Contacts of the helix formed by residues 226 - 233 (chain B) in PDB entry 4HYY
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 MET 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B SER* 4.4 0.4 + - - -
225B ILE* 1.3 79.0 - - + +
227B ALA* 1.3 59.8 + - - +
228B LEU 3.2 3.1 - - - -
229B PHE* 2.7 41.8 + - + +
230B ARG* 3.1 15.7 + - + +
242B ARG* 3.9 31.2 - - - +
246B LEU* 3.6 25.1 - - + -
268B ASN* 3.9 12.0 - - - +
288B ILE* 3.7 23.1 - - + -
289B GLY* 3.4 31.9 - - - +
293B LEU* 3.9 18.6 - - + -
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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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295A HIS* 4.1 13.9 - - + -
161B THR* 4.4 2.9 - - - +
162B GLU* 3.7 15.0 - - - +
224B SER* 3.5 22.4 + - - +
225B ILE 3.8 0.4 - - - -
226B MET* 1.3 76.8 - - - +
228B LEU* 1.3 62.2 + - - +
230B ARG* 3.1 13.0 + - - +
231B VAL* 3.1 26.3 + - - +
269B GLN* 3.9 19.8 + - - +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A HIS* 3.4 31.9 - - + +
161B THR* 3.9 12.7 + - + -
193B ALA* 3.6 29.2 - - + +
194B TYR 3.8 19.7 - - - +
195B THR* 3.4 20.6 - - - +
196B SER* 3.6 20.4 + - - +
199B GLN* 3.4 28.4 - - - +
226B MET 3.2 0.4 - - - -
227B ALA* 1.3 74.9 - - - +
229B PHE* 1.3 57.5 + - - +
231B VAL* 3.7 8.5 - - + -
232B ASP* 3.0 27.6 + - - +
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Residues in contact with PHE 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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196B SER* 3.5 33.2 - - - -
199B GLN* 3.6 30.1 - - - -
200B MET* 5.6 2.7 - - + -
225B ILE 4.1 0.2 - - - -
226B MET* 2.7 39.6 + - + +
228B LEU* 1.3 72.1 - - - +
230B ARG* 1.3 63.3 + - - +
233B PHE* 3.3 21.4 + + - -
242B ARG* 3.4 26.9 - - + +
245B LYS* 4.0 15.0 - - + -
246B LEU* 3.7 38.1 - - + -
249B MET* 3.9 28.3 - - + -
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Residues in contact with ARG 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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291A HIS* 3.2 54.8 + - + +
226B MET* 3.1 16.1 + - + +
227B ALA* 3.1 10.7 + - - +
229B PHE* 1.3 74.3 - - - +
231B VAL* 1.3 62.5 + - - +
233B PHE 3.5 1.8 - - - +
234B SER* 3.3 27.7 + - - -
242B ARG* 4.3 16.2 - - - +
269B GLN* 3.9 21.0 + - - +
270B MET 4.0 16.2 + - - -
271B THR* 4.2 14.3 - - - +
288B ILE* 3.4 47.0 - - + +
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Residues in contact with VAL 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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243A GLN* 5.2 2.6 - - - +
247A ALA* 4.3 10.9 - - + +
291A HIS* 3.8 14.4 - - + +
292A ILE* 3.7 44.3 - - + +
295A HIS* 3.5 40.8 - - + +
194B TYR 6.1 0.4 - - - +
227B ALA 3.1 15.8 + - - +
228B LEU* 3.7 13.5 - - + +
229B PHE 3.1 0.6 - - - -
230B ARG* 1.3 79.3 - - + +
232B ASP* 1.3 70.7 + - - +
233B PHE 3.3 0.9 + - - -
234B SER* 4.2 3.3 + - - -
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Residues in contact with ASP 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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244A GLN* 5.3 12.7 - - - +
247A ALA* 4.6 10.6 - - - +
194B TYR 5.2 0.7 - - - +
195B THR* 3.6 16.0 - - - +
196B SER* 2.9 43.1 + - - +
197B GLU* 4.2 1.4 + - - +
228B LEU* 3.0 14.5 + - - +
231B VAL* 1.3 86.9 - - - +
233B PHE* 1.3 79.4 + - + +
234B SER 3.9 0.9 - - - -
238B GLU* 5.0 2.6 - - - +
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Residues in contact with PHE 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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196B SER* 3.6 24.5 - - - -
197B GLU* 6.4 1.3 - - + -
229B PHE* 3.3 13.9 + + - +
230B ARG 3.5 6.0 - - - +
231B VAL 3.2 0.6 - - - -
232B ASP* 1.3 91.7 - - + +
234B SER* 1.3 62.2 + - - +
235B GLY 3.9 5.9 - - - +
238B GLU* 4.0 27.7 - - + +
239B LEU* 4.4 3.3 - - - +
241B GLU* 4.0 24.0 - - + -
242B ARG* 3.5 60.6 + - + -
245B LYS* 4.2 22.0 - - + -
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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