Contacts of the helix formed by residues 769 - 782 (chain F) in PDB entry 5A31
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 769 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767F ASP* 4.2 0.8 - - - +
768F PRO* 1.3 76.2 - - + +
770F GLY* 1.3 64.5 + - - +
771F ALA 3.1 1.8 - - - -
772F ASN* 2.9 20.5 + - - +
773F ASN* 3.4 8.4 + - - +
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Residues in contact with GLY 770 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737F SER* 5.0 8.7 - - - -
738F LEU* 4.7 3.9 - - - +
767F ASP* 3.6 18.2 - - - +
769F LYS* 1.3 78.2 - - - +
771F ALA* 1.3 51.1 + - - +
773F ASN* 3.1 12.5 + - - +
774F GLN* 2.6 38.4 + - - +
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Residues in contact with ALA 771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737F SER* 5.2 1.0 + - - -
764F MET* 4.7 24.5 - - + -
767F ASP* 3.7 16.7 + - - +
768F PRO 3.6 17.3 - - - +
770F GLY* 1.3 74.3 - - - +
772F ASN* 1.3 59.8 + - - +
774F GLN* 3.6 7.5 + - - +
775F ILE* 3.4 20.4 + - - +
362R HIS 5.5 6.5 - - - +
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Residues in contact with ASN 772 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768F PRO 4.7 1.3 + - - +
769F LYS* 2.9 12.8 + - - +
771F ALA* 1.3 77.6 - - - +
773F ASN* 1.3 61.2 + - - +
775F ILE* 3.6 18.0 + - - +
776F LYS* 3.6 7.6 + - - +
362R HIS* 5.5 8.5 + - - +
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Residues in contact with ASN 773 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738F LEU* 5.0 7.8 - - + +
769F LYS 3.4 4.0 + - - +
770F GLY* 3.1 17.7 + - - +
772F ASN* 1.3 77.4 - - - +
774F GLN* 1.3 63.8 + - - +
776F LYS* 3.3 10.8 + - - +
777F GLU* 3.1 21.4 + - - +
487R ASN* 6.3 0.9 - - - +
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Residues in contact with GLN 774 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737F SER* 5.3 2.7 - - - +
738F LEU* 3.8 25.5 - - + +
741F PHE* 4.6 30.0 - - + -
763F ALA* 6.5 0.2 - - + -
770F GLY 2.6 22.0 + - - +
771F ALA* 3.6 10.3 - - - +
773F ASN* 1.3 72.0 - - - +
775F ILE* 1.3 61.8 + - - +
777F GLU* 3.3 3.9 + - - +
778F ALA* 3.2 22.7 + - - +
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Residues in contact with ILE 775 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741F PHE* 6.0 1.1 - - - -
771F ALA 3.4 10.0 + - - +
772F ASN* 3.6 11.9 - - - +
773F ASN 3.2 0.6 - - - -
774F GLN* 1.3 76.8 - - - +
776F LYS* 1.3 64.2 + - - +
777F GLU 3.3 0.3 + - - -
778F ALA* 3.6 7.9 + - - +
779F ILE* 3.5 19.1 + - - +
320R ALA* 6.4 2.2 - - + -
364R ARG* 5.9 7.2 - - + -
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Residues in contact with LYS 776 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772F ASN 3.6 6.3 + - - +
773F ASN* 3.3 15.4 + - - +
775F ILE* 1.3 79.2 - - - +
777F GLU* 1.3 62.6 + - - +
779F ILE* 3.6 6.4 + - - +
780F ASP* 3.5 18.7 + - - +
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Residues in contact with GLU 777 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707F PHE* 6.2 3.8 - - + -
738F LEU* 4.9 16.6 - - + -
773F ASN 3.1 10.5 + - - +
774F GLN* 3.7 10.3 - - - +
775F ILE 3.2 0.6 - - - -
776F LYS* 1.3 76.0 - - - +
778F ALA* 1.3 66.1 + - - +
779F ILE 3.1 2.0 - - - -
780F ASP* 3.2 16.9 + - - +
781F LYS* 3.2 13.0 + - - +
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Residues in contact with ALA 778 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741F PHE* 4.5 8.4 - - + -
745F LYS* 3.0 34.8 + - - +
774F GLN 3.2 11.7 + - - +
775F ILE* 3.6 12.3 - - - +
777F GLU* 1.3 73.8 - - - +
779F ILE* 1.3 61.6 + - - +
781F LYS* 3.3 8.4 + - - +
782F ARG* 3.1 23.3 + - - +
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Residues in contact with ILE 779 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775F ILE 3.5 8.9 + - - +
776F LYS* 3.8 10.1 - - - +
777F GLU 3.1 1.0 - - - -
778F ALA* 1.3 76.7 - - - +
780F ASP* 1.3 65.9 + - - +
782F ARG* 3.3 21.5 + - - +
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Residues in contact with ASP 780 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646F TYR* 4.7 14.6 - - - +
680F HIS* 4.8 7.3 + - - -
681F ALA* 5.8 4.9 - - - +
776F LYS 3.5 9.9 + - - +
777F GLU* 3.2 11.8 + - - +
779F ILE* 1.3 78.4 - - - +
781F LYS* 1.3 61.1 + - - +
782F ARG 4.7 1.7 - - - -
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Residues in contact with LYS 781 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680F HIS* 4.1 20.8 + - + -
711F SER* 4.2 20.4 - - - +
714F PHE* 5.7 11.7 - - + -
715F ALA* 5.0 8.0 - - + +
777F GLU 3.2 8.8 + - - +
778F ALA* 3.7 10.3 - - - +
779F ILE 3.2 0.6 - - - -
780F ASP* 1.3 79.8 - - - +
782F ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 782 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683F LYS* 5.7 4.2 + - - -
778F ALA 3.1 16.4 + - - +
779F ILE* 3.3 15.8 + - - +
780F ASP 4.7 1.8 - - - -
781F LYS* 1.3 80.5 - - - +
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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