Contacts of the helix formed by residues 222 - 240 (chain A) 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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A THR* 1.3 61.1 + - - +
224A GLU* 4.5 9.2 - - + +
225A GLU* 3.0 48.1 + - + +
226A LEU* 3.1 29.1 + - - +
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Residues in contact with THR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A THR* 1.3 72.1 - - - +
224A GLU* 1.3 81.4 + - - +
226A LEU* 4.0 6.2 - - + +
227A LYS* 3.4 20.6 + - - +
256A ASP* 5.5 7.0 - - - +
258A LEU* 5.6 1.0 - - - +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A THR* 4.5 7.1 - - + +
223A THR* 1.3 91.4 + - - +
225A GLU* 1.3 62.4 + - + +
227A LYS* 3.4 9.1 - - - +
228A GLN* 3.3 28.1 + - - +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A THR* 3.0 39.0 + - + +
223A THR 3.3 0.4 - - - -
224A GLU* 1.3 79.2 - - + +
226A LEU* 1.3 62.3 + - - +
227A LYS 3.2 0.2 - - - -
228A GLN* 3.2 36.8 - - - +
229A GLN* 3.3 13.6 + - - +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LYS 6.1 0.7 - - - +
222A THR 3.1 21.5 + - - +
223A THR* 4.0 7.0 - - + +
224A GLU 3.4 0.2 - - - -
225A GLU* 1.3 75.2 - - - +
227A LYS* 1.3 58.5 + - - +
229A GLN* 3.4 19.4 + - - +
230A PHE* 2.9 29.3 + - - +
258A LEU* 4.4 21.1 - - + +
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A THR 3.4 12.9 + - - +
224A GLU* 3.4 13.2 - - - +
226A LEU* 1.3 80.0 - - - +
228A GLN* 1.3 56.9 + - - +
230A PHE* 3.3 29.5 - - + +
231A ASP* 2.9 60.7 + - - +
253A SER* 4.7 9.3 + - - -
258A LEU* 4.0 16.3 - - + +
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Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU* 3.3 6.6 + - - +
225A GLU* 3.2 43.0 - - - +
227A LYS* 1.3 77.1 - - - +
229A GLN* 1.3 60.7 + - - +
231A ASP* 3.7 9.6 - - - +
232A GLN* 2.8 28.1 + - - +
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU 3.3 15.2 + - - +
226A LEU* 3.6 23.1 - - + +
227A LYS 3.3 0.2 - - - -
228A GLN* 1.3 74.2 - - - +
230A PHE* 1.3 61.5 - - - +
232A GLN* 3.2 16.7 + - - +
233A GLU* 2.9 30.5 + - - +
331A GLY* 3.1 32.6 - - - +
332A LEU* 4.4 9.0 - - - +
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Residues in contact with PHE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU 2.9 14.6 + - - +
227A LYS* 3.3 40.2 - - + +
229A GLN* 1.3 75.8 - - - +
231A ASP* 1.3 63.0 + - - +
233A GLU* 3.5 4.4 + - - +
234A ILE* 3.3 48.8 + - + +
251A PHE* 3.9 18.8 - + + -
252A SER 4.0 9.9 - - - -
253A SER* 4.1 11.9 - - - -
258A LEU* 3.7 33.2 - - + -
259A CYS 3.4 21.8 - - - -
260A LEU* 4.0 22.6 - - + +
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LYS* 2.9 54.8 + - - +
228A GLN* 3.8 8.9 - - - +
230A PHE* 1.3 79.0 - - - +
232A GLN* 1.3 65.6 + - - +
234A ILE* 3.6 8.2 + - - +
235A LYS* 3.1 24.8 + - - +
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Residues in contact with GLN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLN 2.8 19.2 + - - +
229A GLN* 3.2 21.5 + - - +
231A ASP* 1.3 75.3 - - - +
233A GLU* 1.3 64.7 + - - +
235A LYS* 3.2 12.5 - - + +
236A VAL* 3.1 27.0 + - + +
330A PHE 6.2 0.2 - - - +
