Contacts of the helix formed by residues 782 - 789 (chain F) in PDB entry 6C3P
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 THR 782 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781F ALA* 1.3 79.8 - - - +
783F VAL* 1.3 68.6 + - - +
784F GLU* 3.3 15.7 - - + +
785F GLU* 2.8 23.8 + - - +
786F ASN* 2.9 15.1 + - - +
818F ASP 3.2 20.2 - - - +
819F GLN* 3.5 22.8 - - + +
820F THR 3.5 4.5 - - - -
821F GLN* 2.2 30.2 + - - -
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Residues in contact with VAL 783 (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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781F ALA 3.6 0.6 + - - -
782F THR* 1.3 68.9 - - - +
784F GLU* 1.3 63.5 + - - +
786F ASN* 2.6 26.6 - - - +
787F ILE* 3.0 30.7 + - + +
798F TYR* 4.9 0.7 - - - +
807F LEU* 5.0 10.5 - - + -
811F ILE* 5.0 9.6 - - + -
814F LEU* 3.9 22.0 - - + -
817F GLY 3.9 4.0 - - - +
818F ASP* 3.1 20.6 - - - +
820F THR* 3.0 18.9 + - - +
822F ILE* 3.9 19.9 - - + +
837F ILE* 5.2 11.0 - - + -
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Residues in contact with GLU 784 (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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782F THR* 3.2 12.4 - - + +
783F VAL* 1.3 79.4 - - - +
785F GLU* 1.3 56.8 + - - +
787F ILE* 4.4 1.8 - - - -
788F ILE* 2.8 47.8 + - + +
793F PHE* 5.7 1.6 - - + -
798F TYR* 3.6 15.3 - - + +
818F ASP* 3.1 26.6 + - - +
819F GLN* 5.1 5.2 - - + +
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Residues in contact with GLU 785 (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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781F ALA* 3.6 13.0 - - + -
782F THR* 2.8 35.7 + - - +
784F GLU* 1.3 79.6 - - - +
786F ASN* 1.3 57.9 + - - +
788F ILE* 3.7 5.5 - - - +
789F PHE* 3.0 26.0 + - - -
790F GLU 4.8 0.5 + - - -
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Residues in contact with ASN 786 (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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778F LEU* 4.2 0.6 - - - +
779F LEU* 4.1 27.4 + - + +
781F ALA* 4.6 1.3 + - - +
782F THR 2.9 13.5 + - - +
783F VAL* 2.6 16.1 - - - +
785F GLU* 1.3 75.4 - - - +
787F ILE* 1.3 87.2 + - - +
789F PHE* 3.8 13.2 + - - +
822F ILE* 3.1 33.9 - - - +
837F ILE* 3.9 9.0 - - - +
841F ARG* 2.8 51.1 + - - +
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Residues in contact with ILE 787 (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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783F VAL* 3.0 39.6 + - + +
784F GLU* 3.9 3.1 - - - +
786F ASN* 1.3 88.0 + - - +
788F ILE* 1.3 65.8 + - - +
789F PHE* 4.3 2.8 - - - +
798F TYR* 3.8 29.8 - - + +
801F VAL* 5.4 3.6 - - + -
802F ILE* 5.2 10.1 - - + -
807F LEU* 4.7 15.0 - - + -
811F ILE* 5.9 0.2 - - + -
837F ILE* 4.1 16.4 - - + -
840F ALA* 4.6 22.0 - - + -
841F ARG* 4.4 13.4 - - - +
844F TYR* 3.5 21.8 - - + +
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Residues in contact with ILE 788 (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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784F GLU* 2.8 31.1 + - + +
785F GLU* 3.7 4.7 - - - +
787F ILE* 1.3 79.0 - - - +
789F PHE* 1.3 67.7 + - - +
790F GLU* 3.5 5.4 - - - +
791F SER* 3.2 50.0 - - - +
793F PHE* 3.6 38.4 - - + -
798F TYR* 4.7 5.6 - - + -
844F TYR* 3.6 16.4 - - + -
845F GLN* 4.9 2.9 - - - +
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Residues in contact with PHE 789 (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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777F TRP* 6.4 1.6 - + - -
779F LEU* 5.3 14.4 - - + -
785F GLU 3.0 13.5 + - - -
786F ASN* 3.9 13.9 - - - +
787F ILE 3.4 2.9 - - - +
788F ILE* 1.3 78.6 - - - +
790F GLU* 1.3 70.4 + - + +
791F SER* 4.5 1.2 - - - -
841F ARG* 5.5 8.3 - - + +
845F GLN* 3.2 24.9 + - - +
1212F THR* 6.1 0.7 - - - -
1213F ILE* 5.2 4.9 - - + -
1216F PHE* 3.2 50.9 - + + -
1218F TYR* 3.3 32.6 - + + -
1222F PHE* 3.7 34.1 - + - -
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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