Contacts of the helix formed by residues 250 - 261 (chain B) in PDB entry 1OBY
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 LYS 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B GLY 3.8 1.6 + - - -
249B LEU* 1.3 76.8 - - - +
251B ASP* 1.3 65.6 + - - +
252B SER* 3.7 19.7 - - - +
253B GLN* 3.0 44.6 + - - +
254B ILE* 3.1 11.4 + - - +
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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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213B PHE* 3.7 19.2 - - + -
214B LYS* 3.4 10.3 - - - +
215B ASN* 2.7 25.4 + - - -
216B GLY* 2.9 28.6 + - - -
249B LEU 5.0 0.7 - - - +
250B LYS* 1.3 72.9 - - - +
252B SER* 1.3 52.6 + - - +
254B ILE* 3.2 6.5 + - - +
255B ALA* 2.8 35.3 + - - +
2Q ASN 4.4 5.9 - - - +
4Q PHE* 3.7 21.8 - - + -
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Residues in contact with SER 252 (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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250B LYS* 3.7 20.6 - - - +
251B ASP* 1.3 77.6 - - - +
253B GLN* 1.3 61.8 + - - +
255B ALA* 3.6 4.3 + - - +
256B ASP* 2.9 36.8 + - - +
4Q PHE* 4.2 17.8 - - - -
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Residues in contact with GLN 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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249B LEU* 3.5 32.6 - - + +
250B LYS* 3.0 43.1 + - + +
252B SER* 1.3 81.5 + - - +
254B ILE* 1.3 60.2 + - - +
255B ALA 3.2 0.2 - - - -
256B ASP* 3.2 7.1 + - + +
257B ILE* 2.9 37.9 + - + +
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Residues in contact with ILE 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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213B PHE* 3.6 19.7 - - + -
216B GLY* 4.1 24.9 - - - +
238B ILE* 4.4 13.9 - - + +
241B ILE* 4.0 13.2 - - + -
246B VAL* 4.3 23.8 - - + +
249B LEU* 3.8 29.6 - - + +
250B LYS 3.1 9.1 + - - +
251B ASP* 3.6 12.8 - - - +
253B GLN* 1.3 77.0 - - - +
255B ALA* 1.3 62.2 + - - +
257B ILE* 3.2 9.3 + - - +
258B LEU* 3.0 34.5 + - + +
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Residues in contact with ALA 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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213B PHE* 3.9 9.8 - - + -
251B ASP 2.8 20.7 + - - +
252B SER* 3.8 5.2 - - - +
254B ILE* 1.3 73.7 - - - +
256B ASP* 1.3 58.4 + - - +
258B LEU* 3.4 7.2 + - - +
259B SER* 3.0 30.7 + - - -
4Q PHE* 3.5 30.7 - - + -
5Q TYR 6.2 0.2 - - - +
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Residues in contact with ASP 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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252B SER* 2.9 27.6 + - - +
253B GLN* 3.5 9.2 - - + +
254B ILE 3.2 0.2 - - - -
255B ALA* 1.3 75.3 - - - +
257B ILE* 1.3 55.4 + - + +
259B SER* 3.4 4.4 + - - -
260B THR* 2.8 50.1 + - + +
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Residues in contact with ILE 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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241B ILE* 3.9 31.2 - - + +
242B ASN* 6.1 1.6 - - + +
244B GLN* 3.5 40.6 - - - +
246B VAL* 3.9 17.0 - - + -
249B LEU* 4.0 12.1 - - + -
253B GLN* 2.9 23.5 + - + +
254B ILE* 3.2 5.6 + - - +
256B ASP* 1.3 75.7 - - + +
258B LEU* 1.3 58.4 + - - +
260B THR* 3.2 7.0 + - - +
261B SER* 2.9 29.7 + - - -
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Residues in contact with LEU 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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203B LYS* 2.8 36.5 + - - -
209B VAL* 5.4 2.2 - - + -
211B PHE* 4.0 12.1 - - + -
213B PHE* 3.9 11.4 - - + -
238B ILE* 5.6 0.2 - - + -
241B ILE* 4.0 15.5 - - + -
254B ILE* 3.0 37.5 + - + +
255B ALA* 3.8 4.9 - - - +
256B ASP 3.2 0.4 - - - -
257B ILE* 1.3 78.4 - - - +
259B SER* 1.3 52.0 + - - +
261B SER* 3.3 10.1 - - - -
265B VAL* 3.8 29.3 - - + +
267B ILE* 4.0 16.4 - - + -
6Q ALA* 3.8 29.6 - - + +
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Residues in contact with SER 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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203B LYS* 3.4 14.0 + - - +
207B GLY 5.8 1.3 - - - -
255B ALA 3.0 17.1 + - - -
256B ASP* 3.9 5.2 - - - -
258B LEU* 1.3 77.3 - - - +
260B THR* 1.3 64.1 + - - +
261B SER 3.7 1.6 - - - +
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Residues in contact with THR 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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256B ASP* 2.8 34.1 + - + +
257B ILE* 3.2 11.3 + - - +
259B SER* 1.3 79.2 - - - +
261B SER* 1.3 66.8 + - - +
262B GLY 3.7 0.3 + - - -
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Residues in contact with SER 261 (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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203B LYS* 2.7 24.2 + - - +
241B ILE* 5.6 2.2 - - - -
242B ASN* 2.9 29.2 + - - +
257B ILE* 2.9 14.7 + - - -
258B LEU* 3.3 16.6 - - - -
259B SER 3.7 2.1 - - - +
260B THR* 1.3 81.4 + - - +
262B GLY* 1.3 69.5 + - - +
264B VAL 3.5 4.9 + - - -
265B VAL* 3.7 10.4 - - - +
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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