Contacts of the helix formed by residues 224 - 235 (chain B) in PDB entry 2I6A
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 GLU 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B ASN* 1.3 88.7 - - - +
225B THR* 1.3 77.8 + - - +
227B ALA* 3.5 1.6 + - - +
228B ALA* 3.0 28.8 + - - +
241B ILE* 4.1 17.4 - - + +
265B THR 2.9 3.1 + - - +
266B GLN* 3.3 49.8 - - + +
267B GLY* 4.6 1.8 + - - -
295B THR* 5.8 3.8 - - - +
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Residues in contact with THR 225 (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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200B PRO* 4.6 12.9 - - - +
223B ASN* 3.0 21.3 + - - +
224B GLU* 1.3 90.8 + - - +
226B GLU* 1.3 60.4 + - - +
228B ALA* 3.4 6.4 + - - +
229B THR* 2.8 34.3 + - - -
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 3.9 9.4 + - - -
196B ASN* 4.0 1.9 - - - +
197B LEU* 3.6 19.9 - - + +
198B SER 2.8 32.1 + - - +
199B ALA* 3.5 28.8 - - - +
200B PRO* 3.8 7.0 - - + +
203B SER* 4.2 2.6 + - - -
222B GLY* 3.5 7.8 - - - -
223B ASN* 2.7 53.6 + - - +
225B THR* 1.3 74.1 - - - +
227B ALA* 1.3 55.0 + - - +
229B THR* 3.5 6.8 + - - -
230B PHE* 2.9 30.5 + - - +
296B ASN* 5.4 0.3 + - - -
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Residues in contact with ALA 227 (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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197B LEU* 3.8 10.0 - - - +
223B ASN 3.1 18.4 + - - +
224B GLU 3.8 0.7 - - - +
225B THR 3.4 0.2 - - - -
226B GLU* 1.3 73.4 - - - +
228B ALA* 1.3 61.0 + - - +
230B PHE* 3.4 2.4 + - - +
231B ALA* 3.0 28.1 + - - +
241B ILE* 3.7 26.2 - - + -
244B ILE* 3.6 12.2 - - + +
264B PHE* 3.8 26.2 - - + -
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Residues in contact with ALA 228 (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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224B GLU 3.0 17.6 + - - +
225B THR* 3.6 7.4 - - - +
227B ALA* 1.3 72.8 - - - +
229B THR* 1.3 67.8 + - - +
231B ALA* 3.1 5.6 + - - +
232B ARG* 3.0 22.1 + - - +
238B THR 5.8 0.4 - - - -
239B LYS* 6.0 4.3 - - - +
244B ILE* 4.1 13.0 - - + +
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Residues in contact with THR 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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200B PRO* 3.2 27.0 - - + +
203B SER* 3.6 12.1 - - - -
204B GLN* 3.6 36.3 - - + +
225B THR 2.8 19.8 + - - -
226B GLU 3.7 4.7 - - - -
228B ALA* 1.3 79.2 - - - +
230B PHE* 1.3 63.2 + - - +
232B ARG* 3.4 6.4 + - + +
233B GLU* 3.0 27.2 + - + +
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Residues in contact with PHE 230 (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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197B LEU* 4.1 17.3 - - + -
203B SER* 3.3 23.1 + - - +
210B LEU* 3.6 24.7 - - + -
211B MET* 3.9 11.7 - - - -
214B MET* 3.8 22.2 - - + -
220B LEU* 5.1 0.4 - - + -
226B GLU 2.9 19.2 + - - +
227B ALA* 3.7 5.6 - - - +
228B ALA 3.2 0.2 - - - -
229B THR* 1.3 77.8 - - - +
231B ALA* 1.3 65.2 + - - +
233B GLU* 3.3 2.8 + - + +
234B GLN* 2.9 53.0 + - + +
236B PHE* 4.1 12.1 - + - -
244B ILE* 5.0 1.1 - - + -
248B THR* 3.8 33.7 - - + -
251B LEU* 4.0 5.6 - - + -
264B PHE* 5.8 0.9 - + - -
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Residues in contact with ALA 231 (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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227B ALA 3.0 14.7 + - - +
228B ALA* 3.2 10.1 - - - +
230B PHE* 1.3 76.0 - - - +
232B ARG* 1.3 64.0 + - - +
234B GLN* 3.0 10.6 + - - -
235B GLY 3.0 10.2 + - - -
236B PHE* 3.1 39.5 + - + +
237B GLU 5.1 0.9 - - - -
238B THR 3.9 9.2 - - - +
244B ILE* 3.8 22.4 - - + -
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Residues in contact with ARG 232 (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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228B ALA 3.0 11.6 + - - +
229B THR* 3.8 7.4 - - - +
231B ALA* 1.3 79.1 - - - +
233B GLU* 1.3 73.5 + - + +
235B GLY* 3.2 12.2 + - - -
236B PHE 5.2 0.7 - - - +
237B GLU 5.6 2.2 - - - +
239B LYS* 5.4 9.5 - - - +
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Residues in contact with GLU 233 (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 SER* 3.4 29.2 - - - +
204B GLN* 4.0 23.3 + - - +
207B LYS* 2.4 49.9 + - + +
229B THR* 3.0 25.0 + - + +
230B PHE* 3.7 4.0 - - + +
232B ARG* 1.3 87.7 - - + +
234B GLN* 1.3 67.6 + - - +
235B GLY 3.6 0.3 + - - -
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Residues in contact with GLN 234 (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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207B LYS* 4.3 13.9 - - - +
211B MET* 3.1 48.2 - - + +
230B PHE* 2.9 46.9 + - + +
231B ALA 3.0 1.8 + - - +
233B GLU* 1.3 84.9 - - - +
235B GLY* 1.3 59.7 + - - +
236B PHE* 3.7 24.8 - - + -
251B LEU* 5.7 1.4 - - + +
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Residues in contact with GLY 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 ALA 3.0 3.5 + - - -
232B ARG 3.2 10.5 + - - -
233B GLU 3.4 1.2 - - - -
234B GLN* 1.3 77.7 - - - +
236B PHE* 1.3 62.9 + - - +
237B GLU* 3.3 19.5 - - - +
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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