Contacts of the helix formed by residues 846 - 865 (chain A) in PDB entry 5J3V
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 LYS 846 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808A GLU* 4.6 7.5 + - - -
811A ASP* 3.0 33.7 + - - -
815A ARG* 3.4 15.5 - - - +
842A TRP* 5.2 0.8 - - - -
844A ASN 3.9 1.5 + - - +
845A PRO* 1.3 75.9 - - - +
847A ASP* 1.3 61.8 + - - +
848A ASP* 3.3 13.9 - - - +
849A LEU* 3.1 8.8 + - + +
850A ARG* 2.9 25.3 + - - +
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Residues in contact with ASP 847 (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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845A PRO 4.9 2.4 - - - +
846A LYS* 1.3 74.3 - - - +
848A ASP* 1.3 58.2 + - - +
850A ARG* 3.2 18.0 + - - +
851A ASP* 3.0 37.0 + - - +
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Residues in contact with ASP 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A ARG* 2.3 31.0 + - - +
846A LYS* 3.5 21.2 - - - +
847A ASP* 1.3 75.5 + - - +
849A LEU* 1.3 63.7 + - - -
851A ASP* 3.4 12.2 + - - +
852A MET* 3.1 31.4 + - + +
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Residues in contact with LEU 849 (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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811A ASP* 3.3 20.9 - - - +
814A PHE* 4.1 3.6 - - + +
815A ARG* 4.0 42.6 - - + +
818A CYS* 4.5 0.4 - - - -
842A TRP* 3.8 34.1 - - + -
845A PRO* 4.3 4.0 - - + -
846A LYS 3.1 12.1 + - - +
848A ASP* 1.3 83.1 + - - +
850A ARG* 1.3 57.9 + - - +
852A MET* 3.3 16.2 + - - +
853A PHE* 3.0 56.5 + - + -
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Residues in contact with ARG 850 (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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845A PRO* 4.3 15.4 - - + +
846A LYS 2.9 12.9 + - - +
847A ASP* 3.2 20.6 + - - +
849A LEU* 1.3 74.5 - - - +
851A ASP* 1.3 63.9 + - - +
853A PHE* 3.3 11.8 + - - +
854A CYS* 2.9 28.4 + - + +
886A ALA 5.1 2.0 + - - -
887A PHE* 3.3 56.9 + - - +
888A TYR* 3.9 15.1 - - + -
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Residues in contact with ASP 851 (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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847A ASP* 3.0 25.5 + - - +
848A ASP* 3.6 11.3 - - - +
849A LEU 3.3 0.2 - - - -
850A ARG* 1.3 80.4 - - - +
852A MET* 1.3 57.8 + - + +
854A CYS* 3.8 6.5 - - - +
855A LYS* 2.9 33.4 + - - +
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Residues in contact with MET 852 (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 TYR* 6.0 1.8 - - + -
815A ARG* 4.6 26.9 - - + +
818A CYS* 4.0 30.3 - - + -
819A THR* 5.2 5.4 - - - +
848A ASP* 3.1 22.6 + - + +
849A LEU* 3.4 22.4 - - - +
850A ARG 3.2 0.2 - - - -
851A ASP* 1.3 74.5 - - + +
853A PHE* 1.3 65.6 + - - +
855A LYS* 3.4 6.4 + - - +
856A ILE* 3.1 31.2 + - + +
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Residues in contact with PHE 853 (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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814A PHE* 3.6 30.1 - + - -
818A CYS* 3.5 28.9 - - - -
835A PHE* 4.3 2.9 - + - -
839A VAL* 3.6 39.5 - - + -
842A TRP* 3.7 28.3 - + - -
845A PRO* 4.4 5.2 - - + -
849A LEU* 3.0 44.7 + - + -
850A ARG* 3.3 10.3 + - - +
852A MET* 1.3 76.6 - - - +
854A CYS* 1.3 57.4 + - - +
856A ILE* 3.3 5.1 + - - +
857A LEU* 2.9 35.8 + - - +
888A TYR* 3.9 15.0 - - + -
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Residues in contact with CYS 854 (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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850A ARG* 2.9 17.3 + - + +
851A ASP* 3.8 7.9 - - - +
853A PHE* 1.3 77.5 - - - +
855A LYS* 1.3 57.8 + - - +
857A LEU* 4.6 0.7 - - - -
858A HIS* 3.0 59.4 + - - +
887A PHE 5.6 0.2 - - - -
888A TYR* 3.9 29.8 - - + -
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Residues in contact with LYS 855 (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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851A ASP 2.9 19.1 + - - +
852A MET* 3.8 6.3 - - - +
853A PHE 3.3 0.2 - - - -
854A CYS* 1.3 77.5 - - - +
856A ILE* 1.3 58.9 + - + +
858A HIS* 4.6 2.6 - - - +
859A GLY* 3.2 21.1 + - - -
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Residues in contact with ILE 856 (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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818A CYS* 3.7 36.1 - - + +
