Contacts of the helix formed by residues 240 - 250 (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 ASP 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B THR* 3.2 11.9 + - - +
239B LYS* 1.3 78.8 - - - +
241B ILE* 1.3 61.1 + - - +
242B LYS* 3.7 10.1 + - - +
243B GLU* 2.9 33.9 + - + +
244B ILE* 2.9 30.6 + - - +
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Residues in contact with ILE 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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224B GLU* 4.1 20.6 - - + +
227B ALA* 3.7 30.1 - - + -
239B LYS 3.6 4.4 + - - -
240B ASP* 1.3 71.2 + - - +
242B LYS* 1.3 69.4 + - + +
244B ILE* 3.1 10.8 + - + +
245B ALA* 2.7 32.3 + - - +
264B PHE* 3.9 21.1 - - + -
266B GLN* 3.6 16.6 - - - +
272B ILE* 3.4 34.5 - - + -
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Residues in contact with LYS 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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240B ASP* 3.5 10.4 + - - +
241B ILE* 1.3 81.4 - - + +
243B GLU* 1.3 53.2 + - - +
245B ALA* 3.2 5.7 + - - +
246B LYS* 2.7 34.4 + - - +
272B ILE* 4.2 14.4 - - + -
279B VAL* 3.4 45.2 + - + +
280B THR* 5.7 0.9 - - - +
281B ALA* 5.1 18.1 - - + +
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Residues in contact with GLU 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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238B THR* 3.6 19.3 - - - +
240B ASP* 2.9 27.9 + - + +
242B LYS* 1.3 72.3 - - - +
244B ILE* 1.3 61.0 + - - +
246B LYS* 3.3 22.7 + - - +
247B LYS* 2.9 65.9 + - - +
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Residues in contact with ILE 244 (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* 3.6 32.3 - - + +
228B ALA* 4.1 12.1 - - + -
230B PHE* 5.0 2.0 - - + -
231B ALA* 3.8 9.6 - - + +
236B PHE* 4.0 17.8 - - + -
238B THR* 3.6 29.8 - - + +
239B LYS* 4.2 5.6 - - - +
240B ASP 2.9 26.2 + - - +
241B ILE* 3.1 11.0 + - + +
243B GLU* 1.3 76.8 - - - +
245B ALA* 1.3 55.1 + - - +
248B THR* 2.4 47.6 + - - +
264B PHE* 4.1 13.7 - - + -
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Residues in contact with ALA 245 (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 2.7 17.2 + - - +
242B LYS 3.4 5.8 - - - +
244B ILE* 1.3 76.5 - - - +
246B LYS* 1.3 59.3 + - - +
249B GLN* 3.3 15.2 + - - +
262B VAL* 3.8 9.1 - - + +
264B PHE* 3.5 26.6 - - + -
272B ILE* 3.8 21.1 - - + -
274B ALA* 2.9 27.7 - - + +
279B VAL* 4.7 0.2 - - + -
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Residues in contact with LYS 246 (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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242B LYS 2.7 16.6 + - - +
243B GLU* 3.6 28.7 - - - +
245B ALA* 1.3 77.8 - - - +
247B LYS* 1.3 65.3 + - + +
248B THR 3.2 0.2 - - - -
249B GLN* 3.5 7.5 + - + +
250B ALA* 3.3 21.5 + - + +
274B ALA* 4.2 6.1 - - + -
275B THR 6.0 1.6 - - - +
279B VAL* 4.0 15.5 - - + -
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Residues in contact with LYS 247 (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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236B PHE* 3.7 49.2 + - + +
238B THR* 4.0 17.3 - - + -
243B GLU* 2.9 46.1 + - - +
246B LYS* 1.3 73.2 - - + +
248B THR* 1.3 68.6 + - - +
250B ALA* 3.2 14.1 + - - +
251B LEU* 3.3 15.4 + - - +
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Residues in contact with THR 248 (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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214B MET* 4.7 2.5 - - - -
220B LEU* 3.5 31.6 - - + -
230B PHE* 3.8 19.6 - - + -
236B PHE* 3.4 13.0 - - - -
244B ILE* 2.4 31.4 + - - +
245B ALA 4.2 0.4 - - - -
247B LYS* 1.3 78.2 - - - +
249B GLN* 1.3 62.4 + - - +
251B LEU* 3.0 33.7 + - + +
260B ARG* 3.6 6.3 + - - -
262B VAL* 4.1 14.4 - - + -
264B PHE* 4.3 4.2 - - + -
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Residues in contact with GLN 249 (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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245B ALA 3.3 17.6 + - - +
246B LYS* 3.7 11.0 - - + +
247B LYS 3.2 0.8 - - - -
248B THR* 1.3 78.6 - - - +
250B ALA* 1.3 65.1 + - + +
251B LEU 4.2 0.3 - - - +
259B GLN* 3.7 14.7 - - - +
260B ARG* 2.3 60.2 + - - +
262B VAL* 3.6 17.2 - - + +
274B ALA* 4.1 7.4 - - + +
275B THR* 3.6 26.9 - - - +
276B GLU* 3.5 16.6 - - - +
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Residues in contact with ALA 250 (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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246B LYS* 3.3 14.1 + - + +
247B LYS* 3.2 9.3 + - - +
248B THR 3.0 0.8 - - - -
249B GLN* 1.3 84.5 - - + +
251B LEU* 1.3 66.7 + - - +
252B PRO* 3.6 3.8 - - - +
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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