Contacts of the helix formed by residues 89 - 96 (chain B) in PDB entry 3EXG
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 ALA 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 3.6 17.0 - - + +
60B MET* 3.8 8.7 - - - +
63B ALA* 3.5 28.9 - - + -
80B PHE* 4.1 14.4 - - + -
85B PHE 4.2 0.2 + - - -
86B SER 2.5 15.4 + - - +
88B GLN* 1.3 74.7 - - - +
90B ILE* 1.3 61.2 + - - -
91B ASP 3.0 5.3 + - - -
92B GLN* 3.0 15.5 + - - +
93B VAL* 3.3 11.2 + - - +
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Residues in contact with ILE 90 (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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86B SER 2.8 10.8 + - - +
87B MET* 3.6 17.5 - - + +
88B GLN 3.4 1.0 - - - -
89B ALA* 1.3 77.5 - - - +
91B ASP* 1.3 59.6 + - - +
93B VAL* 3.2 8.8 + - - +
94B ILE* 2.9 32.4 + - + +
132B PHE* 5.1 1.3 - - + -
135B TRP* 3.7 34.3 - - + -
136B TYR* 3.8 28.5 - - + +
87D MET* 3.4 30.7 - - + +
90D ILE* 4.0 9.9 - - + -
135D TRP* 4.0 22.7 - - + -
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 3.3 31.2 - - - +
140A ALA* 4.3 5.4 - - - +
60B MET* 3.5 27.3 - - + +
88B GLN 5.2 0.2 + - - -
89B ALA 3.0 0.8 + - - -
90B ILE* 1.3 77.3 - - - +
92B GLN* 1.3 60.3 + - - +
93B VAL 3.1 0.9 - - - -
94B ILE 4.4 0.2 - - - +
95B ASN* 2.9 57.1 + - - +
96B SER* 3.5 1.2 + - - -
84D ASN 4.5 2.0 - - - +
87D MET* 3.8 34.3 + - + +
88D GLN* 3.7 6.8 - - + +
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Residues in contact with GLN 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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140A ALA* 3.0 33.1 + - - +
143A PRO* 4.1 2.4 - - - +
144A LEU* 3.6 8.3 - - - +
174A GLN* 3.3 17.8 + - - -
60B MET* 3.8 22.1 - - + +
63B ALA* 4.2 9.0 - - + +
64B GLY* 3.5 40.3 - - - +
67B VAL* 4.1 6.8 - - + +
89B ALA 3.0 8.5 + - - +
91B ASP* 1.3 77.9 - - - +
93B VAL* 1.3 61.3 + - - +
96B SER* 3.0 31.0 + - - -
97B ALA* 3.1 22.7 + - - +
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Residues in contact with VAL 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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63B ALA* 5.4 0.2 - - + -
80B PHE* 4.5 12.1 - - + -
86B SER* 5.7 0.2 - - - +
89B ALA* 3.8 11.4 - - + +
90B ILE* 3.2 12.7 + - - +
91B ASP 3.1 0.6 - - - -
92B GLN* 1.3 80.0 - - + +
94B ILE* 1.3 59.0 + - + +
97B ALA* 3.2 7.3 - - - +
98B ALA* 3.1 26.0 + - - +
114B PHE* 3.5 48.9 - - + -
136B TYR* 4.1 24.7 - - + +
142B LEU* 4.1 17.3 - - + -
168B VAL* 4.6 1.3 - - + -
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Residues in contact with ILE 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 ILE* 2.9 25.2 + - + +
93B VAL* 1.3 73.9 - - - +
95B ASN* 1.3 61.8 + - - +
98B ALA* 3.4 11.9 - - + +
99B LYS* 3.4 30.7 + - + +
136B TYR* 4.5 9.2 - - + -
139B CYS* 3.4 34.8 - - + -
142B LEU* 3.9 20.0 - - + -
87D MET* 4.0 12.1 - - + -
130D GLN* 3.5 25.6 - - - +
135D TRP* 3.9 20.9 - - + -
266D TRP* 5.1 0.2 - - + -
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Residues in contact with ASN 95 (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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137A ILE* 4.1 17.9 - - + +
91B ASP* 2.9 26.4 + - - +
94B ILE* 1.3 74.8 - - - +
96B SER* 1.3 67.6 + - - +
99B LYS* 2.8 38.1 + - - +
100B THR* 4.4 0.3 + - - -
103B MET* 4.3 7.4 - - - +
84D ASN 4.5 0.4 + - - -
87D MET* 2.8 32.4 - - - +
127D GLN* 2.8 46.0 + - + +
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Residues in contact with SER 96 (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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135A ASN* 5.7 0.9 - - - -
140A ALA* 4.3 12.0 - - - +
144A LEU* 4.2 15.3 - - - +
67B VAL* 4.0 14.0 - - - +
71B MET* 5.1 2.8 - - - +
91B ASP* 3.5 1.8 + - - -
92B GLN* 3.0 43.2 + - - -
95B ASN* 1.3 80.5 - - - +
97B ALA* 1.3 59.8 + - - +
100B THR* 2.7 31.0 + - - -
110B VAL* 4.5 1.0 - - - +
127D GLN* 4.7 2.3 + - - +
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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