Contacts of the strand formed by residues 782 - 788 (chain G) in PDB entry 5FUR
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 ASP 782 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778G MET* 3.5 35.9 - - + +
779G PRO* 3.2 21.7 + - - +
780G GLU 3.3 1.4 + - - -
781G THR* 1.3 102.7 + - - +
783G PHE* 1.3 64.8 + - - +
797G LEU 4.8 3.5 + - - +
17H ILE* 3.9 13.9 - - + +
18H LEU 3.3 2.9 - - - -
19H ARG* 2.8 41.3 + - - +
29H ARG* 3.3 18.7 + - - -
136H ILE* 4.0 3.3 - - - +
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Residues in contact with PHE 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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778G MET* 5.6 2.0 - - - -
781G THR 3.6 20.9 - - - -
782G ASP* 1.3 76.5 - - - +
784G LEU* 1.3 59.5 - - - +
794G ILE* 3.6 31.0 - - + -
795G ARG 4.0 7.6 - - - +
796G GLU* 4.8 4.9 - - + +
797G LEU* 5.4 2.7 - - - +
17H ILE* 3.5 11.6 - - - +
18H LEU* 2.9 43.6 + - + +
20H LEU* 3.9 24.0 - - + -
25H ALA* 3.4 26.7 - - + -
28H VAL* 3.8 12.1 - - + -
29H ARG* 3.7 44.0 - - + -
32H VAL* 4.6 5.6 - - + -
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Residues in contact with LEU 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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699G LEU* 3.5 32.1 - - + -
701G LEU* 5.7 0.2 - - + -
783G PHE* 1.3 72.5 - - - +
785G ILE* 1.3 72.9 + - - +
786G ILE* 4.1 13.8 + - + +
793G TYR 3.8 0.2 - - - +
794G ILE* 3.3 6.4 - - - +
795G ARG* 2.9 46.4 + - + +
797G LEU* 3.7 23.4 - - + +
15H GLN* 3.8 17.7 - - + +
16H PHE 3.9 8.5 - - - +
17H ILE* 4.4 7.2 - - + -
76H SER* 5.0 1.3 - - - -
91H ILE* 3.8 29.2 - - + -
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Residues in contact with ILE 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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657G VAL* 4.0 9.9 - - + -
783G PHE* 4.9 0.2 - - + -
784G LEU* 1.3 79.7 - - - +
786G ILE* 1.3 64.3 + - - +
787G ARG 4.1 0.2 + - - -
792G TYR* 3.7 22.9 - - + -
793G TYR 3.3 7.0 - - - +
794G ILE* 3.8 31.0 - - + -
15H GLN* 3.3 7.4 - - - +
16H PHE* 2.8 73.1 + - + +
18H LEU* 3.6 32.3 - - + -
45H ILE* 4.5 7.0 - - + -
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Residues in contact with ILE 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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660G LEU* 4.2 11.4 - - + -
694G GLY* 3.5 36.1 - - - +
695G LYS* 3.6 16.8 - - + +
784G LEU* 4.4 9.2 - - + +
785G ILE* 1.3 76.3 - - - +
787G ARG* 1.3 65.0 + - - +
788G THR* 4.5 5.4 - - + -
792G TYR* 3.3 4.9 - - - -
793G TYR* 2.8 50.0 + - + +
795G ARG* 4.5 7.0 - - + -
13H GLU* 3.7 30.3 - - + +
14H SER 3.6 3.1 - - - +
15H GLN* 4.1 17.3 - - + +
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Residues in contact with ARG 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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641G LEU* 3.5 34.6 - - - +
642G LYS 2.5 36.4 + - - +
643G LYS* 4.1 4.6 - - - +
644G TYR* 3.4 44.4 + - - +
649G LEU* 4.1 9.6 - - + +
786G ILE* 1.3 74.7 - - - +
788G THR* 1.3 67.6 + - - +
791G GLY 3.8 2.9 - - - -
792G TYR* 3.9 33.4 + - + -
13H GLU* 4.6 0.5 - - - +
14H SER* 2.8 58.5 + - - +
16H PHE* 4.1 10.1 - - + -
47H LEU* 5.2 2.4 - - - +
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Residues in contact with THR 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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644G TYR* 3.4 10.7 - - - -
649G LEU* 3.3 15.4 - - - +
695G LYS* 4.4 25.8 + - - +
786G ILE* 4.5 8.7 - - + -
787G ARG* 1.3 78.4 - - - +
789G ARG* 1.3 65.5 + - - +
790G GLN* 3.0 25.6 + - - +
791G GLY 3.0 22.2 + - - -
793G TYR* 4.0 6.1 - - + -
13H GLU* 4.6 11.0 - - + +
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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