Contacts of the helix formed by residues 85 - 94 (chain B) in PDB entry 4FQG
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 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B THR 4.0 8.7 - - - +
84B SER* 1.3 78.8 - - - +
86B TRP* 1.3 64.3 + - - +
87B LYS* 3.6 8.1 + - - +
88B GLU* 3.0 39.0 + - - +
89B VAL* 2.9 22.7 + - - +
113B PHE* 3.7 4.3 - - - -
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Residues in contact with TRP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 4.0 17.9 - + - -
85B THR* 1.3 73.6 - - - +
87B LYS* 1.3 62.2 + - + +
89B VAL* 4.5 2.0 - - + +
90B LYS* 2.8 71.5 + - + +
93B ILE* 3.9 26.9 - - + -
99B CYS* 4.2 7.6 - - - -
106B ASP* 3.0 29.3 + - - -
109B LYS* 3.6 29.4 - - + -
110B GLN* 3.6 49.4 - - + +
113B PHE* 3.5 40.5 - + + -
114B GLU* 5.1 2.1 + - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B THR* 3.2 7.9 + - - +
86B TRP* 1.3 86.4 - - + +
88B GLU* 1.3 62.9 + - + +
90B LYS* 4.2 15.5 + - - +
91B LYS* 3.6 31.7 + - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B THR 4.5 1.8 - - - +
84B SER* 3.7 10.5 + - - -
85B THR* 3.0 42.0 + - - +
87B LYS* 1.3 77.0 - - + +
89B VAL* 1.3 66.3 + - + +
91B LYS* 3.2 30.1 + - - +
92B ILE* 3.9 9.1 + - - +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 4.2 2.5 - - + -
77B THR* 5.1 2.0 - - + -
80B ILE* 3.8 35.2 - - + -
84B SER* 3.8 12.6 - - - +
85B THR 2.9 16.3 + - - +
86B TRP* 4.1 4.3 - - + +
88B GLU* 1.3 74.0 - - + +
90B LYS* 1.3 66.3 + - - +
92B ILE* 3.0 22.5 + - + +
93B ILE* 3.3 32.4 + - + +
113B PHE* 3.5 34.8 - - + -
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TRP* 2.8 46.2 + - + +
87B LYS* 4.2 15.4 + - - +
88B GLU 3.3 0.4 - - - -
89B VAL* 1.3 78.3 - - - +
91B LYS* 1.3 65.5 + - - +
93B ILE* 4.1 8.1 - - + -
94B LYS* 3.2 33.0 + - + +
99B CYS* 5.5 2.2 - - - -
106B ASP* 3.4 28.5 - - - +
109B LYS* 5.8 0.9 - - + -
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 3.6 25.5 - - - +
88B GLU* 3.2 15.4 + - - +
89B VAL 3.1 1.0 - - - -
90B LYS* 1.3 83.5 - - + +
92B ILE* 1.3 59.7 + - + +
94B LYS* 3.8 25.5 - - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 4.0 24.5 - - + -
79B ALA* 3.8 30.1 - - + -
88B GLU 4.1 7.4 - - - +
89B VAL* 3.0 22.3 + - + +
91B LYS* 1.3 81.3 - - + +
93B ILE* 1.3 64.0 + - + +
94B LYS* 3.5 2.9 + - - +
95B GLU 4.9 1.0 + - - -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 4.3 3.6 - - + -
73B LEU* 4.1 21.8 - - + -
74B LEU* 4.1 17.9 - - + -
77B THR* 3.6 27.1 - - + +
86B TRP* 3.9 20.6 - - + -
89B VAL* 3.6 19.3 - - + +
90B LYS* 4.1 6.1 - - - +
92B ILE* 1.3 84.2 - - + +
94B LYS* 1.3 64.8 + - - +
95B GLU 3.2 3.1 - - - -
96B ASP* 3.0 17.9 + - - +
99B CYS* 3.6 35.9 - - + +
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS* 3.2 20.5 + - + +
91B LYS* 3.8 24.0 - - - +
92B ILE 3.5 2.0 - - - +
93B ILE* 1.3 77.2 - - - +
95B GLU* 1.3 89.7 + - + +
99B CYS* 4.8 7.3 - - - -
100B ILE* 3.3 23.0 + - - +
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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