Contacts of the helix formed by residues 847 - 865 (chain B) in PDB entry 1PKG
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 847 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789B ILE* 3.5 14.4 - - - +
839B GLU* 3.6 18.2 + - - +
845B VAL* 4.8 15.7 - - + -
846B TYR* 1.3 78.8 - - - +
848B PHE* 1.3 65.3 + - - +
849B GLU* 2.8 29.0 + - - +
850B SER* 2.6 19.9 + - - -
851B ASP 3.5 2.4 + - - -
911B PRO* 5.1 1.6 - - - +
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Residues in contact with PHE 848 (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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784B ALA* 3.3 45.5 - - + -
787B ASN* 3.6 36.8 - - - -
788B CYS 4.3 9.4 - - - -
789B ILE* 4.1 8.7 - - + +
847B THR* 1.3 74.9 - - - +
849B GLU* 1.3 72.8 + - - +
850B SER 3.3 0.2 - - - -
851B ASP* 3.1 28.3 + - - +
852B VAL* 3.2 7.6 + - - +
917B PHE* 3.9 8.5 - - + -
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Residues in contact with GLU 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B THR* 3.6 22.4 + - - +
848B PHE* 1.3 95.4 - - - +
850B SER* 1.3 63.4 + - - +
851B ASP 3.2 0.4 - - - -
852B VAL* 3.2 18.5 + - - +
853B TRP 3.2 5.7 + - - -
911B PRO* 3.8 31.6 - - + +
912B LEU* 4.6 17.8 - - - +
914B ARG* 2.8 27.2 + - + +
915B PRO 5.3 5.4 - - - +
916B THR* 5.5 8.7 - - + +
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Residues in contact with SER 850 (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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789B ILE* 4.6 1.4 - - - +
791B ARG* 5.8 0.7 - - - +
837B ALA* 3.8 9.8 + - - +
839B GLU* 3.5 13.0 - - - -
840B SER* 3.4 24.0 + - - -
846B TYR* 3.6 10.7 - - - +
847B THR* 2.6 32.1 + - - -
849B GLU* 1.3 79.1 - - - +
851B ASP* 1.3 61.0 + - - +
853B TRP* 3.2 17.0 - - - +
854B SER* 3.3 10.4 + - - -
914B ARG* 3.5 10.0 - - - +
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Residues in contact with ASP 851 (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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780B MET* 3.4 26.8 - - + +
788B CYS 4.2 3.1 - - - +
789B ILE* 3.7 14.9 - - - +
790B HIS* 3.0 23.3 + - - +
791B ARG* 3.1 26.7 + - - -
792B ASP 4.6 1.4 + - - -
793B LEU* 4.5 4.6 - - - +
847B THR 3.5 0.4 + - - -
848B PHE* 3.1 17.6 + - - +
849B GLU 3.2 0.2 - - - -
850B SER* 1.3 79.9 + - - +
852B VAL* 1.3 64.1 + - - +
854B SER* 3.2 11.7 + - - +
855B TYR 3.0 17.3 + - - -
917B PHE* 3.4 10.3 - - + -
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Residues in contact with VAL 852 (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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848B PHE 3.2 8.2 + - - +
849B GLU* 3.2 10.9 + - - +
851B ASP* 1.3 75.8 - - - +
853B TRP* 1.3 56.8 + - - +
855B TYR* 2.7 24.1 + - - +
856B GLY 2.8 10.7 + - - -
906B CYS* 3.7 32.4 - - + +
914B ARG* 4.2 8.5 - - + -
915B PRO* 3.3 29.2 - - + +
916B THR* 4.2 2.0 - - - -
917B PHE* 3.5 42.6 - - + +
920B ILE* 4.2 7.0 - - + -
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Residues in contact with TRP 853 (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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834B LYS 5.0 0.4 + - - -
835B TRP 3.6 14.8 - - - -
836B MET 3.2 14.5 + - - -
837B ALA* 3.6 18.4 - - + -
838B PRO* 3.4 22.7 - - + -
849B GLU 3.2 3.8 + - - -
850B SER 3.2 10.5 - - - +
851B ASP 3.2 0.2 - - - -
852B VAL* 1.3 78.6 - - - +