331A GLY 4.7 6.2 - - - +
332A LEU 5.7 0.9 - - - -
333A ALA 3.8 14.7 + - - +
334A ARG* 3.7 33.7 + - - +
335A ALA 5.8 0.4 - - - +
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LYS* 2.8 26.7 + - - -
229A GLN* 2.9 15.5 + - + +
230A PHE* 4.1 4.0 - - - +
231A ASP 3.4 0.2 - - - -
232A GLN* 1.3 73.8 - - - +
234A ILE* 1.3 62.1 + - - +
236A VAL* 3.2 7.4 + - - +
237A MET* 2.9 46.0 + - + +
260A LEU* 3.4 15.4 - - + +
262A TYR* 2.4 37.1 + - - -
329A ASP* 5.6 0.2 - - - -
330A PHE* 3.7 26.3 + - + +
331A GLY* 3.6 16.9 - - - +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP* 4.4 15.0 - - + +
165A PHE* 3.8 27.2 - - + -
230A PHE* 3.3 50.3 + - + +
231A ASP* 3.9 10.1 - - - +
233A GLU* 1.3 75.9 - - - +
235A LYS* 1.3 52.4 + - - +
237A MET* 3.3 1.2 + - - +
238A ALA* 2.8 34.0 + - - +
248A LEU* 4.3 11.2 - - + -
251A PHE* 4.2 18.8 - - + -
260A LEU* 3.7 19.5 - - + -
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP 5.4 2.2 - - - +
231A ASP 3.1 14.8 + - - +
232A GLN* 3.2 15.9 - - + +
234A ILE* 1.3 76.8 - - - +
236A VAL* 1.3 61.0 + - + +
238A ALA* 3.5 6.6 + - - +
239A LYS* 3.3 22.9 + - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLN* 3.1 19.5 + - + +
233A GLU* 3.2 9.8 + - - +
235A LYS* 1.3 75.7 - - + +
237A MET* 1.3 58.8 + - + +
239A LYS* 3.3 1.7 + - - -
240A CYS* 2.9 44.3 + - + +
302A LEU* 5.3 1.1 - - + -
307A HIS* 4.1 30.3 - - + +
330A PHE* 4.4 22.4 - - + +
333A ALA* 4.3 32.8 - - + +
334A ARG 5.9 0.2 - - - -
335A ALA 6.0 0.2 - - - +
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Residues in contact with MET 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 3.8 8.9 - - - -
233A GLU* 2.9 45.1 + - + +
234A ILE 3.8 0.2 - - - +
236A VAL* 1.3 76.3 - - + +
238A ALA* 1.3 65.4 + - - +
240A CYS* 3.7 27.2 - - + +
241A GLN* 4.4 8.0 - - - +
245A LEU* 5.4 0.4 - - + -
246A VAL* 3.4 24.7 - - - +
247A GLU* 5.3 0.4 - - - -
248A LEU* 3.8 35.8 + - + +
262A TYR* 4.2 14.4 - - - -
330A PHE* 3.5 39.7 - - + -
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP 3.4 21.8 - - - +
163A THR* 3.3 30.5 + - - +
165A PHE* 3.6 13.6 - - + -
234A ILE 2.8 17.6 + - - +
235A LYS* 3.6 7.4 - - - +
236A VAL 3.3 0.2 - - - -
237A MET* 1.3 79.3 - - - +
239A LYS* 1.3 59.4 + - + +
241A GLN* 4.8 9.0 - - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LYS 3.3 14.3 + - - +
236A VAL 3.9 3.1 - - - +
238A ALA* 1.3 81.2 - - + +
240A CYS* 1.3 59.3 + - - +
241A GLN* 3.7 4.3 + - - +
301A PHE* 4.2 8.5 - - - -
305A ASN* 2.8 48.3 + - - +
306A HIS* 5.0 5.1 - - - +
307A HIS* 3.6 19.4 - - + +
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Residues in contact with CYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 2.9 24.0 + - + +
237A MET* 3.7 21.9 + - + +
238A ALA 3.5 0.8 - - - -
239A LYS* 1.3 77.4 - - - +
241A GLN* 1.3 60.7 + - - +
245A LEU* 3.7 26.2 - - + +
246A VAL 5.1 1.0 - - - +
301A PHE* 3.5 13.9 - - + -
302A LEU* 4.0 16.8 - - + -
305A ASN* 4.9 5.2 - - - -
307A HIS* 3.4 35.7 - - - -
330A PHE* 5.8 0.4 - - + -
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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