Contacts of the helix formed by residues 249 - 260 (chain B) 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 VAL 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A PHE 5.8 1.1 - - - +
232A LEU* 5.5 3.8 - - + -
249A VAL* 3.8 30.5 - - + -
250A ASP* 6.1 0.2 - - - -
253A ILE* 3.6 29.2 - - + -
226B ILE* 4.1 7.5 - - + +
231B PHE 3.8 17.7 - - - +
232B LEU* 2.8 33.4 + - + +
233B ALA* 4.6 0.2 - - - +
247B VAL 4.2 0.2 + - - -
248B THR* 1.3 71.4 - - - +
250B ASP* 1.3 68.8 + - + +
252B ILE* 3.1 7.7 + - + +
253B ILE* 3.0 23.3 + - - +
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Residues in contact with ASP 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASP* 3.6 47.4 - - + +
249A VAL* 6.0 0.2 - - - -
401A MG 4.0 6.5 - - - -
170B GLU* 4.4 8.0 - - - +
248B THR* 2.4 33.1 + - - -
249B VAL* 1.3 82.0 - - + +
251B ASP* 1.3 71.9 + - - +
253B ILE* 3.6 21.1 + - - +
254B ASP* 3.8 12.5 + - - +
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Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASP* 3.1 8.2 - - - +
99B ASN* 4.9 5.5 - - - +
141B ILE* 4.4 17.4 - - + +
247B VAL* 5.5 2.0 - - + -
248B THR* 3.1 18.0 + - - +
250B ASP* 1.3 82.4 - - - +
252B ILE* 1.3 66.4 + - - +
253B ILE 3.0 2.0 - - - -
254B ASP* 3.0 25.5 + - - +
255B VAL* 3.1 16.3 + - + +
408B MG 2.1 32.7 - - - -
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 4.9 8.3 - - + -
141B ILE* 4.1 16.8 - - + -
219B GLN 4.2 2.2 - - - +
222B VAL* 4.0 11.0 - - + -
223B ALA* 3.6 37.5 - - + +
226B ILE* 4.3 29.4 - - + -
247B VAL* 3.7 19.3 - - + -
248B THR 3.1 9.6 + - - +
249B VAL* 3.1 11.4 + - - +
251B ASP* 1.3 78.1 - - - +
253B ILE* 1.3 59.1 + - - +
255B VAL* 3.2 7.7 + - + +
256B ILE* 2.8 40.0 + - + +
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ILE* 4.4 15.3 - - + +
227A ARG* 3.6 36.6 - - + -
249A VAL* 3.5 31.2 - - + -
252A ILE* 5.0 1.3 - - + -
253A ILE* 3.9 23.8 - - + -
256A ILE* 3.9 19.5 - - + +
249B VAL 3.0 17.5 + - - +
250B ASP* 3.7 13.7 - - - +
251B ASP 3.0 0.6 - - - -
252B ILE* 1.3 75.0 - - - +
254B ASP* 1.3 60.6 + - - +
256B ILE* 3.3 8.7 + - - +
257B ASP* 2.9 27.8 + - - +
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Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ARG* 4.3 12.3 - - - +
230A ASP* 5.7 1.2 - - - +
401A MG 4.1 10.4 - - - -
250B ASP 3.8 12.6 - - - +
251B ASP* 3.0 19.8 + - - +
253B ILE* 1.3 75.1 - - - +
255B VAL* 1.3 60.4 + - + +
257B ASP* 3.2 8.4 + - - +
258B ASP* 2.9 38.6 + - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ILE* 4.2 25.1 - - + -
219B GLN* 3.5 54.5 - - + +
223B ALA* 4.8 5.2 - - + -
251B ASP 3.1 14.8 + - - +
252B ILE* 3.2 17.3 - - + +
254B ASP* 1.3 76.7 - - + +
256B ILE* 1.3 53.3 + - - +
258B ASP* 3.1 8.6 + - - +
259B GLU* 2.8 40.5 + - + +
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ILE* 5.5 8.1 - - + -
256A ILE* 4.4 18.6 - - + -
257A ASP* 3.9 11.0 - - - +
220B GLU* 5.3 7.6 - - - +
223B ALA* 3.2 29.4 - - + -
227B ARG* 3.0 33.9 - - - +
252B ILE* 2.8 30.4 + - + +
253B ILE* 3.6 8.7 - - + +
254B ASP 3.2 0.2 - - - -
255B VAL* 1.3 75.0 - - + +
257B ASP* 1.3 65.5 + - - +
259B GLU* 3.4 5.6 + - + +
260B ALA* 3.1 23.5 + - + +
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ARG* 2.6 50.9 + - - +
256A ILE* 3.9 11.1 - - - +
253B ILE* 2.9 17.2 + - - +
254B ASP* 3.2 14.1 + - - +
256B ILE* 1.3 77.2 - - - +
258B ASP* 1.3 68.5 + - - +
260B ALA* 3.2 17.9 + - - +
261B ALA 4.3 3.5 + - - +
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Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLN* 5.2 6.8 + - - +
254B ASP* 2.9 22.6 + - - +
255B VAL* 3.3 11.4 - - - +
257B ASP* 1.3 80.2 - - - +
259B GLU* 1.3 64.8 + - - +
260B ALA 3.0 6.9 + - - +
261B ALA 4.1 7.6 - - - +
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLU* 4.6 1.0 - - - +
219B GLN* 3.0 20.1 + - - +
220B GLU* 3.0 44.5 - - + +
255B VAL* 2.8 28.1 + - + +
256B ILE* 3.8 9.4 - - + +
258B ASP* 1.3 73.2 - - - +
260B ALA* 1.3 68.4 + - - +
407B MG 2.5 28.5 - - - -
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ALA* 4.2 25.1 - - + -
256B ILE* 3.1 12.1 + - + +
257B ASP* 3.3 15.3 - - - +
258B ASP 3.0 2.6 + - - +
259B GLU* 1.3 89.1 - - - +
261B ALA* 1.3 71.5 + - + +
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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