854B SER* 1.3 63.1 + - - +
856B GLY* 3.1 4.5 + - - -
857B ILE* 3.1 31.4 + - + +
870B TYR* 4.6 10.4 + - - -
883B ILE* 4.3 14.1 - - + -
888B ARG* 3.4 35.7 - - - -
906B CYS 3.5 14.8 + - - +
907B TRP* 3.4 45.8 + + + -
908B ASP 3.9 5.6 - - - -
914B ARG* 3.4 22.4 - - - +
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Residues in contact with SER 854 (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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791B ARG 5.6 1.6 - - - -
792B ASP 5.3 2.3 + - - -
793B LEU* 3.8 32.2 + - - +
835B TRP* 2.7 29.7 + - - +
836B MET* 4.7 1.6 - - - -
850B SER 3.3 8.3 + - - -
851B ASP* 3.2 14.0 + - - -
852B VAL 3.2 0.4 - - - -
853B TRP* 1.3 74.9 - - - +
855B TYR* 1.3 53.3 + - - +
857B ILE* 2.6 27.4 + - - +
858B PHE* 2.6 19.4 + - - +
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Residues in contact with TYR 855 (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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773B SER* 2.3 35.3 + - - -
776B VAL* 3.4 35.7 - - + -
777B ALA* 3.3 18.1 - - + +
793B LEU* 3.8 10.2 - - + +
851B ASP 3.0 6.7 + - - +
852B VAL 2.7 15.2 + - - +
854B SER* 1.3 71.2 - - - +
856B GLY* 1.3 61.7 + - - -
858B PHE* 3.2 9.5 + + - +
859B LEU* 2.9 48.6 + - + +
906B CYS* 4.4 0.9 - - - -
917B PHE* 3.4 27.6 - + + -
920B ILE* 3.7 30.7 - - + -
924B ILE* 3.3 12.2 - - + +
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Residues in contact with GLY 856 (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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852B VAL 2.8 9.9 + - - -
853B TRP 3.1 5.8 + - - -
854B SER 3.0 0.2 - - - -
855B TYR* 1.3 76.8 - - - +
857B ILE* 1.3 56.1 + - - +
859B LEU* 2.9 23.8 + - - +
860B TRP 3.3 7.8 + - - -
903B MET* 3.8 6.9 - - - +
906B CYS* 3.7 19.5 - - - +
907B TRP* 3.4 21.5 - - - -
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Residues in contact with ILE 857 (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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834B LYS 3.9 8.5 - - - +
835B TRP* 3.4 31.9 - - + -
853B TRP* 3.1 28.6 + - + +
854B SER* 2.6 13.3 + - - +
856B GLY* 1.3 71.4 - - - +
858B PHE* 1.3 58.4 + - - -
860B TRP* 3.4 3.8 + - - +
861B GLU* 3.3 21.2 + - - +
869B PRO* 3.6 24.0 - - + +
870B TYR* 3.0 34.1 - - + +
889B MET* 3.9 7.6 - - + -
907B TRP* 3.2 24.2 - - + +
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Residues in contact with PHE 858 (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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678B LEU* 3.6 29.6 - - + -
772B PHE 3.9 8.5 - - - -
773B SER* 4.4 1.8 - - - -
776B VAL* 3.5 44.9 - - + -
793B LEU* 4.7 3.4 - - + -
794B ALA* 4.1 15.3 - - - +
795B ALA* 3.7 25.4 - - + -
798B ILE* 3.9 9.9 - - + -
835B TRP* 4.8 1.4 - - - -
854B SER 2.6 14.7 + - - +
855B TYR* 3.3 23.3 - + - +
857B ILE* 1.3 74.1 - - - +
859B LEU* 1.3 59.8 + - + +
860B TRP 3.2 0.2 + - - -
861B GLU* 3.3 10.9 - - - +
862B LEU* 2.9 52.8 + - + +
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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
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773B SER* 3.4 35.9 - - - +
855B TYR* 2.9 46.6 + - + +
856B GLY* 2.9 11.7 + - - +
858B PHE* 1.3 78.2 - - + +
860B TRP* 1.3 56.5 + - - +
862B LEU* 3.7 11.2 - - + -
863B PHE* 3.0 37.5 + - + +
899B MET* 4.5 9.2 - - - +
902B ILE* 3.8 23.6 - - + -
903B MET* 3.7 26.4 - - + +
