Contacts of the helix formed by residues 89 - 95 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59V GLU* 3.7 14.6 - - + +
60V MET* 4.1 7.9 - - - +
63V ALA* 3.6 27.8 - - + -
80V PHE* 3.9 17.0 - - + -
86V SER 2.7 9.1 + - - +
88V GLN* 1.3 78.8 - - - +
90V ILE* 1.3 63.7 + - - +
91V ASP* 3.1 3.6 - - - -
92V GLN* 2.9 18.4 + - - +
93V VAL* 3.2 11.7 + - - +
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Residues in contact with ILE 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86V SER* 2.8 11.7 + - - +
87V MET* 3.4 22.0 + - + +
89V ALA* 1.3 78.3 - - - +
91V ASP* 1.3 59.3 + - - +
93V VAL* 3.2 4.5 + - - +
94V ILE* 2.8 31.8 + - + +
132V PHE* 5.2 0.7 - - + -
135V TRP* 4.0 19.5 - - + -
136V TYR* 3.5 38.1 - - + +
87X MET* 3.6 24.5 - - + +
90X ILE* 4.3 8.3 - - + -
135X TRP* 3.6 33.4 - - + -
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Residues in contact with ASP 91 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137U ILE* 3.5 30.5 - - - +
140U ALA* 4.3 10.4 - - - +
60V MET* 4.7 10.1 - - - -
88V GLN 5.1 0.4 + - - -
89V ALA 3.1 1.0 + - - -
90V ILE* 1.3 83.2 - - - +
92V GLN* 1.3 61.0 + - - +
95V ASN* 2.8 54.9 + - - +
96V SER* 3.4 1.4 + - - -
84X ASN 4.3 2.8 - - - +
87X MET* 4.1 33.3 + - + +
88X GLN* 4.1 15.0 - - + +
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Residues in contact with GLN 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140U ALA* 3.5 19.9 + - - +
143U PRO* 3.9 4.0 - - - +
144U LEU* 4.0 5.9 - - - +
174U GLN* 3.0 27.1 + - - -
60V MET* 3.7 28.3 + - + +
63V ALA* 4.4 11.9 - - + +
64V GLY* 3.6 26.7 - - - -
67V VAL* 4.2 5.4 - - + +
89V ALA 2.9 10.1 + - - +
91V ASP* 1.3 75.8 + - - +
93V VAL* 1.3 67.7 + - + +
96V SER* 2.9 35.4 + - - -
97V ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63V ALA* 5.5 0.2 - - + -
80V PHE* 4.7 10.3 - - + -
86V SER 5.8 0.2 - - - +
89V ALA 3.2 13.2 + - - +
90V ILE* 3.2 8.5 + - - +
92V GLN* 1.3 79.2 - - + +
94V ILE* 1.3 58.1 + - - +
97V ALA* 3.6 5.0 - - - +
98V ALA* 3.0 27.0 + - - +
114V PHE* 3.6 46.2 - - + -
136V TYR* 4.0 27.4 - - + +
142V LEU* 3.8 23.6 - - + -
168V VAL* 4.7 2.5 - - + -
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Residues in contact with ILE 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90V ILE* 2.8 24.1 + - + +
93V VAL* 1.3 73.1 - - + +
95V ASN* 1.3 67.3 + - - +
98V ALA* 3.2 22.6 + - + +
99V LYS* 3.3 31.6 + - - +
136V TYR* 4.5 8.7 - - + -
139V CYS* 3.4 33.0 - - + -
142V LEU* 3.8 21.8 - - + -
87X MET* 4.1 8.3 - - + -
130X GLN* 3.8 15.3 - - - +
135X TRP* 4.0 22.9 - - + -
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Residues in contact with ASN 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137U ILE* 3.7 17.9 - - + +
91V ASP* 2.8 37.1 + - - +
94V ILE* 1.3 76.0 - - - +
96V SER* 1.3 60.0 + - - +
99V LYS* 3.0 46.0 + - - +
100V THR* 4.5 0.2 + - - -
103V MET* 4.3 5.0 - - - +
84X ASN 4.5 2.0 + - - -
87X MET* 3.0 28.3 - - - +
127X GLN* 2.9 43.4 + - - +
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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