Contacts of the helix formed by residues 89 - 95 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59R GLU* 3.6 15.0 - - + +
60R MET* 4.1 8.1 - - - +
63R ALA* 3.4 29.4 - - + -
80R PHE* 4.1 17.0 - - + -
86R SER 2.6 11.9 + - - +
88R GLN* 1.3 72.9 - - - +
90R ILE* 1.3 66.2 + - - +
91R ASP* 3.0 3.6 - - - -
92R GLN* 2.9 17.4 + - - +
93R VAL* 3.3 11.3 + - - +
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Residues in contact with ILE 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86R SER* 2.8 9.9 + - - +
87R MET* 3.4 20.5 + - + +
88R GLN 3.4 0.2 - - - -
89R ALA* 1.3 77.4 - - - +
91R ASP* 1.3 62.3 + - - +
93R VAL* 3.0 8.5 + - - +
94R ILE* 2.9 38.3 + - + +
132R PHE* 5.2 0.9 - - + -
135R TRP* 3.9 31.0 - - + -
136R TYR* 3.6 36.6 - - + +
87T MET* 3.7 28.3 - - + +
90T ILE* 4.1 8.5 - - + -
135T TRP* 4.1 12.8 - - + -
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Residues in contact with ASP 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q ILE* 3.5 25.4 - - - +
140Q ALA* 4.3 10.0 - - - +
174Q GLN* 5.0 0.2 - - - +
60R MET* 4.1 21.7 - - + +
89R ALA 3.0 0.4 + - - -
90R ILE* 1.3 85.1 - - - +
92R GLN* 1.3 60.3 + - - +
95R ASN* 2.9 50.5 + - - +
96R SER* 3.7 1.0 + - - -
84T ASN 5.1 0.5 - - - +
87T MET* 4.1 25.9 + - + +
88T GLN* 3.4 21.7 - - + +
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Residues in contact with GLN 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Q ALA* 3.4 22.6 + - - +
143Q PRO* 4.1 3.8 - - - +
144Q LEU* 3.6 12.3 - - - +
174Q GLN* 3.2 25.5 + - - -
60R MET* 3.7 23.4 - - - +
63R ALA* 4.2 8.7 - - + +
64R GLY* 3.6 31.2 - - - +
67R VAL* 4.1 5.6 - - + +
89R ALA 2.9 8.3 + - - +
91R ASP* 1.3 80.2 + - - +
93R VAL* 1.3 59.9 + - + +
96R SER* 2.8 33.7 + - - -
97R ALA* 3.1 26.7 + - - +
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Residues in contact with VAL 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63R ALA* 5.4 0.2 - - + -
80R PHE* 4.6 10.8 - - + -
86R SER 5.8 0.2 - - - +
89R ALA* 3.6 16.2 - - + +
90R ILE* 3.0 10.7 + - - +
92R GLN* 1.3 80.8 - - + +
94R ILE* 1.3 60.1 + - + +
97R ALA* 3.2 7.0 - - - +
98R ALA* 3.1 24.8 + - - +
114R PHE* 3.6 46.7 - - + -
136R TYR* 4.1 27.1 - - + +
142R LEU* 4.3 14.8 - - + +
168R VAL* 4.8 1.3 - - + -
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Residues in contact with ILE 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90R ILE* 2.9 19.0 + - + +
93R VAL* 1.3 77.9 - - - +
95R ASN* 1.3 63.4 - - - +
98R ALA* 3.4 20.7 - - + +
99R LYS* 3.4 21.0 + - - +
136R TYR* 4.4 11.7 - - + -
139R CYS* 3.5 33.9 - - + -
142R LEU* 4.1 20.0 - - + -
87T MET* 4.1 11.7 - - + -
130T GLN* 3.7 25.8 - - - +
135T TRP* 4.1 19.1 - - + -
266T TRP* 5.0 0.9 - - + -
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Residues in contact with ASN 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q ILE* 3.8 19.0 - - + +
91R ASP* 2.9 27.3 + - - +
94R ILE* 1.3 79.9 - - - +
96R SER* 1.3 63.8 + - - +
99R LYS* 2.9 33.0 + - - +
103R MET* 3.8 11.3 - - - +
84T ASN* 4.5 0.8 + - - +
87T MET* 2.6 35.0 - - - +
127T GLN* 2.9 45.9 + - - +
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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