Contacts of the helix formed by residues 228 - 236 (chain E) in PDB entry 2OME
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 228 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E TYR* 3.5 13.5 - - - -
226E VAL* 3.6 4.3 - - - +
227E TYR* 1.3 85.6 - - + +
229E LEU* 1.3 63.5 + - - +
230E GLN* 3.8 10.3 + - - +
231E ASP* 3.2 39.0 + - - +
232E LEU* 3.3 9.0 + - - +
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Residues in contact with LEU 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E ILE* 4.0 28.3 - - + -
209E TYR* 3.5 32.3 + - + +
228E THR* 1.3 73.4 - - - +
230E GLN* 1.3 62.3 + - - +
232E LEU* 3.1 4.9 + - + +
233E LEU* 2.9 44.3 + - + +
252E LEU* 3.9 34.1 - - + +
253E ILE* 5.3 2.0 - - + -
257E THR* 4.3 22.0 - - + -
260E GLN* 5.1 0.7 - - - +
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Residues in contact with GLN 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E THR* 3.9 9.9 + - - +
229E LEU* 1.3 78.4 - - - +
231E ASP* 1.3 63.7 + - - +
233E LEU* 3.2 3.4 + - - +
234E TYR* 2.8 70.4 + - + -
256E PHE* 5.7 1.0 - - - -
260E GLN* 3.8 34.9 + - - +
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Residues in contact with ASP 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E VAL* 4.2 11.6 - - + +
227E TYR 5.6 1.0 + - - -
228E THR* 3.2 24.6 + - - +
230E GLN* 1.3 85.8 - - - +
232E LEU* 1.3 63.3 + - - +
234E TYR* 4.3 11.7 - - - -
235E GLN* 3.0 50.5 + - - +
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Residues in contact with LEU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E GLY* 4.3 5.4 - - - -
185E LEU 3.2 39.0 - - - +
186E ILE* 3.9 19.5 - - + -
207E ILE* 4.5 3.6 - - + +
208E PHE* 4.1 4.5 - - - +
209E TYR* 3.6 24.0 - - + +
226E VAL* 3.8 16.9 - - + +
228E THR 3.3 7.0 + - - +
229E LEU* 3.1 9.4 + - + +
231E ASP* 1.3 77.2 - - - +
233E LEU* 1.3 79.2 + - + +
235E GLN* 3.5 2.3 + - - -
236E SER* 2.7 41.5 + - - +
239E VAL* 4.3 9.0 - - + -
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Residues in contact with LEU 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E ILE* 4.9 0.2 - - + -
229E LEU* 2.9 36.5 + - + +
230E GLN 3.7 3.6 - - - +
232E LEU* 1.3 82.1 - - + +
234E TYR* 1.3 64.4 + - - +
235E GLN 3.3 0.7 + - - -
236E SER* 3.5 13.8 + - - +
239E VAL* 3.8 21.8 - - + +
253E ILE* 4.3 13.7 - - + -
257E THR* 3.2 33.0 - - - +
260E GLN* 3.7 30.7 - - + +
261E MET* 3.8 34.7 - - + +
262E ARG 3.9 1.6 + - - -
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Residues in contact with TYR 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLY* 4.3 0.7 - - - -
348A ARG* 3.5 23.4 + - + +
351A GLU* 3.5 38.5 + - + +
352A SER* 3.0 32.1 - - - +
230E GLN* 2.8 58.6 + - + +
231E ASP* 3.9 14.1 - - - +
233E LEU* 1.3 77.6 - - - +
235E GLN* 1.3 59.0 + - + +
260E GLN* 3.0 44.4 + - + +
262E ARG* 2.9 26.5 + - - +
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Residues in contact with GLN 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A THR* 3.3 46.2 + - - +
347A GLY* 4.2 2.9 - - - -
352A SER* 5.5 0.4 - - - +
182E THR* 3.2 21.1 + - + +
207E ILE* 4.5 13.0 - - + +
224E GLN* 5.5 1.9 - - - +
226E VAL* 3.7 26.1 - - - +
231E ASP* 3.0 33.3 + - - +
232E LEU* 4.2 2.7 - - - +
234E TYR* 1.3 80.3 - - + +
236E SER* 1.3 60.5 + - - +
262E ARG* 3.4 17.4 + - - +
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Residues in contact with SER 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E THR* 3.8 7.5 - - - +
184E GLY* 3.2 35.6 + - - -
207E ILE* 4.1 3.3 - - - +
232E LEU* 2.7 24.1 + - - +
233E LEU 3.5 5.2 + - - +
234E TYR 3.5 1.0 - - - -
235E GLN* 1.3 79.8 - - - +
237E ASP* 1.3 63.8 + - - +
238E CYS 4.0 5.2 - - - -
239E VAL* 4.0 15.3 - - - +
261E MET* 5.9 0.2 - - - +
262E ARG* 3.4 20.1 + - - +
265E ALA* 4.4 5.2 - - - +
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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
------------------------------------------------------------
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