Contacts of the helix formed by residues 178 - 188 (chain A) in PDB entry 2OA8
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 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A HIS* 3.6 0.2 - - - -
176A SER* 3.3 11.5 + - - -
177A TYR* 1.3 79.8 - - - +
179A LEU* 1.3 67.6 + - - +
180A GLY* 3.9 2.7 + - - -
181A SER* 2.9 32.4 + - - -
182A ILE* 3.2 8.3 + - - +
2D A 3.7 12.9 + - - -
3D C 3.5 22.9 - - - -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A HIS* 3.1 21.5 - - + +
178A SER* 1.3 72.2 - - - +
180A GLY* 1.3 61.6 + - - +
182A ILE* 3.3 4.3 + - - +
183A TYR* 3.2 21.3 + - - +
200A ASP* 3.6 42.6 - - + +
203A THR* 3.8 20.6 - - + -
204A LEU* 3.8 25.6 - - + +
207A ILE* 3.8 26.7 - - + +
3D C 2.8 18.8 + - - +
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER* 3.2 3.4 + - - -
179A LEU* 1.3 77.9 - - - +
181A SER* 1.3 60.5 + - - +
183A TYR* 3.9 0.7 - - - +
184A THR* 3.0 34.5 + - - -
191A PRO* 3.9 22.4 - - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 3.4 32.3 + - - -
178A SER* 2.9 23.8 + - - -
180A GLY* 1.3 74.1 - - - +
182A ILE* 1.3 65.1 + - - +
184A THR* 4.0 3.7 - - - -
185A ARG* 3.1 30.4 + - - +
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A HIS* 3.2 31.6 - - + +
155A SER 5.4 0.2 - - - +
156A ILE* 5.4 0.2 - - - -
159A LEU* 3.9 24.2 - - + -
163A GLU* 4.9 2.0 - - - +
177A TYR* 3.5 41.7 - - + +
178A SER 3.2 8.3 + - - +
179A LEU 3.8 3.6 - - - +
181A SER* 1.3 76.6 - - - +
183A TYR* 1.3 64.2 + - - +
185A ARG* 3.2 19.0 + - - +
186A LEU* 3.0 52.3 + - + +
207A ILE* 4.0 15.0 - - + -
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.4 27.2 - - + +
179A LEU 3.2 14.8 + - - +
180A GLY 3.9 2.7 - - - +
182A ILE* 1.3 81.4 - - - +
184A THR* 1.3 55.4 + - - +
187A TYR* 3.0 46.4 + + + +
189A GLN* 3.3 32.9 + - + -
190A ALA 3.7 14.1 + - - -
191A PRO* 3.6 19.0 - - + +
192A THR* 5.0 5.6 + - - -
203A THR* 3.6 37.0 - - + -
206A SER* 3.7 24.0 - - - -
207A ILE* 3.9 12.3 - - + +
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLY 3.0 19.6 + - - -
181A SER* 4.2 4.5 - - - -
183A TYR* 1.3 75.5 - - - +
185A ARG* 1.3 59.4 + - - +
188A TRP* 2.9 29.4 + - - +
189A GLN 3.2 30.7 + - - +
190A ALA* 4.1 2.9 - - - +
191A PRO* 4.1 8.1 - - - +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLU* 2.9 43.3 + - - -
175A LYS* 3.7 28.0 - - - +
176A SER* 2.4 41.6 + - - +
177A TYR* 4.1 2.6 - - - -
181A SER* 3.1 28.9 + - - +
182A ILE* 3.2 20.0 + - - +
184A THR* 1.3 78.1 - - - +
186A LEU* 1.3 63.5 - - + +
188A TRP* 3.5 15.4 + - - -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PRO* 3.9 4.3 - - - +
55A PRO* 3.7 18.7 - - - +
159A LEU* 4.4 1.8 - - + -
163A GLU* 3.6 24.2 - - - +
182A ILE* 3.0 34.1 + - + +
185A ARG* 1.3 82.9 - - + +
187A TYR* 1.3 78.5 + - + +
188A TRP* 4.1 1.7 + - - -
207A ILE* 4.1 17.9 - - + -
210A TRP* 3.8 61.0 + - + +
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO* 3.8 13.0 - - - +
55A PRO* 3.7 30.2 - - + +
56A PRO 3.8 7.9 - - - -
57A VAL* 4.0 20.6 - - + -
58A PRO* 3.2 30.7 - - + +
183A TYR* 3.0 40.3 + + + +
186A LEU* 1.3 97.0 - - + +
188A TRP* 1.3 71.9 + - - +
189A GLN* 3.4 13.7 + - + +
206A SER* 2.5 38.6 + - - -
207A ILE* 4.2 5.2 - - + -
210A TRP* 3.4 20.5 - + + +
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Residues in contact with TRP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS* 3.7 19.7 - - + -
54A PRO* 3.5 39.1 - - + +
184A THR* 2.9 27.3 + - - -
185A ARG* 3.5 23.6 + - - -
186A LEU 4.3 1.4 + - - -
187A TYR* 1.3 82.4 - - - +
189A GLN* 1.3 60.0 + - - +
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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