Contacts of the helix formed by residues 765 - 786 (chain A) 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 ASP 765 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A PHE* 3.5 4.2 - - - -
690A ILE* 3.6 5.4 - - - -
691A CYS 3.4 0.9 - - - -
692A SER* 3.0 26.5 + - - -
693A LYS* 3.5 28.5 + - - +
763A ALA 4.1 0.8 + - - +
764A LEU* 1.3 74.0 - - - +
766A LEU* 1.3 69.6 + - - +
767A GLU* 3.6 20.2 + - + +
768A ASP* 3.5 34.9 + - - +
769A LEU* 3.4 25.5 + - - +
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Residues in contact with LEU 766 (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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689A PHE* 4.2 9.9 - - + -
690A ILE 3.4 5.5 + - - -
691A CYS* 3.8 31.2 - - + -
692A SER 5.3 0.2 - - - +
765A ASP* 1.3 76.6 + - - +
767A GLU* 1.3 58.5 + - - +
768A ASP 3.2 0.2 - - - -
769A LEU* 3.1 9.9 + - + +
770A LEU* 2.9 33.9 + - + +
863A PHE* 3.9 21.1 - - + -
894A HIS 3.9 21.3 - - - +
896A PRO* 4.2 17.9 - - + -
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Residues in contact with GLU 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ASP* 3.4 19.5 + - + +
766A LEU* 1.3 78.1 - - - +
768A ASP* 1.3 54.3 + - - +
770A LEU* 3.5 15.6 - - + +
771A SER* 2.7 35.1 + - - -
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Residues in contact with ASP 768 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PHE* 5.9 0.2 - - - -
763A ALA 3.9 10.0 - - - +
764A LEU* 4.0 14.2 - - + +
765A ASP* 3.5 35.5 + - - +
767A GLU* 1.3 77.2 - - - +
769A LEU* 1.3 61.0 + - - +
771A SER* 3.3 6.8 + - - -
772A PHE* 2.9 41.5 + - + -
804A ARG* 3.2 39.5 + - - +
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Residues in contact with LEU 769 (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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682A LEU* 4.1 13.9 - - + -
689A PHE* 3.4 26.7 - - + -
764A LEU* 4.0 26.5 - - + -
765A ASP 3.4 12.1 + - - +
766A LEU* 3.1 8.8 + - + +
768A ASP* 1.3 74.8 - - - +
770A LEU* 1.3 67.1 + - - +
772A PHE* 3.2 10.8 + - + -
773A SER* 3.0 24.5 + - - -
862A LEU* 3.5 32.2 - - + +
863A PHE* 3.5 37.5 - - + +
865A LEU* 4.2 3.8 - - + -
894A HIS* 5.1 0.2 - - + -
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Residues in contact with LEU 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A LEU* 2.9 19.4 + - + +
767A GLU* 3.5 18.8 - - + +
769A LEU* 1.3 74.5 - - - +
771A SER* 1.3 55.1 + - - +
773A SER* 2.7 27.7 + - - -
774A TYR* 2.9 13.4 + - - +
863A PHE* 4.3 6.5 - - + -
896A PRO* 4.8 6.5 - - + -
899A MET* 4.1 20.9 - - + -
924A ILE* 4.3 7.9 - - + +
927A GLN* 3.6 56.1 - - + +
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Residues in contact with SER 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A GLU 2.7 21.3 + - - -
768A ASP* 3.3 11.2 + - - -
770A LEU* 1.3 73.0 - - - +
772A PHE* 1.3 57.3 + - - +
774A TYR* 3.5 7.6 + - - +
775A GLN* 3.0 45.4 + - - +
804A ARG* 4.2 10.4 + - - +
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Residues in contact with PHE 772 (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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678A LEU* 3.7 38.1 - - + -
681A PHE* 4.2 5.4 - + - -
682A LEU* 5.5 1.6 - - + -
764A LEU* 3.9 22.7 - - + -
768A ASP* 2.9 35.8 + - + +
769A LEU* 3.8 9.2 - - + +
770A LEU 3.2 0.4 - - - -
771A SER* 1.3 74.7 - - - +
773A SER* 1.3 63.9 + - - +
775A GLN* 4.1 0.2 - - - +
776A VAL* 3.1 29.3 + - - +
800A LEU* 3.6 26.9 - - + -
