Contacts of the helix formed by residues 226 - 237 (chain B) in PDB entry 7C2Y
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B THR* 1.3 83.6 + - - +
227B LEU* 1.3 64.4 + - - +
228B ASN* 3.4 6.0 + - - +
229B ASP* 2.6 39.1 + - + +
230B PHE* 2.9 26.3 + - - +
262B LEU* 5.4 0.7 - - - -
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Residues in contact with LEU 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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225B THR 4.3 0.6 + - - -
226B THR* 1.3 71.7 - - - +
228B ASN* 1.3 60.9 + - - +
230B PHE* 4.0 5.9 - - - +
231B ASN* 3.0 34.7 + - - +
242B LEU* 5.6 7.7 - - + +
243B THR 6.6 0.2 - - - -
244B GLN* 6.1 1.6 - - - +
247B VAL* 5.9 7.0 - - + -
262B LEU* 5.4 3.7 - - - +
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 3.1 6.0 + - - +
227B LEU* 1.3 78.3 - - - +
229B ASP* 1.3 66.5 + - - +
231B ASN* 3.1 9.9 + - - +
232B LEU* 3.0 24.6 + - - +
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Residues in contact with ASP 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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225B THR* 4.0 12.6 - - - +
226B THR* 2.6 27.4 + - + +
228B ASN* 1.3 76.1 - - - +
230B PHE* 1.3 59.7 + - - +
232B LEU* 3.6 7.0 + - - +
233B VAL* 3.2 20.4 + - - +
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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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201B THR* 3.6 23.8 - - + -
225B THR* 4.0 14.2 + - + -
226B THR 2.9 16.8 + - - +
227B LEU* 4.0 4.7 - - - +
229B ASP* 1.3 79.3 - - - +
231B ASN* 1.3 54.8 + - - +
233B VAL* 2.8 9.1 + - + +
234B ALA* 2.6 50.9 + - + +
239B TYR* 5.2 1.3 - + - -
242B LEU* 4.2 18.6 - - + -
265B CYS* 3.8 47.1 - - + -
268B LEU* 3.7 33.2 - - + -
269B LYS* 4.3 15.3 - - + -
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Residues in contact with ASN 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 LEU* 3.0 23.8 + - - +
228B ASN* 3.1 11.0 + - - +
230B PHE* 1.3 80.7 - - - +
232B LEU* 1.3 57.9 + - - +
234B ALA* 3.7 4.3 - - - +
235B MET* 2.8 31.2 + - - +
241B PRO* 3.3 18.2 - - + +
242B LEU* 2.7 49.4 + - - +
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Residues in contact with LEU 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 ASN* 3.0 18.4 + - - +
229B ASP* 3.9 7.2 - - - +
230B PHE 3.2 0.2 - - - -
231B ASN* 1.3 77.2 - - - +
233B VAL* 1.3 61.5 + - - +
235B MET* 3.8 6.0 + - - +
236B LYS* 3.6 18.0 + - - +
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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
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229B ASP 3.2 14.3 + - - +
230B PHE* 2.8 14.6 + - + +
232B LEU* 1.3 76.4 - - - +
234B ALA* 1.3 61.7 + - - +
236B LYS* 3.3 12.1 + - - +
237B TYR* 3.5 25.1 + - + +
269B LYS* 4.8 18.2 - - + -
273B GLN* 5.1 10.5 - - - +
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Residues in contact with ALA 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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230B PHE* 2.6 38.2 + - + +
231B ASN* 3.3 11.9 + - - +
233B VAL* 1.3 70.6 - - - +
235B MET* 1.3 66.0 + - - +
237B TYR* 3.1 9.7 + - - -
239B TYR* 3.0 50.2 + - + +
240B GLU 4.1 8.3 - - - +
241B PRO* 5.1 0.7 - - + -
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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 ASN 2.8 20.6 + - - +
232B LEU* 4.1 7.2 - - - +
234B ALA* 1.3 73.3 - - - +
236B LYS* 1.3 60.4 + - - +
237B TYR 3.6 0.2 + - - -
238B ASN* 3.6 9.2 + - - -
239B TYR 4.2 6.9 + - - -
241B PRO* 6.2 0.2 - - - +
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Residues in contact with LYS 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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232B LEU 3.6 10.1 + - - +
233B VAL* 3.3 10.4 + - - +
234B ALA 3.1 1.0 - - - -
235B MET* 1.3 79.3 - - - +
237B TYR* 1.3 68.0 + - + +
238B ASN* 3.4 2.0 + - - +
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Residues in contact with TYR 237 (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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233B VAL* 3.5 20.3 + - + +
234B ALA* 3.1 5.7 + - - +
236B LYS* 1.3 84.9 - - + +
238B ASN* 1.3 68.9 + - - +
239B TYR* 3.5 20.8 - - + -
272B LEU* 3.0 43.2 + - + -
273B GLN* 3.6 30.7 + - + +
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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