Contacts of the strand formed by residues 291 - 298 (chain C) in PDB entry 5AQO
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 ILE 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245C PHE* 3.8 18.4 - - + -
249C HIS* 3.5 45.1 - - + +
251C LYS* 3.6 36.8 - - + -
287C LEU* 2.8 29.5 + - - +
288C TYR 3.0 15.2 + - - +
289C GLU 3.8 9.0 - - - +
290C GLY* 1.3 76.8 - - - +
292C ASP* 1.4 70.9 + - - +
293C PHE 3.7 0.9 + - - -
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Residues in contact with ASP 292 (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 HIS* 4.5 5.4 + - - -
284C ILE 3.5 4.9 - - - +
285C ASP* 3.5 11.7 - - - +
286C SER* 2.9 20.3 + - - +
290C GLY 3.6 2.7 + - - +
291C ILE* 1.4 84.0 - - - +
293C PHE* 1.3 59.5 + - - +
294C TYR* 3.7 29.2 + - + -
238D LYS* 2.8 34.9 + - - -
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Residues in contact with PHE 293 (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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241C PHE* 3.8 39.3 - + + -
244C GLU* 3.5 27.8 - - + -
245C PHE* 3.5 36.6 - + + -
248C LYS* 4.6 8.3 - - + -
249C HIS* 4.6 7.4 - - - -
263C LEU* 3.9 12.6 - - + -
282C ILE* 3.5 7.2 - - + +
284C ILE* 2.7 43.3 + - + +
287C LEU* 3.7 30.3 - - + -
291C ILE 3.7 0.4 + - - -
292C ASP* 1.3 69.7 - - - +
294C TYR* 1.3 62.7 + - - +
295C THR* 3.6 22.2 - - + -
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Residues in contact with TYR 294 (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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248C LYS* 4.1 11.3 + - - -
282C ILE 3.3 4.9 - - - +
283C GLU* 3.8 26.0 - - + +
284C ILE 4.2 4.9 - - - -
285C ASP* 2.6 31.0 + - - -
292C ASP* 3.7 25.3 + - + -
293C PHE* 1.3 83.6 - - - +
295C THR* 1.3 63.1 + - - +
234D ARG* 3.6 41.5 + - - +
237D ARG* 3.1 16.1 + - - -
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Residues in contact with THR 295 (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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241C PHE* 3.5 25.1 - - + -
244C GLU* 2.7 28.5 + - - -
248C LYS* 4.1 3.7 + - - +
281C SER* 3.5 3.8 - - - -
282C ILE* 2.8 42.2 + - + +
293C PHE* 3.6 26.7 - - + -
294C TYR* 1.3 77.1 - - - +
296C SER* 1.3 75.5 + - - +
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Residues in contact with SER 296 (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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240C HIS* 5.0 1.6 + - - -
241C PHE* 4.0 7.9 - - - -
244C GLU* 4.7 2.6 - - - +
279C GLN* 4.2 13.1 - - - +
280C ALA 3.2 16.2 - - - -
281C SER* 3.9 12.8 - - - -
282C ILE* 4.7 1.1 - - - +
295C THR* 1.3 86.6 + - - +
297C ILE* 1.3 62.0 + - - +
298C THR* 6.2 0.2 - - - +
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Residues in contact with ILE 297 (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 MET* 3.9 28.0 - - + -
240C HIS* 4.0 10.3 - - + +
241C PHE* 3.8 15.7 - - + -
270C ALA* 4.5 3.4 - - + -
274C LEU* 3.6 15.6 - - + +
279C GLN* 3.3 3.9 - - - +
280C ALA* 2.9 42.8 + - + +
282C ILE* 5.1 1.1 - - + -
296C SER* 1.3 74.1 - - - +
298C THR* 1.3 74.7 + - - +
301C ARG* 3.9 16.8 - - + -
302C PHE* 4.1 11.0 - - + +
305C LEU* 3.8 29.4 - - + -
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Residues in contact with THR 298 (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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274C LEU* 3.9 2.2 - - - -
278C THR 3.3 13.7 - - - +
279C GLN* 4.0 11.4 - - + +
296C SER* 6.2 0.2 - - - +
297C ILE* 1.3 82.7 - - - +
299C ARG* 1.3 64.2 + - - +
300C ALA* 3.6 9.2 + - - +
301C ARG* 3.1 23.7 + - + +
302C PHE* 3.1 18.4 + - - +
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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