Contacts of the helix formed by residues 853 - 876 (chain A) in PDB entry 1JQO
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 LEU 853 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737A ARG* 3.6 34.1 - - + +
740A GLU* 3.5 23.6 - - + +
741A TYR* 3.5 42.0 - - + +
744A SER* 6.1 0.4 - - - -
849A VAL* 3.9 15.3 - - + +
850A ALA* 3.4 31.0 - - + +
852A GLU* 1.3 72.2 - - + +
854A LYS* 1.3 67.4 + - - +
855A PRO* 3.3 2.5 - - - -
856A PHE* 3.1 29.7 + - + +
857A GLY 3.4 3.1 + - - -
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Residues in contact with LYS 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A ASP* 3.8 17.0 - - + +
846A GLU* 3.3 36.0 + - + +
849A VAL* 3.5 26.5 + - + +
850A ALA 3.0 5.7 + - - +
851A GLU* 2.8 50.9 + - - +
853A LEU* 1.3 75.9 - - - +
855A PRO* 1.4 60.2 - - + +
857A GLY* 3.0 20.4 + - - -
858A LYS* 3.5 6.8 + - - +
861A ARG* 4.3 3.5 + - - +
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Residues in contact with PRO 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A GLU 3.3 8.5 - - - +
852A GLU 3.4 14.4 - - - +
854A LYS* 1.4 94.0 - - + +
856A PHE* 1.3 63.9 + - - +
858A LYS* 3.1 20.6 + - + +
859A GLN* 3.2 18.1 + - - +
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Residues in contact with PHE 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A VAL* 3.4 34.3 - - + -
735A GLU* 4.2 26.0 - - + -
737A ARG* 5.0 2.9 - - + -
738A PHE* 3.8 30.1 - + - -
741A TYR* 3.9 29.4 - + + -
853A LEU* 3.1 21.8 + - + +
855A PRO* 1.3 76.8 - - - +
857A GLY* 1.3 67.1 + - - +
859A GLN* 3.2 36.2 + - + +
860A LEU* 3.3 17.0 + - + +
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Residues in contact with GLY 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A TYR* 3.4 29.3 + - - -
786A PHE* 5.4 0.2 - - - -
845A ASP* 3.6 7.0 - - - -
853A LEU 3.4 2.6 + - - -
854A LYS 3.0 9.9 + - - -
856A PHE* 1.3 80.4 - - - +
858A LYS* 1.3 63.5 + - - +
860A LEU* 2.8 10.3 + - - +
861A ARG* 2.8 27.2 + - - +
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Residues in contact with LYS 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A LYS 3.5 2.5 + - - +
855A PRO* 3.1 17.2 + - + +
857A GLY* 1.3 76.1 - - - +
859A GLN* 1.3 62.1 + - - +
861A ARG* 3.0 34.2 + - + +
862A ASP* 2.8 54.5 + - - +
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Residues in contact with GLN 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A PRO* 3.2 13.2 + - - +
856A PHE* 3.2 32.9 - - + +
857A GLY 3.0 0.6 + - - -
858A LYS* 1.3 75.1 - - - +
860A LEU* 1.3 64.9 + - + +
862A ASP* 3.1 12.4 + - - +
863A LYS* 3.0 36.0 + - + +
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Residues in contact with LEU 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A VAL* 4.0 24.0 - - + -
738A PHE* 5.1 4.0 - - + -
741A TYR* 3.6 34.1 - - + +
781A TRP* 5.8 0.2 - - + -
786A PHE* 3.8 20.1 - - + -
788A LEU* 3.9 25.6 - - + -
791A TRP* 3.9 1.7 - - - -
792A LEU* 4.6 9.4 - - + -
856A PHE* 3.7 31.2 - - + +
857A GLY 2.8 5.2 + - - +
859A GLN* 1.3 77.4 - - + +
861A ARG* 1.3 67.2 + - - +
863A LYS* 2.9 25.6 + - + +
864A TYR* 2.9 12.6 + - - +
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Residues in contact with ARG 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A TYR* 5.0 2.0 + - - -
786A PHE* 3.8 13.9 - - - -
838A PRO* 3.8 33.8 + - + +
841A ALA* 4.3 9.8 - - - -
842A GLY* 4.2 21.0 - - - +
845A ASP* 3.3 27.5 + - - +
854A LYS* 4.3 4.6 + - - +
857A GLY 2.8 11.7 + - - +
