Contacts of the helix formed by residues 273 - 284 (chain B) in PDB entry 2QFZ
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 HIS 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B TYR* 5.8 5.4 - + - -
274B GLN* 1.3 66.6 + - - +
275B ASP* 3.2 4.3 - - - +
276B THR* 3.7 16.9 + - - +
277B TYR* 3.2 21.8 + - - +
307B PHE* 3.6 23.2 - + + -
311B ILE* 3.7 34.3 + - + +
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Residues in contact with GLN 274 (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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273B HIS* 1.3 78.3 - - - +
275B ASP* 1.3 58.6 + - - +
277B TYR* 3.4 7.8 + - - +
278B ARG* 2.8 28.6 + - - +
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Residues in contact with ASP 275 (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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404A HIS* 5.8 1.4 + - - -
405A ARG* 3.7 10.9 + - - -
273B HIS* 3.2 1.6 - - - +
274B GLN* 1.3 77.6 - - - +
276B THR* 1.3 63.6 + - - +
277B TYR 3.2 0.2 - - - -
278B ARG* 3.2 34.8 + - - +
279B GLN* 3.2 35.5 + - - +
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Residues in contact with THR 276 (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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273B HIS* 3.7 21.8 + - - +
274B GLN 3.5 0.2 - - - -
275B ASP* 1.3 78.2 - - - +
277B TYR* 1.3 65.2 + - - +
279B GLN* 3.4 10.8 + - - +
280B ILE* 3.1 40.7 + - + +
307B PHE* 4.1 12.3 - - + -
310B ALA* 3.8 23.7 - - + +
311B ILE* 5.4 2.0 - - + -
317B GLY* 5.9 1.0 - - - -
318B TYR* 4.1 11.7 + - + +
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Residues in contact with TYR 277 (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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265B TYR* 4.4 16.2 - + - -
273B HIS 3.2 14.9 + - - +
274B GLN* 3.6 6.7 - - - +
275B ASP 3.2 0.4 - - - -
276B THR* 1.3 81.8 - - - +
278B ARG* 1.3 59.6 + - - +
280B ILE* 3.1 7.5 + - + +
281B HIS* 2.9 69.1 + + + +
303B GLU* 3.4 26.2 + - + -
307B PHE* 4.2 22.4 - + + -
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Residues in contact with ARG 278 (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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404A HIS* 4.8 12.9 + - - -
405A ARG* 3.3 64.5 - - - +
408A ASP* 4.1 9.1 + - - +
274B GLN 2.8 18.8 + - - +
275B ASP* 3.2 31.2 + - - +
276B THR 3.3 0.2 - - - -
277B TYR* 1.3 80.7 - - - +
279B GLN* 1.3 74.7 + - - +
281B HIS* 3.4 6.8 + - - +
282B ILE* 3.1 54.4 + - + +
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Residues in contact with GLN 279 (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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404A HIS* 6.1 2.5 - - - -
408A ASP* 4.6 18.1 - - - +
275B ASP* 3.2 27.7 + - - +
276B THR* 3.6 11.1 - - - +
278B ARG* 1.3 90.9 - - - +
280B ILE* 1.3 65.1 + - - +
282B ILE* 3.3 9.5 + - - +
283B ASP* 3.2 28.6 + - - +
318B TYR* 3.9 32.0 + - + +
320B GLN 5.8 1.0 + - - -
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Residues in contact with ILE 280 (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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276B THR* 3.1 30.3 + - + +
277B TYR* 3.6 8.5 - - + +
279B GLN* 1.3 78.6 - - - +
281B HIS* 1.3 58.1 + - - +
283B ASP 3.3 0.7 + - - -
284B ILE* 3.0 53.9 + - + +
303B GLU* 3.8 23.3 - - + +
306B LEU* 4.0 10.3 - - + +
307B PHE* 3.6 38.8 - - + +
318B TYR* 3.7 31.0 - - + -
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Residues in contact with HIS 281 (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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277B TYR* 2.9 48.6 + + + +
278B ARG* 3.7 7.4 - - - +
280B ILE* 1.3 78.3 - - - +
282B ILE* 1.3 58.3 + - + +
285B PRO* 3.0 30.1 - - + +
299B THR* 6.1 0.4 - - + -
303B GLU* 3.0 29.3 + - - -
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Residues in contact with ILE 282 (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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405A ARG* 5.8 1.8 - - + +
408A ASP* 3.5 24.7 - - + +
409A GLN* 4.0 25.1 - - - +
278B ARG* 3.1 41.2 + - + +
279B GLN* 3.7 5.6 - - - +
280B ILE 3.2 0.2 - - - -
281B HIS* 1.3 81.5 - - + +
283B ASP* 1.3 66.7 + - - +
285B PRO* 3.6 4.9 - - - +
286B ARG* 3.5 44.1 + - - +
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Residues in contact with ASP 283 (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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411A GLU* 4.7 1.7 - - - +
279B GLN 3.2 9.9 + - - +
280B ILE 4.0 1.1 - - - +
282B ILE* 1.3 83.8 - - - +
284B ILE* 1.3 66.3 + - + +
286B ARG* 3.1 25.9 + - - +
287B MET* 3.3 10.1 + - - +
318B TYR* 2.6 38.1 + - - +
320B GLN* 3.0 20.5 + - - +
323B ASN* 4.5 9.6 + - - +
1011B UNX 2.5 29.9 - - - -
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Residues in contact with ILE 284 (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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280B ILE* 3.0 33.9 + - + +
283B ASP* 1.3 74.6 - - - +
285B PRO* 1.3 72.7 - - + +
286B ARG 2.9 1.7 + - - -
287B MET* 3.0 27.7 + - - +
293B ILE* 3.1 18.8 - - + +
299B THR* 3.6 24.9 - - + +
302B PHE* 3.8 21.1 - - + -
303B GLU* 3.7 15.0 - - + +
306B LEU* 3.7 28.5 - - + -
318B TYR* 4.6 2.7 - - - +
323B ASN* 3.8 17.9 - - + -
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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