0 24.9 + - - -
981B SER* 3.7 12.0 + - - +
982B GLN 3.8 18.8 - - - +
983B ALA* 3.8 1.8 - - - -
984B PRO* 3.8 4.4 - - - +
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Residues in contact with PHE 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B ILE* 4.0 11.2 - - + -
818B PRO 3.6 20.6 - - - -
819B ALA* 3.3 32.3 - - + -
822B THR* 3.8 28.3 - - + -
823B LEU* 4.4 12.6 - - + -
848B PHE* 4.2 23.1 - + - -
862B ARG 3.0 14.6 + - - +
863B VAL* 3.1 13.4 + - - +
865B ALA* 1.3 76.7 - - - +
867B LEU* 1.3 67.7 + - + +
869B THR* 3.2 10.0 + - - -
870B MET* 3.0 57.6 + - + +
981B SER* 5.3 0.4 - - - -
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Residues in contact with LEU 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B TYR* 3.6 36.6 - - + +
811B PHE* 4.5 25.1 - - + -
815B ILE* 5.1 0.4 - - + -
846B LEU* 4.8 2.9 - - + -
848B PHE* 4.2 21.1 - - + -
863B VAL* 3.0 20.1 + - + +
864B GLU* 3.3 13.6 + - - +
866B PHE* 1.3 82.5 - - + +
868B ILE* 1.3 62.1 + - + +
870B MET* 3.1 7.4 + - + +
871B GLU 3.1 18.2 + - - -
940B TYR* 3.5 23.7 + - + +
944B LEU* 4.6 8.1 - - + +
945B ALA* 6.2 0.2 - - - -
951B ARG* 4.1 13.2 - - - +
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Residues in contact with ILE 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864B GLU 3.4 4.8 + - - +
865B ALA* 3.8 6.7 - - - +
866B PHE 3.3 0.4 - - - -
867B LEU* 1.3 73.2 - - + +
869B THR* 1.3 65.3 + - - +
870B MET 3.0 2.8 + - - -
871B GLU* 3.3 13.7 + - - +
872B LYS* 3.2 36.9 + - - +
940B TYR* 4.2 11.2 - - - +
946B VAL* 5.1 9.6 - - + +
982B GLN 4.7 9.2 - - - +
984B PRO* 3.6 45.1 - - + -
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Residues in contact with THR 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822B THR* 5.7 5.7 - - + +
865B ALA 3.0 14.1 + - - -
866B PHE* 3.2 16.2 + - + -
868B ILE* 1.3 78.8 - - - +
870B MET* 1.3 66.1 + - + +
872B LYS* 3.8 17.6 + - - +
873B SER* 3.1 27.5 + - - -
981B SER* 3.7 19.9 + - - -
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Residues in contact with MET 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811B PHE* 5.0 7.2 - - + -
814B ILE* 4.5 6.3 - - - +
815B ILE* 3.7 30.5 - - + -
818B PRO* 3.6 30.5 - - + -
822B THR* 5.5 1.3 - - - +
866B PHE* 3.0 47.2 + - + +
867B LEU* 3.4 11.9 - - + +
868B ILE 3.0 0.6 - - - -
869B THR* 1.3 86.1 - - + +
871B GLU* 1.3 64.8 + - - +
872B LYS 3.2 1.1 - - - -
873B SER* 3.3 20.9 + - - +
874B ILE* 3.0 32.9 + - + +
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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
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867B LEU 3.1 5.9 + - - -
868B ILE* 3.7 17.9 - - - +
870B MET* 1.3 75.5 - - - +
872B LYS* 1.3 63.7 + - - +
874B ILE* 3.4 9.0 + - - +
875B GLU* 3.1 37.7 + - + +
937B ILE* 5.1 5.9 - - + +
940B TYR* 3.4 50.5 + - + +
941B LYS* 3.5 25.9 + - - +
945B ALA* 5.4 0.7 - - - +
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Residues in contact with LYS 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PRO* 5.7 4.9 - - + -
868B ILE* 3.2 30.7 + - - +
869B THR* 3.8 17.0 - - - +
871B GLU* 1.3 82.9 - - - +
873B SER* 1.3 57.1 - - - +
875B GLU* 3.3 10.9 + - + +
876B ASP* 3.0 46.4 + - - +
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Residues in contact with SER 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B ILE* 5.6 2.4 - - - +
818B PRO* 6.0 0.2 - - - +
869B THR* 3.1 19.3 + - - -
870B MET* 3.3 24.5 + - - +
872B LYS* 1.3 73.9 - - - +
874B ILE* 1.3 64.4 + - - +
876B ASP* 3.8 7.3 - - - +
877B MET* 3.0 32.6 + - - +
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Residues in contact with ILE 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B PHE* 3.9 32.5 - - + -
814B ILE* 4.0 29.6 - - + -
815B ILE* 5.3 0.2 - - + -
870B MET* 3.0 25.7 + - + +
871B GLU* 3.7 8.3 - - - +
873B SER* 1.3 75.7 - - - +
875B GLU* 1.3 63.0 + - - +
877B MET* 3.4 22.8 - - + +
882B PHE* 5.5 0.2 - - + -
933B LYS* 3.3 28.0 - - + +
936B ILE* 4.3 14.8 - - + +
937B ILE* 3.8 26.2 - - + -
940B TYR* 5.9 2.0 - - + -
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Residues in contact with GLU 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS* 3.3 32.0 + - + +
55A THR* 3.5 8.5 + - - -
56A LYS 5.3 0.2 + - - -
871B GLU* 3.1 38.0 + - - +
872B LYS* 3.4 12.6 - - + +
873B SER 3.3 0.2 - - - -
874B ILE* 1.3 75.7 - - - +
876B ASP* 1.3 63.1 + - - +
933B LYS* 2.8 25.6 + - - +
937B ILE* 3.8 11.3 - - + +
941B LYS* 4.5 8.4 + - - -
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Residues in contact with ASP 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 4.0 13.4 - - - +
56A LYS* 4.0 18.7 - - - +
57A SER 4.9 0.2 - - - -
58A PRO* 3.4 40.2 - - + +
422A PHE* 5.9 1.4 - - - -
455A LEU* 6.1 0.5 - - - +
872B LYS* 3.0 35.2 + - - +
873B SER* 4.1 7.0 - - - +
874B ILE 3.4 0.2 - - - -
875B GLU* 1.3 79.7 - - - +
877B MET* 1.3 63.1 + - - +
878B THR* 3.8 2.6 + - - +
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Residues in contact with MET 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.1 2.5 + - - -
814B ILE* 3.9 24.5 - - + -
873B SER* 3.0 16.8 + - - +
874B ILE* 3.4 26.2 - - + +
875B GLU 3.4 0.4 - - - -
876B ASP* 1.3 77.6 - - - +
878B THR* 1.3 63.0 + - - +
881B ALA* 3.8 25.4 - - + -
882B PHE* 3.2 43.3 - - + -
885B HIS* 4.3 11.7 - - - +
933B LYS* 2.9 36.4 + - + -
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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