Contacts of the helix formed by residues 223 - 240 (chain D) in PDB entry 2OIB
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 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D THR* 1.3 79.5 + - - +
224D GLU* 1.3 73.0 + - + +
225D GLU 3.3 0.8 - - - +
226D LEU* 3.4 16.2 + - - +
227D LYS* 3.1 21.5 + - - +
258D LEU* 5.6 1.6 - - - +
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Residues in contact with GLU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D THR 2.6 11.1 + - - +
223D THR* 1.3 84.2 - - + +
225D GLU* 1.3 57.1 + - - +
226D LEU 3.1 2.2 - - - -
227D LYS* 3.4 21.8 - - - +
228D GLN* 3.0 44.6 + - - +
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Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D THR* 3.4 42.3 + - + +
223D THR 3.3 0.2 - - - -
224D GLU* 1.3 78.3 - - - +
226D LEU* 1.3 58.4 + - - +
228D GLN* 3.9 6.0 + - - +
229D GLN* 3.3 36.4 + - - +
347D ARG* 4.8 20.5 + - - +
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 3.7 42.4 - - + +
215D LEU* 3.8 44.7 - - + +
222D THR* 5.0 5.8 - - + +
223D THR* 3.4 21.8 + - - +
224D GLU 3.1 0.4 - - - -
225D GLU* 1.3 78.5 - - - +
227D LYS* 1.3 58.6 + - - +
228D GLN 3.4 0.4 - - - -
229D GLN* 3.6 6.2 + - + +
230D PHE* 3.1 26.3 + - - +
258D LEU* 4.3 4.6 - - + +
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Residues in contact with LYS 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D THR 3.1 14.5 + - - +
224D GLU* 3.4 29.8 - - - +
226D LEU* 1.3 77.4 - - - +
228D GLN* 1.3 62.2 + - - +
230D PHE* 3.2 22.8 - - + +
231D ASP* 2.9 62.1 + - - +
253D SER* 4.7 5.5 - - - -
258D LEU* 3.8 27.8 - - + +
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Residues in contact with GLN 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D GLU* 3.0 39.8 + - - +
225D GLU* 4.1 7.6 - - - +
226D LEU 3.4 0.2 - - - -
227D LYS* 1.3 79.3 - - - +
229D GLN* 1.3 59.1 + - + +
231D ASP* 3.5 21.3 + - - +
232D GLN* 2.8 30.2 + - - +
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Residues in contact with GLN 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 3.3 55.8 - - - -
215D LEU* 5.3 1.6 - - + -
225D GLU* 3.3 26.9 + - - +
226D LEU* 3.6 9.8 + - + +
227D LYS 3.3 0.4 - - - -
228D GLN* 1.3 75.5 - - + +
230D PHE* 1.3 62.6 + - - +
232D GLN* 4.3 0.2 - - - -
233D GLU* 3.1 25.3 + - - +
260D LEU* 5.3 0.2 - - - +
329D ASP* 5.3 0.2 + - - -
331D GLY* 3.7 29.5 - - - +
332D LEU* 3.6 22.0 - - + +
349D VAL* 5.7 1.0 - - - +
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Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LEU* 3.8 24.1 - - + +
226D LEU 3.1 15.2 + - - +
227D LYS* 3.2 29.8 - - - +
229D GLN* 1.3 77.7 - - - +
231D ASP* 1.3 79.9 + - - +
233D GLU* 3.4 3.3 + - - +
234D ILE* 3.2 38.2 + - + +
251D PHE* 3.6 29.2 - + - -
252D SER 3.7 13.0 - - - -
253D SER* 4.3 3.8 - - - -
258D LEU* 3.7 24.5 - - + -
259D CYS 3.5 21.1 - - - -
260D LEU* 3.7 21.0 - - + +
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Residues in contact with ASP 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LYS* 2.9 39.1 + - - +
228D GLN* 3.5 20.9 - - - +
230D PHE* 1.3 95.1 - - - +
232D GLN* 1.3 57.7 + - - +
234D ILE* 3.4 9.2 + - - +
235D LYS* 3.0 31.0 + - - +
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Residues in contact with GLN 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D GLN 2.8 18.8 + - - +
229D GLN 4.1 0.7 - - - +
230D PHE 3.3 0.2 - - - -
231D ASP* 1.3 73.6 - - - +
233D GLU* 1.3 66.8 + - - +
235D LYS* 3.4 24.5 + - - +
