Contacts of the helix formed by residues 807 - 813 (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 LEU 807 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783F VAL* 5.0 2.7 - - + -
787F ILE* 4.7 13.9 - - + -
802F ILE* 3.3 17.6 + - + +
805F CYS* 4.2 10.8 - - + +
806F SER* 1.3 75.1 - - - +
808F GLN* 1.3 61.1 + - - +
809F PRO* 3.3 3.6 - - - -
810F ASP* 2.8 25.9 + - + +
811F ILE* 2.8 45.7 + - + +
833F GLN* 4.3 13.5 - - + -
836F ARG* 3.7 25.6 - - + +
837F ILE* 3.9 27.6 - - + +
840F ALA* 6.1 2.0 - - + -
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Residues in contact with GLN 808 (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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799F LYS* 5.6 4.0 - - - +
802F ILE* 3.1 35.0 - - + +
803F GLU* 4.4 24.0 + - + +
806F SER* 3.4 1.3 - - - -
807F LEU* 1.3 77.2 - - - +
809F PRO* 1.3 69.7 - - + +
811F ILE* 3.1 16.2 + - - +
812F ASP* 2.9 23.4 + - - +
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Residues in contact with PRO 809 (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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806F SER* 3.6 15.3 - - - +
807F LEU 3.4 4.5 - - - -
808F GLN* 1.3 94.0 - - + +
810F ASP* 1.3 64.3 + - - +
812F ASP* 3.5 8.1 + - + +
813F ILE* 3.3 21.0 + - - +
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Residues in contact with ASP 810 (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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806F SER 5.0 2.1 - - - +
807F LEU* 2.8 20.7 + - + +
809F PRO* 1.3 80.3 - - - +
811F ILE* 1.3 62.6 + - - +
813F ILE* 3.0 25.7 - - - +
814F LEU* 3.2 14.9 - - - +
833F GLN* 3.2 24.7 + - - +
836F ARG* 2.2 37.1 + - - -
863F LEU* 5.4 0.5 - - - +
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Residues in contact with ILE 811 (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* 5.0 9.6 - - + -
787F ILE* 5.9 0.4 - - + -
798F TYR* 5.6 1.6 - - - +
802F ILE* 3.6 39.9 - - + -
807F LEU* 2.8 34.9 + - + +
808F GLN* 3.1 18.6 + - - +
810F ASP* 1.3 75.5 - - - +
812F ASP* 1.3 66.2 + - - +
814F LEU* 3.1 19.7 + - + +
817F GLY* 3.1 45.3 - - - +
818F ASP* 3.6 12.1 - - + +
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Residues in contact with ASP 812 (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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808F GLN 2.9 12.7 + - - +
809F PRO* 3.7 10.8 - - + +
811F ILE* 1.3 78.5 - - - +
813F ILE* 1.3 60.0 + - - +
814F LEU 3.2 8.3 + - - +
817F GLY* 5.3 0.6 - - - -
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Residues in contact with ILE 813 (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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809F PRO 3.3 7.6 + - - +
810F ASP* 3.0 34.3 - - - +
812F ASP* 1.3 76.9 - - - +
814F LEU* 1.3 68.2 + - + +
815F PRO* 3.7 2.1 - - - +
833F GLN* 4.6 9.2 - - - +
2001F ADP 6.0 1.8 - - - +
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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