858A LYS* 3.1 49.1 - - + +
860A LEU* 1.3 75.0 - - - +
862A ASP* 1.3 59.6 + - - +
864A TYR* 3.1 20.3 - - - +
865A VAL* 3.3 13.7 - - + +
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Residues in contact with ASP 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A LYS* 2.8 52.8 + - - +
859A GLN* 3.3 10.8 - - - +
860A LEU 3.0 0.2 - - - -
861A ARG* 1.3 76.7 - - - +
863A LYS* 1.3 59.8 + - - +
864A TYR 3.1 1.7 + - - -
865A VAL* 3.3 10.1 + - - +
866A GLU* 2.9 30.7 + - - +
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Residues in contact with LYS 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A GLU* 2.6 43.9 + - - +
730A SER* 5.4 0.6 + - - -
731A VAL* 6.0 3.7 - - - +
791A TRP* 4.0 13.9 - - + -
792A LEU* 5.0 9.9 - - + +
859A GLN* 3.0 32.1 + - - +
860A LEU* 2.9 15.8 + - + +
862A ASP* 1.3 72.6 - - + +
864A TYR* 1.3 63.2 + - - +
866A GLU* 3.8 7.8 - - - +
867A THR* 2.6 36.3 + - - +
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Residues in contact with TYR 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A PHE* 3.2 54.1 - + + -
787A HIS* 5.3 0.9 - + - -
791A TRP* 3.5 24.2 - + + -
833A PHE* 3.3 42.1 + + - -
836A GLY* 3.5 17.0 - - - -
837A ASP 4.7 2.5 - - - -
838A PRO* 3.3 31.4 - - + +
860A LEU 2.9 5.9 + - - +
861A ARG 3.1 13.0 - - - +
863A LYS* 1.3 79.9 - - - +
865A VAL* 1.3 71.2 + - + +
867A THR* 3.2 3.1 + - - -
868A GLN* 3.0 39.4 + - - +
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Residues in contact with VAL 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A PRO* 5.0 8.3 - - + -
861A ARG 3.3 17.7 - - - +
862A ASP* 3.3 10.5 + - - +
864A TYR* 1.3 85.0 - - + +
866A GLU* 1.3 64.0 + - - +
868A GLN* 3.0 16.8 + - + +
869A GLN* 3.1 14.1 + - + +
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Residues in contact with GLU 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A GLY* 5.2 5.4 - - - +
799A LYS* 4.4 17.6 - - - +
862A ASP 2.9 17.1 + - - +
863A LYS* 3.8 7.9 - - - +
865A VAL* 1.3 76.7 - - - +
867A THR* 1.3 65.3 + - - +
869A GLN* 3.1 8.8 + - + +
870A LEU* 3.1 42.1 + - + +
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Residues in contact with THR 867 (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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791A TRP* 4.1 15.0 - - + +
792A LEU 5.3 0.3 + - - -
794A VAL* 3.9 19.5 - - + +
795A GLY* 3.2 40.1 + - - +
829A LEU* 5.5 0.4 - - + -
833A PHE* 4.2 18.4 - - + -
863A LYS* 2.6 25.0 + - - +
864A TYR 3.5 3.6 - - - -
866A GLU* 1.3 77.5 - - - +
868A GLN* 1.3 57.2 + - - +
870A LEU* 3.5 5.8 + - + +
871A LEU* 2.9 27.7 + - + +
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Residues in contact with GLN 868 (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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833A PHE* 3.4 27.4 + - + +
864A TYR* 3.0 38.4 + - - +
865A VAL* 3.0 12.3 + - + +
867A THR* 1.3 75.8 - - - +
869A GLN* 1.3 60.1 + - - +
871A LEU* 3.4 6.9 - - + +
872A LEU* 3.0 39.2 + - + +
880A ILE* 2.9 37.4 - - + +
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Residues in contact with GLN 869 (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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865A VAL* 3.1 12.8 + - + +
866A GLU* 3.1 10.3 + - - +
868A GLN* 1.3 73.4 - - - +
870A LEU* 1.3 78.8 + - - +
872A LEU* 2.9 19.8 + - - +
873A GLN* 2.9 52.7 + - - +