236D VAL* 3.1 45.5 + - + +
330D PHE 3.8 6.7 - - - +
331D GLY 3.6 21.3 - - - +
333D ALA 3.0 29.2 + - - +
334D ARG* 4.8 6.3 - - - +
335D ALA* 4.8 6.5 - - - +
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Residues in contact with GLU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LYS* 3.9 10.4 + - - +
229D GLN 3.1 20.1 + - - +
230D PHE 3.5 4.9 - - - +
231D ASP 3.3 0.2 - - - -
232D GLN* 1.3 77.4 - - - +
234D ILE* 1.3 57.3 + - - +
236D VAL* 4.1 1.4 - - - +
237D MET* 3.0 49.3 + - + +
248D LEU* 5.3 0.7 - - + -
260D LEU* 3.9 16.2 - - + -
262D TYR* 2.6 41.5 + - + +
329D ASP* 4.2 4.2 + - - -
330D PHE* 2.5 47.6 + - - +
331D GLY* 3.3 3.3 + - - +
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Residues in contact with ILE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE* 3.7 24.0 - - + -
230D PHE* 3.2 38.2 + - + +
231D ASP* 3.8 9.9 - - - +
232D GLN 3.2 0.6 - - - -
233D GLU* 1.3 77.0 - - - +
235D LYS* 1.3 57.9 + - - +
237D MET* 3.3 2.4 + - - +
238D ALA* 2.8 28.7 + - + +
248D LEU* 4.2 10.3 - - + -
251D PHE* 3.7 40.2 - - + -
260D LEU* 3.7 16.8 - - + -
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Residues in contact with LYS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ASP 3.0 17.7 + - - +
232D GLN* 3.4 39.0 - - - +
234D ILE* 1.3 74.4 - - - +
236D VAL* 1.3 68.2 + - + +
238D ALA* 3.4 7.0 + - - +
239D LYS* 3.3 58.4 + - - +
307D HIS* 5.9 0.2 - - - +
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D GLN* 3.1 37.0 + - - +
233D GLU 4.1 0.2 - - - +
235D LYS* 1.3 76.0 - - + +
237D MET* 1.3 58.4 + - - +
239D LYS* 3.1 3.3 + - - -
240D CYS* 2.8 38.7 + - + +
302D LEU* 4.6 2.5 - - + -
307D HIS* 3.8 37.5 - - + +
330D PHE* 3.8 36.1 - - + +
333D ALA* 4.0 14.6 - - + -
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Residues in contact with MET 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE* 3.5 8.7 - - + -
233D GLU* 3.0 38.3 + - - +
234D ILE 3.7 3.8 - - - +
236D VAL* 1.3 73.0 - - - +
238D ALA* 1.3 60.2 + - - +
239D LYS 3.2 0.2 - - - -
240D CYS* 3.6 13.9 - - - +
241D GLN* 3.0 20.8 + - - +
245D LEU* 5.9 0.4 - - - -
246D VAL* 3.2 50.0 - - + +
248D LEU* 3.9 31.9 - - + +
262D TYR* 3.3 27.1 - - + -
330D PHE* 3.7 20.0 - - + -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D ASP* 3.0 22.7 + - - +
163D THR* 3.1 26.5 + - - +
165D PHE* 3.6 13.0 - - + -
234D ILE* 2.8 18.3 + - + +
235D LYS* 3.6 10.8 - - - +
236D VAL 3.2 0.2 - - - -
237D MET* 1.3 76.1 - - - +
239D LYS* 1.3 58.9 + - + +
241D GLN* 2.8 15.8 + - - +
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ASP 4.3 9.6 - - - +
235D LYS* 3.3 48.0 - - - +
236D VAL 3.1 6.8 + - - +
238D ALA* 1.3 81.0 - - + +
240D CYS* 1.3 67.1 + - - +
241D GLN* 4.0 7.7 + - - +
301D PHE* 4.8 2.4 - - - -
305D ASN* 4.4 9.9 - - - +
307D HIS* 3.9 19.0 + - + +
335D ALA* 4.7 4.9 - - - +
337D GLU* 3.3 26.8 + - - +
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Residues in contact with CYS 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D VAL* 2.8 20.7 + - + +
237D MET* 3.6 18.9 - - - +
238D ALA 3.6 1.0 - - - -
239D LYS* 1.3 81.5 - - - +
241D GLN* 1.3 62.1 + - - +
245D LEU* 3.7 19.8 - - + +
246D VAL 5.2 1.6 - - - +
301D PHE* 3.7 21.1 - - + -
302D LEU* 4.1 16.8 - - + -
305D ASN* 4.2 9.2 - - - -
307D HIS* 3.7 31.2 - - - -
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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
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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