Contacts of the helix formed by residues 218 - 230 (chain A) in PDB entry 2OUX
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 ASP 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLU* 3.6 15.1 - - - +
137A THR* 4.8 2.0 - - - +
216A GLY 3.7 1.2 + - - -
217A ASP* 1.3 73.1 - - - +
219A GLN* 1.3 62.8 + - - +
220A GLU* 3.1 35.9 + - - +
221A ASP* 2.6 48.0 + - - +
222A VAL* 3.1 8.3 + - - -
259A GLU* 5.5 0.7 - - - +
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Residues in contact with GLN 219 (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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136A GLU* 3.0 56.6 + - + +
137A THR* 4.4 0.4 - - - +
138A ALA 5.2 0.9 - - - +
141A ILE* 4.0 24.1 - - + +
217A ASP 3.6 2.6 + - - -
218A ASP* 1.3 74.8 - - - +
220A GLU* 1.3 59.1 + - - +
222A VAL* 3.0 12.3 + - - +
223A ALA* 2.7 31.2 + - - +
255A VAL* 3.5 38.7 + - + +
258A ASP* 5.2 6.5 + - - +
259A GLU* 3.0 27.8 + - - +
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Residues in contact with GLU 220 (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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218A ASP* 2.8 22.5 + - - +
219A GLN* 1.3 78.3 - - - +
221A ASP* 1.3 58.2 + - - +
223A ALA* 3.4 7.9 + - + +
224A GLN* 3.0 26.5 + - - +
227A ARG* 4.5 4.8 + - - +
255A VAL* 5.3 0.9 - - - -
259A GLU* 3.4 49.9 - - + +
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Residues in contact with ASP 221 (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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213A VAL* 5.9 0.4 - - - -
217A ASP* 5.0 7.9 - - + +
218A ASP* 2.6 38.3 + - - +
220A GLU* 1.3 72.7 - - - +
222A VAL* 1.3 65.0 + - - +
224A GLN* 3.1 9.4 + - - +
225A THR* 3.1 24.2 + - - -
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Residues in contact with VAL 222 (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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138A ALA* 4.1 25.8 - - + -
141A ILE* 4.5 2.7 - - + -
213A VAL* 4.3 18.6 - - + -
217A ASP* 4.4 6.7 - - + -
218A ASP 3.1 11.6 + - - +
219A GLN* 3.0 14.5 + - - +
221A ASP* 1.3 77.0 - - - +
223A ALA* 1.3 59.0 + - - +
225A THR* 3.0 11.2 + - - -
226A ILE* 2.7 38.6 - - + +
234A VAL* 4.3 6.1 - - + -
247A VAL* 3.8 35.0 - - + -
252A ILE* 4.5 3.1 - - + -
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Residues in contact with ALA 223 (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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219A GLN 2.7 19.9 + - - +
220A GLU* 3.5 9.6 - - + +
222A VAL* 1.3 74.0 - - - +
224A GLN* 1.3 56.5 + - - +
226A ILE* 3.2 3.7 + - - +
227A ARG* 2.9 37.0 + - - +
252A ILE* 3.9 30.5 - - + +
255A VAL* 4.8 7.0 - - + -
256A ILE* 4.2 17.1 - - + +
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Residues in contact with GLN 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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220A GLU 3.0 14.4 + - - +
221A ASP* 3.1 13.2 + - - +
223A ALA* 1.3 77.8 - - - +
225A THR* 1.3 56.1 + - - +
227A ARG* 3.3 30.9 + - - +
228A ASP* 2.8 71.2 + - - +
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Residues in contact with THR 225 (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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211A ILE* 4.0 19.7 - - + -
213A VAL* 4.3 12.3 - - + +
221A ASP 3.1 11.7 + - - -
222A VAL* 3.0 11.1 + - - -
224A GLN* 1.3 75.3 - - - +
226A ILE* 1.3 66.6 + - + +
228A ASP* 4.7 2.5 - - - -
229A TYR* 2.9 53.3 + - + +
231A PHE* 4.9 2.7 - - + -
234A VAL* 4.3 12.1 - - + -
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Residues in contact with ILE 226 (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 VAL* 2.7 21.0 + - + +
223A ALA 3.2 7.8 + - - +
225A THR* 1.3 83.7 - - + +
227A ARG* 1.3 58.6 + - - +
230A ASP* 3.0 27.9 + - - -
231A PHE* 3.4 29.3 + - + +
233A ALA 5.5 0.9 - - - -
234A VAL* 3.5 34.5 - - + +
247A VAL 5.1 1.1 - - - +
249A VAL* 4.0 22.2 - - + +
252A ILE* 3.2 33.2 - - + -
250B ASP* 5.9 0.2 - - - +
253B ILE* 4.4 7.1 - - + +
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Residues in contact with ARG 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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220A GLU* 4.5 4.8 + - - +
223A ALA* 2.9 20.9 + - - +
224A GLN* 3.3 45.3 + - - +
226A ILE* 1.3 79.5 - - - +
228A ASP* 1.3 61.7 + - - +
230A ASP* 3.1 1.4 - - - +
256A ILE* 3.7 25.7 - - + +
401A MG 2.0 36.8 - - - -
253B ILE* 3.6 23.6 - - + -
254B ASP* 4.3 7.4 - - - +
257B ASP* 2.6 50.5 + - - +
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Residues in contact with ASP 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 GLN* 2.8 55.0 + - - +
225A THR* 4.0 3.5 - - - +
227A ARG* 1.3 77.2 - - - +
229A TYR* 1.3 66.8 + - + +
230A ASP* 3.5 6.6 + - - +
34B HIS* 4.5 0.5 - - - -
36B TYR* 3.6 61.5 + - + +
68B VAL* 5.3 4.3 - - - +
70B GLU* 5.5 2.9 - - - +
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Residues in contact with TYR 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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211A ILE* 3.9 18.6 - - + +
225A THR* 2.9 40.0 + - + +
228A ASP* 1.3 78.1 - - + +
230A ASP* 1.3 72.4 + - - +
231A PHE* 3.2 36.9 + + + -
7B MSE 4.4 5.0 - - - +
34B HIS* 3.1 54.6 + + + -
36B TYR* 3.7 21.9 - + + -
37B GLU* 2.9 38.8 + - + +
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Residues in contact with ASP 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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174A TYR* 4.8 1.7 + - - -
226A ILE 3.0 11.8 + - - -
227A ARG 3.1 0.8 - - - +
228A ASP 4.2 5.1 - - - +
229A TYR* 1.3 79.5 - - - +
231A PHE* 1.3 62.6 + - - +
232A LEU 4.1 0.5 + - - -
401A MG 2.2 32.9 - - - -
34B HIS* 5.7 1.1 - - + -
35B ILE* 5.4 0.9 - - + +
68B VAL* 3.7 26.5 - - - +
250B ASP* 3.6 38.0 - - + +
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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