Contacts of the helix formed by residues 233 - 244 (chain A) in PDB entry 2OQ1
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 THR 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.5 4.7 - - + -
117A PHE* 3.7 7.1 - - + -
156A ALA* 3.4 44.0 - - + +
157A THR* 3.9 11.0 - - + +
160A HIS* 6.1 0.2 - - - -
223A TYR* 3.8 12.9 - - - -
231A PHE* 3.4 10.9 - - - +
232A ASP* 1.3 88.3 - - + +
234A LEU* 1.3 63.3 + - - +
235A TRP 3.6 2.7 + - - -
236A GLN* 2.9 36.7 + - - +
237A LEU* 3.4 14.7 + - - +
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Residues in contact with LEU 234 (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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157A THR 5.2 1.2 + - - -
160A HIS* 3.7 40.6 + - + +
165A TRP* 4.6 3.8 - - + -
191A LEU* 4.6 10.3 - - + -
200A TYR* 3.7 42.6 - - + +
215A ILE* 4.0 27.1 - - + -
223A TYR* 3.7 35.0 - - + +
233A THR* 1.3 72.7 - - - +
235A TRP* 1.3 65.6 + - - +
237A LEU* 3.3 9.3 + - + +
238A VAL* 3.2 26.7 + - - +
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Residues in contact with TRP 235 (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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116A VAL* 3.9 13.7 - - + -
117A PHE* 3.5 65.2 - + + -
120A LEU* 3.6 24.4 - - + +
124A MSE 5.3 0.8 - - + +
156A ALA 5.0 0.7 - - - +
159A ALA* 4.2 22.7 - - + -
160A HIS* 4.3 6.6 + - - +
163A MSE 3.6 44.1 - - + +
165A TRP* 4.1 11.2 - + - -
233A THR* 3.3 5.5 + - - +
234A LEU* 1.3 80.2 - - - +
236A GLN* 1.3 64.1 + - + +
238A VAL* 3.5 1.4 + - - +
239A GLU* 3.1 63.2 + - + +
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Residues in contact with GLN 236 (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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41A CYS 4.8 1.8 + - - -
42A LEU* 3.6 21.5 + - - +
43A ARG 3.4 18.6 - - - +
44A SER 3.2 28.5 + - - +
45A LEU* 4.1 4.7 - - - +
117A PHE* 3.6 30.6 - - + -
231A PHE* 3.8 4.6 - - + -
232A ASP* 3.6 8.1 - - - +
233A THR* 2.9 38.6 + - - +
235A TRP* 1.3 81.7 - - + +
237A LEU* 1.3 59.4 + - - +
239A GLU* 3.8 2.5 - - - +
240A TYR* 2.9 32.2 + - - +
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Residues in contact with LEU 237 (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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191A LEU* 5.1 0.4 - - + -
202A LEU* 4.4 4.7 - - + -
215A ILE* 3.9 46.7 - - + -
223A TYR* 4.4 10.5 - - + -
224A CYS* 4.4 8.5 - - - -
225A ILE* 5.0 4.9 - - + -
231A PHE* 3.6 41.4 - - + -
233A THR 3.4 8.8 + - - +
234A LEU* 3.3 12.5 + - + +
235A TRP 3.3 0.4 - - - -
236A GLN* 1.3 78.8 - - - +
238A VAL* 1.3 76.9 + - + +
240A TYR* 3.5 1.4 - - - +
241A LEU* 3.0 48.0 + - + +
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Residues in contact with VAL 238 (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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165A TRP* 3.7 44.4 - - + +
189A PHE* 3.5 35.7 - - + -
191A LEU* 4.4 14.1 - - + -
202A LEU* 5.5 0.9 - - + -
234A LEU 3.2 16.4 + - - +
235A TRP 3.9 0.7 - - - +
237A LEU* 1.3 88.6 - - + +
239A GLU* 1.3 63.3 + - - +
241A LEU 3.3 1.6 + - - -
242A LYS* 3.2 27.1 + - - +
252A LEU* 3.6 11.1 - - + +
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Residues in contact with GLU 239 (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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116A VAL* 5.7 2.6 - - + +
163A MSE 5.1 2.9 - - - +
165A TRP* 4.3 11.4 + - - -
235A TRP* 3.1 66.6 + - + +
236A GLN* 4.0 3.4 - - - +
238A VAL* 1.3 76.6 - - - +
240A TYR* 1.3 62.3 + - - +
242A LYS* 2.9 52.4 + - + +
243A LEU* 3.6 14.1 - - - +
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Residues in contact with TYR 240 (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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42A LEU* 4.3 22.0 - - + +
43A ARG* 4.1 26.5 - - + -
229A THR* 4.3 3.3 + - + -
231A PHE* 3.4 26.9 - + + -
236A GLN 2.9 18.9 + - - +
237A LEU 3.2 0.9 + - - +
239A GLU* 1.3 72.8 - - - +
241A LEU* 1.3 64.5 + - + +
242A LYS 3.0 4.5 - - - -
243A LEU* 2.9 29.2 + - + +
244A LYS* 3.2 38.8 + - + +
246A ASP* 3.7 21.5 - - - -
313B GLU* 3.8 11.6 - - - +
315B PTR 2.9 41.6 + - - -
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Residues in contact with LEU 241 (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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202A LEU* 3.9 19.1 - - + -
225A ILE* 4.1 14.6 - - + -
231A PHE* 4.8 4.7 - - + -
237A LEU* 3.0 40.6 + - + +
238A VAL 3.3 0.9 + - - -
240A TYR* 1.3 80.8 - - + +
242A LYS* 1.3 57.0 + - - +
243A LEU 3.3 0.2 - - - -
244A LYS 3.3 7.4 - - - +
245A ALA* 3.8 7.4 - - - +
246A ASP* 3.7 37.5 - - + +
248A LEU* 3.9 12.8 - - + -
251A CYS* 3.1 13.9 - - - +
252A LEU* 3.0 34.1 + - + -
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Residues in contact with LYS 242 (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 MSE 5.9 2.2 - - - +
165A TRP* 4.4 10.9 - - - +
189A PHE* 3.9 25.4 - - - -
238A VAL* 3.2 20.0 + - - +
239A GLU* 2.9 41.6 + - - +
240A TYR 3.0 0.8 - - - -
241A LEU* 1.3 78.9 - - - +
243A LEU* 1.3 67.6 + - + +
251A CYS* 4.0 10.0 - - - -
252A LEU* 3.5 31.0 - - + +
253A LYS* 4.5 12.7 + - - +
255A ALA* 5.9 1.6 - - - +
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Residues in contact with LEU 243 (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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18A SER* 4.9 16.2 - - - -
42A LEU* 3.8 28.9 - - + -
239A GLU 3.6 17.0 - - - +
240A TYR* 2.9 14.8 + - + +
242A LYS* 1.3 85.1 - - + +
244A LYS* 1.3 72.1 + - - +
251A CYS* 4.8 5.1 - - - -
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Residues in contact with LYS 244 (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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18A SER* 5.5 3.6 - - - -
19A ARG* 3.8 18.2 - - - +
20A ALA 5.4 0.4 - - - +
42A LEU* 6.3 0.6 - - - +
240A TYR* 3.2 35.6 + - + +
241A LEU* 3.3 21.0 - - - +
242A LYS 3.6 0.2 - - - -
243A LEU* 1.3 90.6 - - - +
245A ALA* 1.3 66.0 + - - +
246A ASP* 3.3 6.5 + - + +
251A CYS* 3.9 6.7 - - - -
313B GLU* 2.9 43.5 + - + +
315B PTR 3.0 20.4 + - - -
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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