Contacts of the helix formed by residues 89 - 95 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59Z GLU* 3.8 5.6 - - + +
60Z MET* 3.6 20.2 - - - +
63Z ALA* 3.5 30.1 - - + -
80Z PHE* 4.3 11.7 - - + -
86Z SER 2.6 15.6 + - - +
88Z GLN* 1.3 73.8 - - - +
90Z ILE* 1.3 62.8 + - - -
91Z ASP 3.2 3.1 - - - -
92Z GLN* 3.0 15.2 + - + +
93Z VAL* 3.3 12.9 + - - +
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Residues in contact with ILE 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872 MET* 3.7 37.7 - - + +
902 ILE* 4.5 4.0 - - + -
1352 TRP* 3.7 28.7 - - + -
86Z SER* 3.0 6.1 + - - +
87Z MET* 3.5 18.5 + - + +
88Z GLN 3.6 0.4 - - - -
89Z ALA* 1.3 77.8 - - - +
91Z ASP* 1.3 66.3 + - - +
93Z VAL* 3.1 4.1 + - - -
94Z ILE* 3.0 26.5 + - + +
132Z PHE* 5.2 0.7 - - + -
135Z TRP* 3.9 22.2 - - + -
136Z TYR* 3.5 39.5 - - + +
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Residues in contact with ASP 91 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842 ASN 5.7 0.4 - - - +
872 MET* 4.1 26.4 + - + +
882 GLN* 4.2 8.5 - - + +
137Y ILE* 3.2 30.0 - - - +
140Y ALA* 4.0 9.9 - - - +
174Y GLN* 3.6 20.4 + - - -
60Z MET* 4.0 18.9 - - + +
89Z ALA 3.2 0.8 - - - -
90Z ILE* 1.3 79.7 - - - +
92Z GLN* 1.3 58.7 + - - +
95Z ASN* 2.9 49.5 + - - +
96Z SER* 3.6 0.9 + - - -
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Residues in contact with GLN 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Y ALA* 3.3 20.3 + - - +
143Y PRO* 4.1 3.6 - - - +
144Y LEU* 4.2 3.8 - - - +
174Y GLN* 3.2 28.3 + - - +
60Z MET* 3.8 23.5 + - - +
63Z ALA* 4.4 6.1 - - + -
64Z GLY* 3.7 35.5 - - - +
67Z VAL* 3.8 8.1 - - + +
89Z ALA 3.0 10.5 + - - +
91Z ASP* 1.3 79.9 + - - +
93Z VAL* 1.3 62.1 + - + +
96Z SER* 2.7 49.9 + - - -
97Z ALA* 3.2 9.2 + - - +
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Residues in contact with VAL 93 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Z ALA* 5.5 0.2 - - + -
80Z PHE* 4.6 11.4 - - + -
86Z SER 5.6 0.2 - - - +
89Z ALA* 3.5 14.8 - - + +
90Z ILE* 3.1 9.0 + - - +
92Z GLN* 1.3 79.7 - - + +
94Z ILE* 1.3 58.9 + - + +
97Z ALA* 3.3 7.0 - - - +
98Z ALA* 3.2 25.1 + - - +
114Z PHE* 3.8 46.7 - - + -
136Z TYR* 4.1 29.6 - - + +
142Z LEU* 4.1 16.8 - - + +
168Z VAL* 4.5 2.2 - - + -
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Residues in contact with ILE 94 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872 MET* 4.0 10.3 - - + -
1302 GLN* 3.7 25.8 - - - +
1352 TRP* 3.9 24.0 - - + -
90Z ILE* 3.0 20.1 + - + +
93Z VAL* 1.3 84.9 - - + +
95Z ASN* 1.3 66.9 + - - +
98Z ALA* 3.5 7.3 - - + +
99Z LYS* 3.4 37.0 + - - +
136Z TYR* 4.8 4.3 - - + -
139Z CYS* 3.3 34.5 - - + -
142Z LEU* 4.4 12.8 - - + -
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Residues in contact with ASN 95 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842 ASN 4.6 3.6 + - - -
872 MET* 3.1 28.0 - - - +
1272 GLN* 2.9 46.0 + - - +
137Y ILE* 3.7 16.7 - - + +
91Z ASP* 2.9 34.0 + - - +
94Z ILE* 1.3 76.5 - - - +
96Z SER* 1.3 62.6 + - - +
99Z LYS* 3.3 43.0 + - - +
100Z THR* 4.1 0.2 + - - -
103Z MET* 4.0 4.2 - - - +
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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