Contacts of the helix formed by residues 184 - 193 (chain B) in PDB entry 3OUY
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 SER 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B LYS* 5.7 1.1 - - - -
147B GLU* 3.2 25.6 - - - -
179B ILE* 3.6 4.9 + - - -
182B TYR 3.0 5.1 + - - +
183B GLY* 1.3 77.8 - - - +
185B PHE* 1.3 59.4 + - - +
186B LEU* 3.5 7.9 + - - +
187B GLU* 3.5 18.5 + - - +
188B THR* 2.4 35.5 + - - -
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Residues in contact with PHE 185 (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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7B LEU* 4.1 24.0 - - + -
147B GLU* 2.8 27.7 + - - +
150B LEU* 3.4 32.3 - - + -
151B LEU* 3.3 32.8 - - + -
154B PHE* 3.7 21.3 - + + -
179B ILE* 3.6 12.1 - - - +
184B SER* 1.3 70.8 - - - +
186B LEU* 1.3 61.9 + - + +
188B THR* 3.3 2.6 + - - -
189B VAL* 3.1 50.2 + - + +
245B PHE* 4.6 10.8 - + - -
254B PHE* 3.4 27.6 - + - -
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Residues in contact with LEU 186 (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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3B VAL* 4.3 27.8 - - + -
4B GLU* 4.8 14.4 - - + +
7B LEU* 4.4 22.2 - - + +
147B GLU* 4.4 0.6 + - - -
184B SER* 3.2 7.6 + - - +
185B PHE* 1.3 82.9 - - + +
187B GLU* 1.3 61.1 + - - +
189B VAL* 4.1 4.5 - - - +
190B LYS* 3.1 50.4 + - + +
246B MET* 4.9 12.8 - - + +
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Residues in contact with GLU 187 (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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182B TYR* 3.1 32.2 - - + +
184B SER* 3.5 10.6 + - - +
185B PHE 3.4 0.4 - - - -
186B LEU* 1.3 78.7 - - - +
188B THR* 1.3 62.4 + - - +
190B LYS* 3.3 28.3 + - - +
191B ASN* 2.9 50.5 + - - +
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Residues in contact with THR 188 (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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151B LEU* 4.4 18.4 - - + -
178B LEU* 3.7 26.4 + - + -
179B ILE* 3.5 10.8 - - - +
182B TYR* 3.4 32.5 - - + +
184B SER 2.4 27.2 + - - -
185B PHE* 3.5 7.4 - - - -
186B LEU 3.3 0.2 - - - -
187B GLU* 1.3 75.8 - - - +
189B VAL* 1.3 65.2 + - - +
191B ASN* 3.4 2.3 + - - +
192B ALA* 3.0 25.6 + - - +
195B TRP* 5.1 4.5 - - + -
238B PHE* 5.1 4.3 - - + -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 5.7 2.2 - - + -
154B PHE* 4.6 9.6 - - + -
185B PHE* 3.1 46.1 + - + +
186B LEU* 4.1 5.2 - - - +
188B THR* 1.3 76.5 - - - +
190B LYS* 1.3 64.5 + - - +
191B ASN 3.4 0.3 + - - -
192B ALA* 3.5 7.6 + - - +
193B ARG* 3.4 15.6 - - - +
238B PHE* 5.3 3.4 - - + -
242B CYS* 3.6 37.1 - - + +
245B PHE* 4.5 11.4 - - + -
246B MET* 3.8 25.1 - - + -
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Residues in contact with LYS 190 (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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186B LEU* 3.1 40.8 + - + +
187B GLU* 3.3 31.1 + - - +
189B VAL* 1.3 77.4 - - - +
191B ASN* 1.3 62.5 + - - +
193B ARG* 3.0 42.6 + - - +
194B ARG* 3.9 29.2 + - - +
246B MET* 4.2 13.5 - - - -
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Residues in contact with ASN 191 (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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182B TYR* 3.2 44.6 - - + +
187B GLU* 2.9 40.5 + - - +
190B LYS* 1.3 74.3 - - - +
192B ALA* 1.3 67.3 + - - +
193B ARG 3.1 2.2 - - - -
194B ARG* 2.9 45.1 + - + +
195B TRP* 3.4 13.2 - - + -
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Residues in contact with ALA 192 (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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188B THR 3.0 18.4 + - - +
189B VAL 3.5 7.6 + - - +
191B ASN* 1.3 76.6 - - - +
193B ARG* 1.3 63.7 + - - +
195B TRP* 2.9 39.6 + - + +
238B PHE* 3.5 31.9 - - + -
239B VAL* 3.3 13.0 - - - +
242B CYS* 3.7 9.4 - - - -
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Residues in contact with ARG 193 (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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352A GLU* 5.1 9.0 + - - +
189B VAL 3.4 10.5 - - - +
190B LYS* 3.0 46.6 + - - +
192B ALA* 1.3 76.8 - - - +
194B ARG* 1.3 69.9 + - + +
195B TRP 3.6 2.9 + - - +
239B VAL* 3.9 12.7 - - - +
242B CYS* 3.8 5.4 - - + -
243B ARG* 3.4 72.3 + - + +
246B MET* 3.3 32.7 - - - +
247B GLU* 6.0 2.2 - - - +
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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