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Residues in contact with LEU 870 (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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794A VAL 5.7 0.2 - - - +
795A GLY* 3.4 31.9 - - - +
798A PHE* 3.9 21.5 - - + -
799A LYS* 4.0 20.0 - - + +
802A ILE* 4.3 23.3 - - + -
809A PHE* 5.5 2.0 - - + -
866A GLU* 3.1 26.6 + - + +
867A THR* 3.6 7.0 - - + +
869A GLN* 1.3 92.4 - - - +
871A LEU* 1.3 62.6 + - - +
873A GLN* 3.4 9.4 + - - +
874A ILE* 3.2 30.0 + - + +
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Residues in contact with LEU 871 (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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794A VAL* 5.9 2.9 - - + -
798A PHE* 4.7 10.3 - - + -
826A LEU* 3.6 40.6 - - + +
829A LEU* 3.9 9.9 - - + -
830A GLU* 3.9 32.8 - - + +
833A PHE* 3.5 33.2 - - + -
867A THR* 2.9 20.9 + - + +
868A GLN* 3.4 8.3 - - + +
870A LEU* 1.3 77.3 - - - +
872A LEU* 1.3 64.7 + - + +
874A ILE* 3.6 1.4 + - - +
875A ALA* 3.2 22.5 + - + +
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Residues in contact with LEU 872 (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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830A GLU* 3.4 25.4 - - + +
868A GLN* 3.0 30.2 + - + +
869A GLN* 2.9 7.8 + - - +
871A LEU* 1.3 78.0 - - + +
873A GLN* 1.3 53.2 + - - +
875A ALA* 3.6 1.7 - - - -
876A GLY* 2.7 28.9 + - - -
877A HIS* 2.8 42.3 + - + +
878A LYS 5.0 2.9 - - - +
879A ASP* 4.7 3.8 - - - -
880A ILE* 3.9 39.0 - - + +
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Residues in contact with GLN 873 (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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802A ILE* 6.0 0.2 - - - +
809A PHE* 3.4 33.6 - - + -
813A LYS* 4.3 11.6 - - - -
869A GLN* 2.9 45.9 + - - +
870A LEU* 3.7 14.2 - - - +
872A LEU* 1.3 75.0 - - - +
874A ILE* 1.3 68.0 + - - +
876A GLY* 3.0 14.0 + - - -
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Residues in contact with ILE 874 (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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798A PHE* 3.5 18.8 - - + -
802A ILE* 5.3 1.6 - - + -
809A PHE* 3.9 25.8 - - + +
812A LEU* 3.5 58.3 - - + +
813A LYS* 4.1 22.0 + - + +
816A TYR* 4.0 10.6 - - + -
817A ASN* 5.4 0.9 + - - -
822A PHE* 4.5 2.7 - - + -
826A LEU* 3.7 23.1 - - + -
870A LEU* 3.2 18.4 + - + +
871A LEU 3.9 3.6 - - - +
873A GLN* 1.3 78.1 - - - +
875A ALA* 1.3 61.8 + - - +
876A GLY* 4.5 0.2 - - - -
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Residues in contact with ALA 875 (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 TYR* 3.5 43.5 - - + +
817A ASN* 5.7 0.9 + - - -
826A LEU* 5.1 2.2 - - + -
827A ASP* 5.5 0.4 - - - +
830A GLU* 4.6 4.7 - - - +
871A LEU* 3.2 18.2 + - + +
872A LEU* 3.9 4.9 - - - +
873A GLN 3.2 0.6 - - - -
874A ILE* 1.3 82.0 - - - +
876A GLY* 1.3 61.5 + - - +
877A HIS* 4.0 23.7 + - + +
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Residues in contact with GLY 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A LYS* 5.9 4.3 - - - -
872A LEU 2.7 13.1 + - - -
873A GLN* 3.0 12.0 + - - -
874A ILE 4.5 0.2 - - - -
875A ALA* 1.3 76.1 - - - +
877A HIS* 1.3 67.0 + - - -
878A LYS* 4.2 3.5 + - - +
882A GLU* 4.3 2.6 - - - +
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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
------------------------------------------------------------
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