Contacts of the helix formed by residues 228 - 243 (chain B) in PDB entry 2OY0
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 ASN 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B GLN* 5.6 0.9 - - - +
227B GLY* 1.3 66.4 - - - -
229B VAL* 1.3 66.4 + - - +
230B VAL* 3.2 13.3 + - - +
231B HIS* 2.8 44.9 + - + +
232B SER* 2.9 12.3 + - - -
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Residues in contact with VAL 229 (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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186B PRO 5.7 0.2 - - - +
192B ILE* 4.5 13.7 - - + +
195B MET* 4.2 33.2 - - + -
196B GLU* 4.4 23.8 - - + +
199B GLN* 3.6 28.0 - - + +
206B LEU* 4.2 15.5 - - + +
227B GLY 3.1 8.0 + - - +
228B ASN* 1.3 69.5 + - - +
230B VAL* 1.3 68.0 + - - +
232B SER* 3.0 16.6 + - - -
233B VAL* 3.0 29.0 - - + +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 3.9 32.1 - - + -
196B GLU* 4.1 11.7 - - - +
228B ASN* 3.2 9.6 + - - +
229B VAL* 1.3 80.7 - - - +
231B HIS* 1.3 59.9 + - - +
233B VAL* 3.8 6.9 - - + +
234B ASN* 2.9 53.3 + - - +
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Residues in contact with HIS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASN* 2.8 32.6 + - + +
230B VAL* 1.3 78.9 - - - +
232B SER* 1.3 62.1 + - - +
234B ASN* 3.2 5.7 + - + -
235B MET* 3.0 60.9 + - + +
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 4.1 25.4 + - - -
219B MET* 3.7 8.0 - - - +
226B SER 4.8 3.3 + - - -
227B GLY* 4.3 13.9 + - - -
228B ASN 2.9 12.8 + - - -
229B VAL* 3.0 10.3 + - - -
231B HIS* 1.3 78.0 - - - +
233B VAL* 1.3 64.4 + - - +
235B MET* 3.6 19.6 + - - +
236B THR* 3.3 17.5 + - - -
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 3.8 28.9 - - + +
187B TYR* 4.3 16.4 - - + -
192B ILE* 4.6 10.3 - - + -
206B LEU* 4.0 22.9 - - + -
217B HIS* 3.5 5.7 - - + -
219B MET* 3.8 19.3 - - - -
229B VAL* 3.0 22.8 + - + +
230B VAL* 3.9 6.1 - - + +
232B SER* 1.3 75.0 - - - +
234B ASN* 1.3 62.6 + - + +
235B MET 3.4 0.2 - - - -
236B THR* 3.7 0.8 + - - -
237B SER* 2.7 34.3 + - - +
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Residues in contact with ASN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 5.4 3.3 - - - -
8B LEU* 4.0 30.9 + - + +
9B GLY 5.1 0.5 + - - -
230B VAL* 2.9 37.8 + - - +
231B HIS* 3.8 8.3 - - + +
232B SER 3.2 0.2 - - - -
233B VAL* 1.3 83.1 - - - +
235B MET* 1.3 63.4 + - - +
237B SER* 3.6 5.7 + - - -
238B GLN* 3.4 26.3 + - - +
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Residues in contact with MET 235 (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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231B HIS* 3.0 66.7 + - + +
232B SER* 3.6 13.9 + - - +
233B VAL 3.4 0.2 - - - -
234B ASN* 1.3 75.6 - - + +
236B THR* 1.3 67.2 + - - +
238B GLN* 3.0 27.7 + - - +
239B VAL* 3.1 18.2 + - + +
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Residues in contact with THR 236 (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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208B ARG* 3.6 34.4 - - + +
217B HIS* 4.3 10.1 - - + +
219B MET* 3.5 21.7 - - + +
232B SER 3.3 13.4 + - - -
233B VAL 3.9 7.4 - - - -
234B ASN 3.3 0.2 - - - -
235B MET* 1.3 74.8 - - - +
237B SER* 1.3 58.4 + - - +
238B GLN 2.9 1.3 - - - -
239B VAL* 2.7 29.5 + - + +