804A ARG* 3.8 35.9 - - + -
806A THR* 3.6 22.9 - - + -
858A PHE* 4.4 0.7 - - - -
862A LEU* 4.2 14.8 - - + -
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Residues in contact with SER 773 (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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769A LEU 3.0 14.1 + - - -
770A LEU* 2.7 16.9 + - - -
772A PHE* 1.3 69.6 - - - +
774A TYR* 1.3 65.0 + - - -
777A ALA* 3.1 13.5 + - - +
855A TYR* 2.9 22.3 + - - -
858A PHE* 4.8 1.8 - - - -
859A LEU* 3.6 14.3 - - - +
862A LEU* 3.2 18.1 - - - +
863A PHE* 3.4 18.4 - - - -
899A MET* 4.5 7.2 - - - -
924A ILE* 3.6 11.7 - - - -
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Residues in contact with TYR 774 (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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770A LEU 2.9 10.4 + - - +
771A SER* 3.6 12.6 - - - +
773A SER* 1.3 76.5 - - - +
775A GLN* 1.3 64.5 + - + +
777A ALA* 3.2 3.1 + - - +
778A LYS* 2.8 63.1 + - + +
921A VAL* 3.7 36.8 - - + +
924A ILE* 3.7 23.0 - - + +
925A GLU* 3.6 33.6 + - + +
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Residues in contact with GLN 775 (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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652A ASN* 2.7 34.4 + - - +
771A SER* 3.0 29.7 + - - +
772A PHE 3.6 1.1 + - - +
773A SER 3.4 0.2 - - - -
774A TYR* 1.3 83.0 - - + +
776A VAL* 1.3 58.5 + - - +
778A LYS* 3.5 9.6 - - + +
779A GLY 3.0 20.3 + - - -
803A GLY 5.2 0.2 + - - -
804A ARG 2.7 27.9 + - - -
805A ILE* 3.2 12.9 - - - +
806A THR* 2.6 41.7 + - - +
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Residues in contact with VAL 776 (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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678A LEU* 5.3 0.4 - - + -
772A PHE 3.1 19.6 + - - +
775A GLN* 1.3 75.0 - - - +
777A ALA* 1.3 56.0 + - - +
779A GLY* 3.2 1.1 + - - +
780A MET* 2.7 47.4 + - + +
793A LEU* 3.9 16.4 - - + -
798A ILE* 3.5 50.3 - - + -
806A THR* 4.4 8.5 - - - +
808A ILE* 4.1 9.9 - - + +
855A TYR* 3.9 14.6 - - + -
858A PHE* 3.8 14.4 - - + -
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Residues in contact with ALA 777 (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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773A SER 3.1 18.6 + - - +
774A TYR 3.7 2.7 - - - +
776A VAL* 1.3 76.0 - - - +
778A LYS* 1.3 52.1 + - - +
780A MET* 3.2 5.2 + - - -
781A ALA* 2.8 35.7 + - - +
855A TYR* 3.4 25.5 - - + +
917A PHE* 3.7 6.1 - - + +
920A ILE* 3.8 17.9 - - + -
921A VAL* 3.5 13.3 - - + +
924A ILE* 3.9 5.2 - - + -
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Residues in contact with LYS 778 (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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650A HIS* 4.7 12.3 + - + +
651A MET* 5.9 3.2 - - - +
652A ASN* 3.9 17.8 + - - +
774A TYR* 2.8 53.0 + - + +
775A GLN* 3.5 10.3 - - + +
777A ALA* 1.3 76.6 - - - +
779A GLY* 1.3 61.0 + - - +
781A ALA* 3.3 4.2 + - - +
782A PHE* 3.1 20.3 + - - +
921A VAL* 3.6 16.9 - - + +
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Residues in contact with GLY 779 (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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650A HIS* 4.4 3.8 - - - -
652A ASN* 4.0 12.8 - - - +
653A ILE* 3.8 11.7 - - - +
775A GLN 3.0 12.2 + - - -
776A VAL 3.6 2.9 - - - -
778A LYS* 1.3 77.9 - - - +
780A MET* 1.3 59.5 + - - +
782A PHE* 3.1 9.8 + - - +
