Contacts of the helix formed by residues 272 - 283 (chain C) in PDB entry 6Q2J
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 SER 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243C LYS 4.6 3.8 + - - -
246C GLN* 5.6 1.6 + - - -
270C SER* 3.2 12.8 - - - -
271C GLY* 1.3 82.2 - - - +
273C ASP* 1.3 63.4 + - - +
274C ASP* 3.8 17.4 + - - +
275C CYS* 3.2 23.4 + - - +
276C LYS* 3.5 6.8 + - - +
317C PHE* 4.5 0.2 - - - -
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Residues in contact with ASP 273 (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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180C PHE* 4.7 12.3 - - + -
184C GLN* 4.9 3.6 + - - -
271C GLY 4.7 2.1 - - - +
272C SER* 1.3 72.5 - - - +
274C ASP* 1.3 61.7 + - - +
275C CYS 3.3 0.2 - - - -
276C LYS* 3.3 30.3 + - + +
277C ALA* 2.9 27.9 + - - +
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Residues in contact with ASP 274 (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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243C LYS* 3.7 37.0 - - + +
272C SER* 3.2 11.9 + - - +
273C ASP* 1.3 78.2 - - - +
275C CYS* 1.3 57.3 + - - +
277C ALA* 3.8 5.7 - - - +
278C ALA* 2.9 30.1 + - - +
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Residues in contact with CYS 275 (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 PHE* 4.7 2.7 - - - -
243C LYS* 4.0 6.6 - - - +
244C CYS* 2.0 56.7 - - + -
269C CYS* 4.3 10.3 - - - -
270C SER 3.5 20.9 - - - +
272C SER* 3.2 14.2 + - - +
274C ASP* 1.3 76.3 - - - +
276C LYS* 1.3 59.6 + - - +
278C ALA* 3.4 0.4 + - - -
279C TYR* 3.0 30.3 + - - +
316C CYS* 4.7 2.9 - - - -
317C PHE* 4.4 11.4 - - + -
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Residues in contact with LYS 276 (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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180C PHE* 4.5 11.9 - - + -
184C GLN* 3.1 32.9 - - + +
188C PHE* 3.5 28.0 - - + -
271C GLY 5.0 2.6 + - - -
272C SER 3.9 4.3 - - - +
273C ASP* 3.3 34.0 + - - +
274C ASP 3.3 0.4 - - - -
275C CYS* 1.3 77.7 - - - +
277C ALA* 1.3 56.7 + - - +
279C TYR* 3.3 5.0 + - - +
280C ILE* 3.0 38.7 + - + +
317C PHE* 3.6 42.1 - - + -
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Residues in contact with ALA 277 (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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180C PHE* 4.2 23.3 - - + -
273C ASP 2.9 17.3 + - - +
274C ASP* 3.9 7.0 - - - +
275C CYS 3.3 0.2 - - - -
276C LYS* 1.3 75.4 - - - +
278C ALA* 1.3 57.2 + - - +
280C ILE* 3.5 2.5 + - - +
281C ASP* 2.9 40.3 + - - +
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Residues in contact with ALA 278 (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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236C HIS 4.7 0.4 - - - +
239C THR* 4.0 21.1 - - + +
240C PHE* 3.7 33.4 - - + +
243C LYS* 4.4 3.6 - - + -
274C ASP 2.9 17.5 + - - +
275C CYS* 3.8 4.7 - - - +
276C LYS 3.3 0.2 - - - -
277C ALA* 1.3 78.1 - - - +
279C TYR* 1.3 56.9 - - - +
281C ASP* 3.2 7.9 + - - +
282C ILE* 3.0 32.6 + - - +
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Residues in contact with TYR 279 (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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187C ALA* 4.7 4.9 - - + -
188C PHE* 3.5 40.8 - + + -
240C PHE* 3.8 22.4 - + + -
275C CYS* 3.0 19.1 + - - +
276C LYS 3.9 2.9 - - - +
278C ALA* 1.3 73.2 - - - +
280C ILE* 1.3 67.3 + - - +
282C ILE* 3.2 37.1 - - + +
283C LEU* 3.4 36.1 + - + +
287C LEU 6.1 1.3 - - - -
311C LEU 4.3 17.8 + - - -
312C HIS 5.1 3.4 - - - -
313C ARG* 3.8 26.2 - - + +
317C PHE* 6.5 0.4 - - + -
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Residues in contact with ILE 280 (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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175C TYR* 4.1 35.8 - - + +
180C PHE* 4.0 25.4 - - + -
183C ALA* 4.0 8.5 - - + +
184C GLN* 3.8 34.8 - - + +
187C ALA* 4.2 18.6 - - + -
188C PHE* 5.4 3.4 - - + -
276C LYS* 3.0 24.3 + - + +
277C ALA* 3.9 4.9 - - - +
278C ALA 3.3 0.2 - - - -
279C TYR* 1.3 81.4 - - + +
281C ASP* 1.3 64.0 + - - +
283C LEU* 3.2 24.6 + - + +
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Residues in contact with ASP 281 (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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172C ARG* 5.7 2.8 - - - +
176C GLN* 5.4 10.0 + - - +
232C LEU* 5.8 0.9 - - - +
236C HIS* 3.4 37.3 + - + +
239C THR* 5.8 4.5 - - + +
277C ALA* 2.9 28.2 + - - +
278C ALA* 3.2 8.4 + - - +
280C ILE* 1.3 81.2 - - - +
282C ILE* 1.3 59.2 + - - +
283C LEU 4.3 3.9 - - - +
285C THR* 5.3 3.5 - - - +
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Residues in contact with ILE 282 (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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236C HIS* 3.4 36.3 - - + +
237C TYR 4.1 1.3 - - - +
240C PHE* 4.0 25.8 - - + -
278C ALA 3.0 15.1 + - - +
279C TYR* 3.2 41.5 - - + +
280C ILE 3.2 0.2 - - - -
281C ASP* 1.3 75.1 - - - +
283C LEU* 1.3 63.1 + - + +
284C GLY 3.2 1.4 + - - -
285C THR* 2.8 27.4 + - - +
287C LEU* 4.0 38.7 - - + +
288C GLN 4.8 1.4 + - - -
311C LEU* 5.0 4.5 - - + -
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Residues in contact with LEU 283 (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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171C ILE* 3.9 10.3 - - + +
172C ARG* 4.3 9.9 - - - +
175C TYR* 3.8 36.4 - - + +
187C ALA* 3.7 31.2 - - + +
206C HIS* 6.2 3.1 - - + -
279C TYR* 3.4 38.9 + - + +
280C ILE* 3.2 18.3 + - - +
281C ASP 4.3 3.5 - - - +
282C ILE* 1.3 75.1 - - + +
284C GLY* 1.3 57.7 + - - +
285C THR 3.7 0.2 - - - -
288C GLN* 3.8 34.5 - - + +
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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