240B LEU* 2.8 40.4 + - + +
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.6 28.3 - - - -
9B GLY* 3.6 12.5 + - - -
12B TRP* 5.2 1.1 - - - +
187B TYR* 4.8 0.3 - - - +
217B HIS* 2.6 32.4 + - - -
233B VAL* 2.7 19.0 + - - +
234B ASN* 3.7 6.6 + - - -
236B THR* 1.3 78.1 - - - +
238B GLN* 1.3 57.4 + - - +
240B LEU* 4.0 3.1 - - - +
241B LEU* 3.0 35.7 + - - +
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Residues in contact with GLN 238 (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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8B LEU* 3.6 21.2 - - + +
234B ASN* 3.4 14.2 + - - +
235B MET* 3.0 22.9 + - - +
236B THR 2.9 0.6 - - - -
237B SER* 1.3 75.3 - - - +
239B VAL* 1.3 61.4 + - + +
241B LEU* 3.4 6.7 + - + +
242B GLY* 2.9 24.6 + - - -
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Residues in contact with VAL 239 (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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208B ARG* 6.4 2.5 - - + -
235B MET* 3.1 16.1 + - + +
236B THR* 2.7 20.1 + - + +
238B GLN* 1.3 71.6 - - + +
240B LEU* 1.3 60.3 + - + +
242B GLY* 2.7 22.3 + - - -
243B ARG* 3.0 46.4 + - + +
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Residues in contact with LEU 240 (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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12B TRP* 3.5 28.3 - - + +
27B TYR* 2.8 20.3 + - - +
208B ARG* 3.9 19.3 - - - +
214B ASN* 3.3 43.7 - - - +
216B THR 4.7 4.5 - - - +
217B HIS* 4.6 7.6 - - + -
236B THR* 2.8 58.1 + - + +
237B SER* 4.2 5.2 - - - +
239B VAL* 1.3 80.0 - - + +
241B LEU* 1.3 60.3 + - - +
242B GLY 3.6 0.2 + - - -
243B ARG* 3.8 8.7 + - - +
244B MET* 3.2 9.9 - - - +
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Residues in contact with LEU 241 (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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8B LEU* 3.9 24.0 - - + +
11B VAL* 3.7 26.2 - - + -
12B TRP* 4.1 15.3 - - + +
15B ARG* 4.3 12.3 - - - +
237B SER 3.0 24.6 + - - +
238B GLN* 3.8 7.0 - - + +
239B VAL 3.1 0.2 - - - -
240B LEU* 1.3 77.4 - - - +
242B GLY* 1.3 62.1 + - - +
244B MET* 3.2 40.5 - - + +
245B GLU* 3.6 16.1 - - - +
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Residues in contact with GLY 242 (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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238B GLN 2.9 11.1 + - - -
239B VAL* 2.7 9.4 + - - -
241B LEU* 1.3 75.6 - - - +
243B ARG* 1.3 55.0 + - - -
244B MET 2.9 10.5 + - - -
245B GLU* 3.1 14.4 + - - +
246B LYS* 3.4 15.3 + - - +
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Residues in contact with ARG 243 (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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27B TYR* 3.9 13.3 - - + -
30B GLU* 3.6 12.0 - - + +
31B ALA* 3.1 34.8 + - + +
32B ILE* 4.1 12.3 - - - +
208B ARG* 5.3 6.5 - - - +
210B PRO* 5.6 8.5 + - - +
214B ASN* 3.2 35.6 + - - +
239B VAL* 3.0 39.1 + - + +
240B LEU* 3.8 4.0 + - - +
241B LEU 3.5 0.2 - - - -
242B GLY* 1.3 74.7 - - - +
244B MET* 1.3 56.6 + - - +
245B GLU 3.4 0.2 - - - -
246B LYS* 3.9 24.8 + - + +
249B TRP* 3.2 27.5 - - - -
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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