783A LEU* 3.1 22.7 + - - +
808A ILE* 3.8 16.4 - - - -
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Residues in contact with MET 780 (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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776A VAL* 2.7 31.5 + - + +
777A ALA 3.7 0.2 - - - +
779A GLY* 1.3 69.6 - - - +
781A ALA* 1.3 63.0 + - - +
783A LEU* 3.4 30.3 + - + +
784A ALA* 3.3 23.0 + - - +
790A HIS* 4.0 8.1 - - + -
793A LEU* 3.7 35.2 - - + -
808A ILE* 4.0 8.5 - - + -
851A ASP* 3.5 40.4 - - + +
917A PHE* 3.6 35.5 - - + -
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Residues in contact with ALA 781 (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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777A ALA 2.8 18.1 + - - +
778A LYS 3.5 6.5 - - - +
779A GLY 3.3 0.2 - - - -
780A MET* 1.3 78.0 - - - +
782A PHE* 1.3 60.0 + - - +
784A ALA* 3.7 5.9 + - - +
785A SER* 3.4 20.8 + - - -
917A PHE* 3.6 18.3 - - + +
918A LYS* 3.9 19.0 - - + +
921A VAL* 4.0 8.3 - - + -
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Residues in contact with PHE 782 (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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647A LEU* 3.7 35.0 - - + -
649A ASN 4.8 1.6 - - - -
650A HIS* 3.5 52.9 - + + +
653A ILE* 3.8 20.0 - - + -
778A LYS 3.1 12.7 + - - +
779A GLY 3.3 7.4 - - - +
780A MET 3.1 0.2 - - - -
781A ALA* 1.3 73.8 - - - +
783A LEU* 1.3 65.2 + - - +
784A ALA 3.1 1.6 - - - -
785A SER* 2.4 26.9 + - - -
786A LYS* 3.2 31.5 + - + +
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Residues in contact with LEU 783 (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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647A LEU* 3.7 40.4 - - + -
653A ILE* 4.2 11.0 - - + -
779A GLY 3.1 12.5 + - - +
780A MET* 3.6 39.0 - - + +
782A PHE* 1.3 76.7 - - + +
784A ALA* 1.3 57.9 + - - +
786A LYS* 3.1 7.9 + - - +
787A ASN 3.0 8.0 + - - -
788A CYS* 2.8 46.2 + - + +
789A ILE 5.9 0.2 - - - -
790A HIS* 4.1 13.9 - - + +
808A ILE* 5.1 0.4 - - + -
811A PHE* 3.7 25.6 - - + -
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Residues in contact with ALA 784 (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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780A MET 3.3 13.8 + - - +
781A ALA* 3.8 8.5 - - - +
782A PHE 3.1 0.6 - - - -
783A LEU* 1.3 75.5 - - - +
785A SER* 1.3 62.2 + - - +
786A LYS 3.0 1.8 - - - -
787A ASN* 2.9 20.1 + - - +
788A CYS 3.8 9.2 - - - +
848A PHE* 3.4 28.8 - - + +
917A PHE* 5.0 9.0 - - + -
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Residues in contact with SER 785 (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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781A ALA 3.4 8.9 + - - -
782A PHE* 2.4 41.2 + - - -
784A ALA* 1.3 78.8 - - - +
786A LYS* 1.3 57.6 + - - +
787A ASN* 3.1 12.6 + - - +
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Residues in contact with LYS 786 (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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646A TYR* 2.7 74.0 + - + +
647A LEU* 3.2 37.6 + - + -
782A PHE* 3.6 30.7 - - + +
783A LEU* 3.1 13.8 + - - +
784A ALA 3.0 0.6 - - - -
785A SER* 1.3 79.7 + - - +
787A ASN* 1.3 65.7 + - - +
788A CYS* 3.4 2.1 + - - -
816A ASP* 4.1 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
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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