Contacts of the helix formed by residues 782 - 789 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781G ALA* 1.3 79.8 - - - +
783G VAL* 1.3 68.9 + - - +
784G GLU* 3.3 15.5 - - + +
785G GLU* 2.8 23.4 + - - +
786G ASN* 2.9 15.2 + - - +
818G ASP 3.2 19.1 - - - +
819G GLN* 3.5 22.6 - - + +
820G THR 3.5 4.3 - - - -
821G GLN* 2.2 30.5 + - - -
822G ILE* 4.5 0.2 - - - -
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Residues in contact with VAL 783 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781G ALA 3.6 0.6 + - - -
782G THR* 1.3 69.7 - - - +
784G GLU* 1.3 62.2 + - - +
786G ASN* 2.6 26.0 - - - +
787G ILE* 3.0 32.0 + - + +
798G TYR* 4.9 0.7 - - - +
807G LEU* 5.0 10.8 - - + -
811G ILE* 5.0 9.6 - - + -
814G LEU* 3.9 22.2 - - + -
817G GLY 3.9 4.0 - - - +
818G ASP* 3.1 20.0 - - - +
820G THR* 3.0 18.7 + - - +
822G ILE* 3.9 19.5 - - + -
837G ILE* 5.2 10.8 - - + -
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Residues in contact with GLU 784 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782G THR* 3.2 12.3 - - + +
783G VAL* 1.3 79.0 - - - +
785G GLU* 1.3 57.3 + - - +
787G ILE* 4.4 2.2 - - - -
788G ILE* 2.8 47.5 + - + +
793G PHE* 5.7 1.6 - - + -
798G TYR* 3.6 14.8 - - + +
818G ASP* 3.1 27.5 + - - +
819G GLN* 5.1 5.2 - - + +
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Residues in contact with GLU 785 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781G ALA* 3.6 13.2 - - + -
782G THR* 2.8 35.9 + - - +
784G GLU* 1.3 80.4 - - - +
786G ASN* 1.3 57.8 + - - +
788G ILE* 3.7 6.0 - - - +
789G PHE* 3.0 25.5 + - - -
790G GLU 4.8 0.7 + - - -
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Residues in contact with ASN 786 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778G LEU* 4.2 0.6 - - - +
779G LEU* 4.1 27.0 - - + +
781G ALA 5.3 1.1 - - - +
782G THR 2.9 14.1 + - - +
783G VAL* 2.6 15.7 - - - +
785G GLU* 1.3 74.5 - - - +
787G ILE* 1.3 89.3 + - - +
789G PHE* 3.8 14.3 + - - +
822G ILE* 3.1 34.1 - - - +
837G ILE* 3.9 8.6 - - - +
841G ARG* 2.8 51.4 + - - +
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Residues in contact with ILE 787 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783G VAL* 3.0 38.5 + - + +
784G GLU* 3.9 3.1 - - - +
786G ASN* 1.3 88.1 + - - +
788G ILE* 1.3 67.5 + - - +
789G PHE* 4.3 2.4 - - - +
798G TYR* 3.8 30.1 - - + +
801G VAL* 5.4 3.6 - - + -
802G ILE* 5.2 10.5 - - + -
807G LEU* 4.7 14.8 - - + -
811G ILE* 5.9 0.2 - - + -
837G ILE* 4.1 15.7 - - + +
840G ALA* 4.6 21.8 - - + -
841G ARG* 4.4 14.1 - - - +
844G TYR* 3.5 22.1 - - + +
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Residues in contact with ILE 788 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784G GLU* 2.8 30.9 + - + +
785G GLU* 3.7 5.2 - - - +
787G ILE* 1.3 78.9 - - - +
789G PHE* 1.3 69.1 + - - +
790G GLU* 3.5 5.4 - - - +
791G SER* 3.2 48.5 - - - +
793G PHE* 3.6 39.0 - - + -
798G TYR* 4.7 5.6 - - + -
844G TYR* 3.6 16.2 - - + -
845G GLN* 4.9 2.6 - - - +
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Residues in contact with PHE 789 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777G TRP* 6.4 1.3 - + - -
779G LEU* 5.3 13.5 - - + -
785G GLU 3.0 15.0 + - - -
786G ASN* 3.8 13.7 + - - +
787G ILE 3.4 2.4 - - - +
788G ILE* 1.3 78.9 - - - +
790G GLU* 1.3 70.3 + - + +
791G SER* 4.5 1.2 - - - -
841G ARG* 5.5 9.0 - - + +
845G GLN* 3.2 25.3 + - - +
1212G THR* 6.1 0.4 - - - -
1213G ILE* 5.2 5.6 - - + -
1216G PHE* 3.2 52.0 - + + -
1218G TYR* 3.3 31.5 - + + -
1222G PHE* 3.7 34.8 - + - -
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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