Contacts of the helix formed by residues 230 - 241 (chain B) in PDB entry 6D6U
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PHE* 3.5 9.0 + - - -
229B GLN* 1.3 92.6 + - - +
231B TYR* 1.3 78.9 + - + +
232B LEU 3.4 1.1 - - - -
233B PRO* 3.5 2.5 - - - -
234B CYS* 3.1 23.8 + - + +
269B LEU* 3.7 31.7 - - + +
273B ALA* 4.1 23.8 - - + +
286B MET* 4.8 10.9 - - - -
289B PHE* 6.2 0.4 - - + -
290B ILE* 5.2 7.6 - - + -
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Residues in contact with TYR 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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147B PRO* 3.4 32.0 - - + +
148B MET* 6.5 0.4 - - - -
223B ILE* 5.6 2.2 - - + -
226B PHE* 3.4 23.9 + - + +
227B VAL* 3.9 9.9 - - + +
230B THR* 1.3 82.0 - - + +
232B LEU* 1.3 57.4 + - - +
234B CYS* 3.3 2.4 + - - +
235B ILE* 2.9 36.5 + - + +
286B MET* 3.4 49.7 - - + +
289B PHE* 3.7 33.3 - + + -
340B TYR* 3.8 14.8 + + - -
341B TRP* 3.3 41.5 - + + -
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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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286A MET* 5.5 11.4 - - + -
227B VAL* 2.8 32.4 + - + +
228B ILE* 4.2 19.1 - - + +
231B TYR* 1.3 74.5 - - - +
233B PRO* 1.3 60.0 - - + +
235B ILE* 3.4 13.0 + - + -
236B MET* 2.9 59.0 + - + +
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Residues in contact with PRO 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL 4.0 1.1 - - - +
228B ILE 4.1 8.5 - - - +
229B GLN 3.2 26.2 - - - +
230B THR* 3.5 14.1 - - - +
232B LEU* 1.3 95.6 - - + +
234B CYS* 1.3 55.7 + - - +
236B MET* 3.4 6.8 + - + +
237B THR* 2.9 35.1 + - - +
269B LEU* 4.8 10.8 - - + -
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Residues in contact with CYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 3.1 20.9 + - + +
231B TYR 3.7 3.6 - - - +
233B PRO* 1.3 75.2 - - - +
235B ILE* 1.3 59.7 + - - +
237B THR* 3.3 4.6 + - - -
238B VAL* 2.9 34.3 + - - +
266B MET* 3.6 16.4 - - - -
269B LEU* 3.8 15.4 - - + +
289B PHE* 3.9 8.5 - - + -
290B ILE* 5.1 9.0 - - - -
293B CYS* 2.0 51.1 - - - -
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B TYR* 2.9 26.9 + - + +
232B LEU* 3.8 13.2 - - + +
234B CYS* 1.3 76.6 - - - +
236B MET* 1.3 65.6 + - + +
238B VAL* 3.3 1.6 + - - +
239B ILE* 2.9 55.1 + - + +
289B PHE* 3.5 23.6 - - + -
333B PHE* 3.9 24.0 - - + -
337B ASN* 4.0 13.9 - - - +
341B TRP* 4.7 9.9 - - + +
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Residues in contact with MET 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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289A PHE* 6.4 3.6 - - + -
232B LEU* 2.9 41.1 + - + +
233B PRO* 3.8 6.3 - - + +
235B ILE* 1.3 85.1 - - + +
237B THR* 1.3 59.5 + - - +
239B ILE* 3.4 25.7 + - + +
240B LEU* 2.8 30.7 + - - +
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Residues in contact with THR 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 PRO* 2.9 19.5 + - - +
234B CYS* 4.6 0.6 - - - -
236B MET* 1.3 75.2 - - - +
238B VAL* 1.3 59.4 + - - +
240B LEU* 3.3 10.4 + - + +
241B SER* 2.9 27.5 + - - -
262B THR* 4.5 25.1 - - + +
265B THR* 4.0 26.2 - - + +
266B MET* 3.6 24.9 - - + -
269B LEU* 6.1 0.4 - - - +
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Residues in contact with VAL 238 (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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234B CYS 2.9 21.4 + - - +
235B ILE 3.8 3.6 - - - +
237B THR* 1.3 76.8 - - - +
239B ILE* 1.3 61.8 + - - +
241B SER* 2.4 29.3 + - - +
242B GLN* 3.8 6.9 + - - +
266B MET* 3.6 18.6 - - + -
293B CYS* 3.8 25.8 - - + -
296B PHE* 4.5 15.7 - - + -
297B VAL* 4.3 6.1 - - + -
333B PHE* 4.0 35.9 - - + -
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Residues in contact with ILE 239 (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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235B ILE* 2.9 42.3 + - + +
236B MET* 3.8 19.5 - - + +
238B VAL* 1.3 76.0 - - - +
240B LEU* 1.3 63.7 + - - +
242B GLN* 3.2 43.1 + - - +
243B VAL* 5.3 0.9 - - - +
333B PHE* 4.6 14.8 - - + -
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Residues in contact with LEU 240 (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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258A VAL* 5.3 13.7 - - + -
259A LEU* 5.6 13.0 - - + -
262A THR* 6.0 1.6 - - - +
289A PHE* 6.3 2.9 - - + -
293A PHE* 5.8 8.1 - - + -
236B MET 2.8 18.8 + - - +
237B THR* 3.6 9.6 - - + +
238B VAL 3.3 0.2 - - - -
239B ILE* 1.3 72.1 - - - +
241B SER* 1.3 58.7 + - - +
242B GLN 2.8 12.1 + - - -
243B VAL* 3.0 19.1 + - + +
258B PHE* 2.9 43.7 - - + -
261B THR* 6.2 2.5 - - + -
262B THR* 4.7 10.5 - - + -
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B THR 2.9 13.6 + - - -
238B VAL* 2.4 32.5 + - - +
240B LEU* 1.3 75.2 - - - +
242B GLN* 1.3 59.7 + - - +
243B VAL 3.2 1.4 + - - -
244B SER* 3.6 9.2 + - - -
245B PHE* 4.1 10.1 - - - -
258B PHE* 3.4 19.9 - - - -
262B THR* 4.1 18.2 - - - -
297B VAL* 4.6 13.2 - - - +
300B ALA* 5.2 10.1 - - - +
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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