Contacts of the helix formed by residues 223 - 237 (chain A) in PDB entry 3OQN
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ASP* 2.2 45.4 + - - -
222A TYR* 1.3 70.5 - - - +
224A TYR* 1.3 69.6 + - + +
225A ASP* 2.8 26.2 - - + +
226A SER* 2.5 26.5 + - - -
227A GLY 3.1 4.7 + - - -
250A GLU* 5.0 0.7 - - - -
251A MET* 3.8 3.0 - - - +
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Residues in contact with TYR 224 (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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222A TYR 3.4 3.8 + - - -
223A THR* 1.3 74.7 - - + +
225A ASP* 1.3 71.5 + - - +
227A GLY 3.5 0.9 + - - -
228A LEU* 3.3 23.1 - - + +
250A GLU* 3.6 23.8 + - - +
253A LEU* 3.5 31.0 - - + -
254A GLY* 3.2 31.9 - - - -
257A HIS* 3.1 27.6 + - - +
279C ARG* 6.5 0.2 - - + -
282C LEU* 4.1 10.8 - - + -
283C MET* 3.5 58.4 - - + -
285C ARG* 3.2 16.2 + - - -
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Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 2.8 16.1 + - + +
224A TYR* 1.3 87.4 - - - +
226A SER* 1.3 62.2 + - - +
227A GLY 2.8 6.2 + - - -
228A LEU* 3.0 28.3 + - - +
229A GLU* 3.0 28.1 + - - +
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLY* 4.2 7.8 - - - -
221A ASP* 2.6 50.9 + - - -
222A TYR 3.7 1.2 + - - -
223A THR* 2.5 31.0 + - - -
225A ASP* 1.3 73.8 - - - +
227A GLY* 1.3 55.5 + - - +
229A GLU* 3.5 15.6 + - - +
230A ALA* 3.1 28.2 + - - +
251A MET* 3.9 4.0 - - - +
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Residues in contact with GLY 227 (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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184A VAL* 5.2 0.7 - - - -
223A THR 3.1 7.1 + - - -
224A TYR 3.5 4.5 + - - -
225A ASP 2.8 2.6 - - - -
226A SER* 1.3 77.1 + - - +
228A LEU* 1.3 63.0 + - - -
230A ALA* 3.0 5.4 + - - +
231A LEU* 2.9 20.1 + - - +
251A MET* 3.7 28.9 - - - -
254A GLY 3.3 7.2 - - - +
255A ILE* 3.4 11.5 - - - +
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Residues in contact with LEU 228 (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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224A TYR* 3.3 40.4 - - + +
225A ASP* 3.0 24.3 + - - +
227A GLY* 1.3 75.3 - - - +
229A GLU* 1.3 65.9 + - + +
230A ALA 3.0 1.2 + - - -
231A LEU* 3.2 11.1 + - - +
232A GLN* 3.2 22.8 + - - +
254A GLY* 2.8 20.1 + - - +
257A HIS* 4.2 10.1 - - + -
258A ALA* 3.2 39.3 - - + +
261A ASP* 5.4 0.9 - - - +
285C ARG* 4.4 8.1 - - - +
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Residues in contact with GLU 229 (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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225A ASP* 3.0 35.7 + - - +
226A SER* 3.5 11.0 + - - +
228A LEU* 1.3 77.7 - - + +
230A ALA* 1.3 59.2 + - - +
232A GLN* 3.7 20.5 + - - +
233A HIS* 3.4 19.4 + - - +
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Residues in contact with ALA 230 (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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184A VAL* 4.2 19.1 - - + -
218A ALA* 4.1 22.8 - - + +
219A GLU 6.0 0.7 - - - -
220A GLY* 5.6 2.7 - - - -
226A SER 3.1 19.5 + - - +
227A GLY 3.0 7.4 + - - +
229A GLU* 1.3 75.8 - - - +
231A LEU* 1.3 66.1 + - - +
232A GLN 3.1 1.1 - - - -
233A HIS* 3.3 6.9 + - - +
234A LEU* 3.2 26.9 + - - +
255A ILE* 5.1 0.2 - - - -
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Residues in contact with LEU 231 (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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227A GLY 2.9 10.8 + - - +
228A LEU 3.2 6.0 + - - +
230A ALA* 1.3 77.6 - - - +
232A GLN* 1.3 62.5 + - + +
234A LEU* 3.4 6.5 + - - +
235A MET* 3.1 39.9 + - + +
244A ILE* 4.5 6.7 - - + -
255A ILE* 3.2 42.8 - - + +
258A ALA* 3.1 43.1 - - + +
259A ALA* 3.2 18.4 - - + +
262A GLN* 3.5 21.5 - - - +
270A LEU* 4.3 4.3 - - + -
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Residues in contact with GLN 232 (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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228A LEU* 3.2 24.9 - - - +
229A GLU* 3.7 20.9 + - - +
231A LEU* 1.3 79.1 - - + +
233A HIS* 1.3 57.6 + - - +
235A MET* 3.0 4.7 + - - +
236A SER* 2.9 28.4 + - - -
258A ALA* 5.0 3.4 - - + +
262A GLN* 3.6 22.7 - - + +
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Residues in contact with HIS 233 (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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215A GLN* 4.4 14.1 - - + -
217A VAL 5.9 2.0 - - - -
218A ALA* 5.6 5.7 - - + +
229A GLU 3.4 9.8 + - - +
230A ALA* 3.3 10.3 + - - +
232A GLN* 1.3 78.7 - - - +
234A LEU* 1.3 66.3 + - + +
236A SER* 3.1 24.3 + - - -
237A LEU* 3.5 25.9 + - + +
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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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182A ALA* 3.4 27.4 - - + -
184A VAL* 4.4 11.2 - - + -
215A GLN 3.2 27.4 - - - +
216A PHE* 3.9 15.9 - - + +
218A ALA* 4.3 12.6 - - + +
230A ALA 3.2 12.8 + - - +
231A LEU 3.8 6.7 - - - +
232A GLN 3.2 0.8 - - - -
233A HIS* 1.3 80.9 + - - +
235A MET* 1.3 66.6 + - - +
236A SER 3.1 1.3 - - - -
237A LEU* 3.3 27.3 - - + +
240A LYS* 4.0 2.1 - - - +
241A PRO* 3.8 17.0 - - + +
244A ILE* 3.5 29.4 - - + -
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Residues in contact with MET 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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231A LEU* 3.1 31.4 + - + +
232A GLN 3.0 5.3 + - - +
234A LEU* 1.3 77.2 - - - +
236A SER* 1.3 64.2 + - - +
237A LEU 3.2 8.2 + - - +
240A LYS* 3.7 37.9 + - + +
241A PRO* 4.8 8.3 - - - +
244A ILE* 4.7 5.6 - - + -
262A GLN* 3.6 24.7 - - - +
264A LEU* 3.5 23.8 - - + -
270A LEU* 3.4 34.5 - - + -
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Residues in contact with SER 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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232A GLN 2.9 12.1 + - - -
233A HIS* 3.1 20.2 - - - -
235A MET* 1.3 76.3 - - - +
237A LEU* 1.3 64.8 + - - +
238A ASP* 5.4 0.9 - - - +
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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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215A GLN* 3.4 57.2 - - + +
216A PHE* 3.7 23.6 - - + -
233A HIS* 3.7 27.1 - - + +
234A LEU* 3.3 21.8 - - + +
235A MET 3.2 8.5 - - - +
236A SER* 1.3 84.7 - - - +
238A ASP* 1.3 67.0 + - - +
239A LYS 3.9 9.9 - - - +
240A LYS* 3.6 8.4 + - - +
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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