Contacts of the helix formed by residues 829 - 849 (chain A) in PDB entry 5XA0
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 ILE 829 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A ASP* 3.1 8.3 - - + +
828A GLU* 1.3 77.3 - - - +
830A LYS* 1.3 64.5 + - - +
831A GLU 3.4 0.4 - - - -
832A ARG* 3.3 12.6 + - + +
833A PHE* 3.1 18.6 + - - +
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Residues in contact with LYS 830 (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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825A SER* 4.2 23.8 - - - +
826A LYS 4.7 2.9 - - - +
827A ASP* 3.2 16.5 + - - +
828A GLU 3.2 1.2 - - - -
829A ILE* 1.3 76.0 - - - +
831A GLU* 1.3 56.3 + - - +
833A PHE* 2.4 39.1 + - - +
834A ALA* 3.1 5.1 + - - +
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Residues in contact with GLU 831 (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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828A GLU 4.0 9.3 + - - +
829A ILE 3.4 0.4 - - - -
830A LYS* 1.3 77.7 - - - +
832A ARG* 1.3 64.1 + - - +
834A ALA* 3.2 15.9 + - - +
835A GLN* 3.7 8.7 + - - +
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Residues in contact with ARG 832 (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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828A GLU 4.7 1.0 + - - +
829A ILE* 3.3 15.2 + - + +
830A LYS 3.1 0.6 - - - -
831A GLU* 1.3 78.0 - - - +
833A PHE* 1.3 55.9 + - - +
834A ALA 3.3 0.3 + - - -
835A GLN* 3.4 8.6 + - - +
836A THR* 2.9 27.0 + - - -
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Residues in contact with PHE 833 (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 3.1 9.5 + - - +
830A LYS* 2.4 29.0 + - + +
832A ARG* 1.3 71.3 - - - +
834A ALA* 1.3 54.6 + - - +
836A THR* 3.1 10.7 + - - -
837A MET* 2.8 28.6 + - - +
873A LEU* 6.4 2.0 - - + -
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Residues in contact with ALA 834 (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 LYS 3.1 7.5 + - - +
831A GLU* 3.2 11.3 + - - +
833A PHE* 1.3 75.7 - - - +
835A GLN* 1.3 57.9 + - - +
837A MET* 3.2 9.3 + - - +
838A GLU* 2.9 27.1 + - - +
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Residues in contact with GLN 835 (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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831A GLU 3.7 5.8 + - - +
832A ARG* 3.4 10.6 + - - +
834A ALA* 1.3 77.8 - - - +
836A THR* 1.3 56.9 + - - +
838A GLU* 3.3 8.5 + - - +
839A PHE* 2.8 30.9 + - - +
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Residues in contact with THR 836 (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 ARG 2.9 14.4 + - - -
833A PHE* 3.1 15.5 + - - -
835A GLN* 1.3 73.4 - - - +
837A MET* 1.3 60.1 + - - +
839A PHE* 3.1 7.6 + - - +
840A VAL* 2.8 30.4 + - - +
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Residues in contact with MET 837 (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 2.8 15.8 + - - +
834A ALA* 3.5 10.5 - - - +
836A THR* 1.3 72.3 - - - +
838A GLU* 1.3 57.4 + - - +
840A VAL* 3.1 10.3 + - - +
841A GLU* 2.9 26.7 + - - +
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Residues in contact with GLU 838 (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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834A ALA 2.9 13.3 + - - +
835A GLN* 3.6 11.9 - - - +
837A MET* 1.3 78.7 - - - +
839A PHE* 1.3 57.1 + - - +
841A GLU* 3.0 12.3 + - - +
842A GLU* 2.9 25.6 + - - +
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Residues in contact with PHE 839 (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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835A GLN 2.8 20.5 + - - +
836A THR* 3.6 7.4 - - - +
838A GLU* 1.3 72.1 - - - +
840A VAL* 1.3 57.1 + - - +
842A GLU* 3.0 10.6 + - - +
843A TYR* 2.8 26.7 + - - +