821A ILE* 3.7 33.7 - - + -
822A SER* 5.6 3.1 - - - +
828A VAL* 5.6 0.7 - - + -
832A PHE* 4.0 15.0 - - + -
835A PHE* 3.7 29.2 - - + -
852A MET* 3.1 19.3 + - + +
853A PHE 3.7 3.1 - - - +
855A LYS* 1.3 78.8 - - + +
857A LEU* 1.3 60.2 + - - +
859A GLY* 3.3 1.4 + - - -
860A PHE* 3.0 27.9 + - - +
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Residues in contact with LEU 857 (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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832A PHE* 3.8 15.5 - - + -
835A PHE* 4.8 11.4 - - + -
836A CYS* 3.8 32.1 - - + -
839A VAL* 4.4 7.9 - - + -
853A PHE* 2.9 21.0 + - - +
854A CYS* 4.0 3.6 - - - +
856A ILE* 1.3 76.8 - - - +
858A HIS* 1.3 58.2 + - - +
860A PHE* 3.3 5.0 + - - +
861A LYS* 2.9 28.0 + - - +
869A TRP* 4.8 13.6 - - + -
884A LEU* 4.0 18.8 - - + +
888A TYR* 3.6 38.4 - - + -
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Residues in contact with HIS 858 (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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854A CYS* 3.0 35.8 + - - +
855A LYS* 4.6 3.4 - - - +
857A LEU* 1.3 75.4 - - - +
859A GLY* 1.3 59.8 + - - +
861A LYS* 3.5 23.3 + - + +
862A ASN* 2.9 46.9 + - - +
888A TYR* 3.6 30.8 - - - +
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Residues in contact with GLY 859 (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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855A LYS 3.2 18.0 + - - -
856A ILE* 3.7 4.3 - - - -
857A LEU 3.2 0.8 - - - -
858A HIS* 1.3 77.2 - - - +
860A PHE* 1.3 58.9 + - - +
862A ASN* 3.4 8.9 + - - +
863A GLN* 3.1 29.2 + - - +
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Residues in contact with PHE 860 (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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829A ILE* 4.2 35.9 - - + -
832A PHE* 3.5 68.4 - + + -
856A ILE 3.0 9.0 + - - +
857A LEU 3.3 2.9 + - - +
859A GLY* 1.3 73.0 - - - +
861A LYS* 1.3 67.1 + - - +
863A GLN* 3.2 17.6 + - + +
864A VAL* 3.3 37.1 + - + +
869A TRP* 3.8 14.6 - + - -
872A PHE* 3.8 30.5 - + + -
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Residues in contact with LYS 861 (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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857A LEU 2.9 18.2 + - - +
858A HIS* 3.3 26.3 + - + +
860A PHE* 1.3 79.3 - - - +
862A ASN* 1.3 64.4 + - - +
864A VAL* 3.7 6.7 - - - +
865A GLY* 2.9 29.1 + - - +
866A ASP* 2.8 41.1 + - - +
869A TRP* 3.6 49.1 - - + +
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Residues in contact with ASN 862 (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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858A HIS* 2.9 34.9 + - - +
859A GLY* 3.8 7.5 - - - +
860A PHE 3.2 0.2 - - - -
861A LYS* 1.3 87.0 + - - +
863A GLN* 1.3 64.0 + - + +
865A GLY* 4.0 6.7 + - - +
866A ASP* 5.0 3.0 - - - +
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Residues in contact with GLN 863 (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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829A ILE* 5.7 9.2 - - + -
859A GLY 3.1 21.9 + - - +
860A PHE* 3.2 14.8 + - + +
862A ASN* 1.3 80.7 - - + +
864A VAL* 1.3 63.7 + - + +
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Residues in contact with VAL 864 (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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829A ILE* 6.2 1.8 - - + -
860A PHE* 3.4 44.6 - - + +
861A LYS* 3.7 5.2 - - - +
863A GLN* 1.3 83.2 - - + +
865A GLY* 1.3 72.1 + - - +
868A ASN* 2.8 41.1 + - + +
869A TRP* 3.9 17.5 - - + +
872A PHE* 6.1 0.7 - - + -
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Residues in contact with GLY 865 (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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861A LYS 2.9 14.7 + - - +
862A ASN* 4.0 6.1 + - - -
863A GLN 3.6 1.4 - - - -
864A VAL* 1.3 79.2 - - - +
866A ASP* 1.3 61.2 + - - -
867A GLU* 3.1 3.6 - - - -
869A TRP* 3.0 31.4 + - - +
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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
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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