Contacts of the helix formed by residues 246 - 256 (chain C) in PDB entry 4RO0
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 GLY 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241C ARG* 4.1 6.7 + - - -
242C SER* 3.9 22.4 - - - -
245C ASP* 1.3 83.2 - - - +
247C TYR* 1.3 65.0 + - - +
248C GLU* 3.1 2.0 - - - -
249C ALA* 3.4 12.7 + - - +
250C MET* 3.5 11.0 + - - +
206c ARG* 5.2 0.5 + - - -
227c GLN* 3.9 8.3 - - - +
266c GLU* 3.2 13.0 + - - -
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Residues in contact with TYR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ASP* 3.5 21.9 + - + -
246C GLY* 1.3 73.5 - - - +
248C GLU* 1.3 59.3 - - - +
250C MET* 3.3 30.3 + - + +
251C PHE* 2.9 28.5 + - - +
266c GLU* 2.9 25.3 + - + +
296c VAL 5.6 15.3 - - - -
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ARG* 3.5 23.4 + - - -
238C LEU* 3.9 15.9 - - + +
241C ARG* 3.9 27.4 + - + +
246C GLY* 4.8 0.7 - - - -
247C TYR* 1.3 76.8 - - - +
249C ALA* 1.3 57.9 - - - +
251C PHE* 3.0 8.9 + - - +
252C VAL* 2.9 34.2 + - + +
255c VAL 5.3 1.0 - - - +
256c LEU* 4.3 5.0 - - - +
264c MET* 3.5 48.3 + - + +
266c GLU* 2.8 21.6 + - + +
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Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LEU* 3.8 23.4 - - + +
242C SER* 3.0 27.3 + - - +
246C GLY* 3.4 6.7 + - - +
247C TYR 3.3 0.2 - - - -
248C GLU* 1.3 78.9 - - - +
250C MET* 1.3 58.3 + - - +
252C VAL* 3.4 3.1 + - - +
253C GLN* 2.8 29.5 + - - +
227c GLN* 3.4 24.1 + - + +
228c VAL 4.7 1.2 - - - +
229c ILE* 5.1 4.3 - - + -
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Residues in contact with MET 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLY 3.5 3.0 + - - +
247C TYR* 3.3 46.4 + - + +
249C ALA* 1.3 76.9 - - - +
251C PHE* 1.3 59.7 + - - +
253C GLN* 4.2 1.3 - - - -
254C ASP* 2.8 49.5 + - - +
227c GLN* 3.3 24.4 - - - +
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Residues in contact with PHE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C TYR 2.9 15.0 + - - +
248C GLU* 3.0 11.2 + - - +
250C MET* 1.3 74.1 - - - +
252C VAL* 1.3 72.5 + - + +
254C ASP* 5.1 0.2 - - - -
255C VAL* 3.0 59.6 + - + +
256C LEU* 4.4 16.4 - - + -
264C MET* 4.4 13.7 - - + -
321C ILE* 4.4 16.6 - - + -
251c PHE* 5.6 3.8 - + - -
256c LEU* 5.2 0.9 - - + -
264c MET* 3.7 36.6 - - + -
294c ILE* 3.9 39.0 - - + -
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ILE* 4.9 3.6 - - + -
238C LEU* 3.8 25.4 - - + -
248C GLU* 2.9 22.4 + - + +
249C ALA 3.6 6.1 - - - +
251C PHE* 1.3 82.2 - - + +
253C GLN* 1.3 60.0 + - - +
256C LEU* 2.9 48.1 + - + +
257C ALA* 3.1 7.6 + - - +
229c ILE* 6.1 0.2 - - + -
234c ILE* 3.7 24.7 - - + -
256c LEU* 3.3 30.7 - - + -
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ALA 2.8 20.4 + - - +
250C MET* 4.1 3.4 - - - +
251C PHE 3.3 0.2 - - - -
252C VAL* 1.3 75.7 - - - +
254C ASP* 1.3 58.8 + - - +
257C ALA* 3.1 19.0 + - - +
258C GLU* 2.9 49.3 + - - +
217c ILE* 3.8 9.2 - - - +
221c ARG* 4.0 10.3 - - - +
227c GLN* 3.8 9.6 - - - +
228c VAL* 3.0 30.2 + - + +
229c ILE* 3.5 2.4 - - - +
230c SER* 2.8 42.7 + - - +
234c ILE* 5.1 2.4 - - - +
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Residues in contact with ASP 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C MET* 2.8 44.4 + - - +
251C PHE* 4.4 0.9 - - - +
253C GLN* 1.3 79.3 - - - +
255C VAL* 1.3 64.6 + - + +
258C GLU* 3.4 17.9 - - - +
259C GLU* 3.4 3.4 + - - -
260C SER* 3.2 41.5 + - - +
261C THR* 4.4 3.8 + - - +
262C ARG 4.1 2.8 + - - +
221c ARG* 4.4 4.9 + - - -
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 3.0 42.4 + - + +
254C ASP* 1.3 86.8 - - + +
256C LEU* 1.3 62.6 + - + +
257C ALA 3.5 0.7 - - - -
259C GLU* 3.4 24.9 - - - +
261C THR* 6.1 0.2 - - - +
262C ARG* 3.9 33.3 - - + +
263C ARG* 4.3 7.6 - - - -
264C MET* 4.1 27.0 + - + +
321C ILE* 4.6 7.0 - - + -
237c ARG* 4.2 4.2 + - - -
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 4.4 9.6 - - + -
252C VAL* 2.9 43.0 + - + +
255C VAL* 1.3 82.4 - - + +
257C ALA* 1.3 59.3 + - - +
259C GLU* 5.1 0.2 - - - -
264C MET* 4.2 22.0 - - + -
233c VAL 5.3 0.2 - - - +
234c ILE* 3.8 19.7 - - + +
237c ARG* 3.1 45.2 + - - +
248c GLU* 4.0 5.8 - - - +
251c PHE* 5.6 1.1 - - + -
252c VAL* 3.9 24.9 - - + -
256c LEU* 3.8 25.8 - - + -
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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