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Residues in contact with VAL 840 (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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836A THR 2.8 13.3 + - - +
837A MET* 3.3 12.8 - - - +
839A PHE* 1.3 76.8 - - - +
841A GLU* 1.3 56.7 + - - +
843A TYR* 3.2 10.4 + - - +
844A LEU* 2.9 26.3 + - - +
894A ILE* 5.3 15.2 - - + +
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Residues in contact with GLU 841 (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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837A MET 2.9 13.1 + - - +
838A GLU* 3.0 15.0 + - - +
840A VAL* 1.3 76.8 - - - +
842A GLU* 1.3 54.5 + - - +
844A LEU* 3.1 11.2 + - - +
845A ARG* 2.8 26.5 + - - +
894A ILE* 6.5 0.2 - - - -
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Residues in contact with GLU 842 (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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838A GLU 2.9 11.4 + - - +
839A PHE* 3.0 11.9 + - - +
841A GLU* 1.3 73.0 - - - +
843A TYR* 1.3 61.2 + - - +
845A ARG* 3.5 10.5 - - - +
846A ASP* 2.8 24.1 + - - +
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Residues in contact with TYR 843 (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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839A PHE 2.8 12.2 + - - +
840A VAL* 3.3 13.5 - - - +
842A GLU* 1.3 75.8 - - - +
844A LEU* 1.3 49.8 + - - +
846A ASP* 2.8 13.6 - - + +
847A VAL* 2.6 33.0 + - - +
863A THR* 6.3 3.8 - - - -
897A CYS 5.3 0.4 - - - -
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Residues in contact with LEU 844 (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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840A VAL 2.9 13.7 + - - +
841A GLU* 3.1 14.3 + - - +
843A TYR* 1.3 71.6 - - - +
845A ARG* 1.3 59.4 + - - +
847A VAL* 2.9 12.2 + - - +
848A VAL* 2.9 26.9 + - - +
893A ALA 5.7 0.2 - - - +
894A ILE* 5.2 9.4 - - + -
897A CYS* 4.1 21.9 + - + +
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Residues in contact with ARG 845 (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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841A GLU 2.8 16.5 + - - +
842A GLU* 3.5 14.1 - - - +
844A LEU* 1.3 69.3 - - - +
846A ASP* 1.3 66.2 + - - +
847A VAL 3.3 0.3 + - - -
848A VAL* 3.4 15.5 + - - +
849A CYS* 3.5 9.7 + - - +
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Residues in contact with ASP 846 (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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842A GLU 2.8 17.2 + - - +
843A TYR* 2.8 17.9 - - + +
845A ARG* 1.3 76.1 - - - +
847A VAL* 1.3 48.1 - - - +
849A CYS* 2.5 38.0 + - - +
859A LYS* 6.1 4.9 - - + -
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Residues in contact with VAL 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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843A TYR 2.6 13.8 + - - +
844A LEU 2.9 12.7 + - - +
846A ASP* 1.3 71.4 - - - +
848A VAL* 1.3 60.7 + - - +
849A CYS 2.6 16.9 - - - +
850A GLN* 3.7 7.4 + - - +
897A CYS* 3.5 35.4 - - + +
898A VAL* 4.4 11.9 - - - +
899A HIS* 6.1 2.9 - - - -
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Residues in contact with VAL 848 (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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844A LEU 2.9 10.7 + - - +
845A ARG* 3.7 11.9 - - - +
846A ASP 3.4 0.4 - - - -
847A VAL* 1.3 75.8 - - - +
849A CYS* 1.3 60.1 + - - +
850A GLN* 3.3 6.1 + - - +
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Residues in contact with CYS 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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845A ARG 3.5 6.6 + - - +
846A ASP* 2.5 32.5 + - - +
847A VAL* 2.6 10.5 - - - +
848A VAL* 1.3 76.7 - - - +
850A GLN* 1.3 56.4 + - - +
851A ARG* 4.1 4.2 + - + -
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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