924B ILE* 6.0 0.4 - - + -
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Residues in contact with TRP 860 (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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856B GLY 3.3 8.9 + - - +
857B ILE 3.6 8.5 - - - +
858B PHE 3.1 0.6 - - - -
859B LEU* 1.3 76.2 - - - +
861B GLU* 1.3 60.5 + - + +
863B PHE 3.1 0.9 + - - -
864B SER* 2.6 61.4 + - - -
867B SER* 3.2 36.6 - - - -
868B SER 3.2 20.4 - - - -
869B PRO* 4.1 5.2 - - + -
871B PRO* 4.0 16.8 - - + -
889B MET* 3.5 41.8 - - + +
890B LEU 3.2 23.7 + - - +
892B PRO* 3.3 29.6 - - + +
903B MET* 4.3 2.0 - - - -
907B TRP* 4.1 15.0 - + + -
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Residues in contact with GLU 861 (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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679B LEU* 3.4 25.0 - - + +
682B LEU* 3.8 3.5 - - - +
683B ARG* 5.3 0.3 + - - -
794B ALA* 3.9 2.3 - - - +
795B ALA* 3.1 34.6 + - + +
796B ARG* 4.6 1.4 + - - +
835B TRP* 3.4 33.7 + - - +
857B ILE 3.3 14.8 + - - +
858B PHE* 3.3 8.4 - - - +
860B TRP* 1.3 79.9 - - + +
862B LEU* 1.3 56.5 + - - +
864B SER* 3.2 6.9 + - - -
865B LEU 3.0 8.8 + - - -
866B GLY 2.9 26.9 + - - -
867B SER 3.1 23.8 - - - +
868B SER* 4.6 0.7 - - - -
869B PRO* 4.1 8.9 - - + +
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Residues in contact with LEU 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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678B LEU* 4.4 4.9 - - + -
682B LEU* 3.8 12.0 - - + +
769B LEU* 3.5 36.6 - - + +
772B PHE* 3.7 24.0 - - + -
773B SER* 3.1 32.5 - - - +
858B PHE* 2.9 36.0 + - + +
859B LEU* 3.5 15.0 - - + +
861B GLU* 1.3 77.0 - - - +
863B PHE* 1.3 73.2 + - + +
865B LEU* 3.3 26.0 - - - +
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Residues in contact with PHE 863 (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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766B LEU* 3.8 16.2 - - + -
769B LEU* 3.9 25.6 - - + -
770B LEU* 3.6 24.5 - - + -
773B SER* 3.4 22.2 - - - -
859B LEU* 3.0 28.7 + - + +
860B TRP 3.5 0.4 - - - -
862B LEU* 1.3 86.4 - - + +
864B SER* 1.3 60.4 + - - +
865B LEU* 3.4 2.7 - - - -
892B PRO* 3.4 13.0 - - + +
894B HIS* 3.5 41.9 + - - +
895B ALA* 3.4 25.6 - - + -
896B PRO* 3.6 14.6 - - + -
899B MET* 4.0 17.7 - - + -
903B MET* 4.7 4.0 - - + -
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Residues in contact with SER 864 (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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686B ARG* 4.6 2.6 + - - -
860B TRP* 2.6 55.8 + - - -
861B GLU* 3.2 7.6 + - - -
863B PHE* 1.3 79.2 - - - +
865B LEU* 1.3 67.0 + - - +
866B GLY 3.7 0.2 + - - -
867B SER* 3.3 20.2 + - - -
892B PRO* 4.0 12.3 - - - -
893B GLU* 5.0 4.0 - - - +
894B HIS* 5.4 3.9 + - - -
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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
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682B LEU* 3.8 29.8 - - + +
683B ARG 4.3 3.1 + - - -
686B ARG* 2.6 62.3 + - + +
689B PHE* 3.0 42.2 - - + -
764B LEU* 4.4 5.4 - - + -
769B LEU* 4.1 15.5 - - + -
861B GLU 3.0 5.4 + - - -
862B LEU 3.3 18.4 - - - +
863B PHE 3.4 2.8 - - - +
864B SER* 1.3 82.2 - - - +
866B GLY* 1.3 53.6 + - - +
894B HIS* 4.4 14.6 - - + +
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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