Contacts of the helix formed by residues 322 - 333 (chain B) in PDB entry 1U2X
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 TYR 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B LEU* 3.0 25.4 + - + +
318B SER 4.1 0.2 + - - -
320B LEU* 3.4 29.4 - - + -
321B GLY* 1.3 78.7 - - - +
323B ARG* 1.3 56.4 + - - +
324B GLU* 3.3 2.9 - - - -
325B LEU* 3.4 11.0 + - + -
326B ALA* 3.0 28.8 + - - +
344B ILE* 3.6 43.6 - - + +
348B GLU* 2.6 37.1 + - + +
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Residues in contact with ARG 323 (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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289B ARG* 3.1 23.4 - - - +
318B SER* 2.9 38.6 + - - +
321B GLY* 3.3 12.4 + - - +
322B TYR* 1.3 76.3 - - - +
324B GLU* 1.3 58.7 + - - +
326B ALA* 3.4 5.4 + - - +
327B ASP* 2.9 50.2 + - - +
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Residues in contact with GLU 324 (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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322B TYR 5.1 0.2 - - - -
323B ARG* 1.3 80.2 - - - +
325B LEU* 1.3 63.7 + - - +
327B ASP* 3.4 7.2 + - - +
328B ARG* 3.2 46.2 + - + +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 3.8 13.7 - - + -
322B TYR* 3.4 15.3 + - + +
324B GLU* 1.3 78.4 - - - +
326B ALA* 1.3 64.6 + - - +
328B ARG* 3.3 29.7 + - - +
329B ILE* 3.0 21.8 + - + +
337B ASP* 4.1 26.5 - - + +
340B LEU* 4.0 12.3 - - + -
341B GLY* 3.7 21.5 - - - +
344B ILE* 3.5 32.8 - - + -
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Residues in contact with ALA 326 (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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314B ALA* 3.4 36.5 - - + +
317B LEU* 3.9 8.0 - - + +
318B SER* 3.7 17.3 - - - +
322B TYR 3.0 17.1 + - - +
323B ARG* 3.7 4.7 - - - +
325B LEU* 1.3 78.7 - - - +
327B ASP* 1.3 59.0 + - - +
329B ILE* 3.1 4.6 + - - +
330B PHE* 2.8 30.5 + - - +
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Residues in contact with ASP 327 (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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323B ARG* 2.9 38.8 + - - +
324B GLU* 3.7 6.6 - - - +
326B ALA* 1.3 75.6 - - - +
328B ARG* 1.3 51.1 + - + +
330B PHE* 3.2 9.2 + - - +
331B THR* 2.7 46.5 + - - +
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Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLU* 3.2 38.8 + - + +
325B LEU* 3.5 29.1 - - - +
327B ASP* 1.3 80.9 - - + +
329B ILE* 1.3 58.1 + - - +
331B THR* 4.5 3.6 - - - -
332B TYR* 2.8 41.2 + - + +
333B ASN 3.9 0.3 + - - -
334B ARG* 3.5 25.5 - - - +
337B ASP* 3.8 22.0 + - - +
340B LEU* 4.7 9.7 - - - +
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Residues in contact with ILE 329 (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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310B GLU* 4.2 22.4 - - + +
313B ILE* 3.6 15.5 - - + -
314B ALA* 4.3 7.9 - - + +
317B LEU* 3.4 33.4 - - + -
325B LEU* 3.0 13.4 + - + +
326B ALA* 3.6 6.3 - - - +
328B ARG* 1.3 73.5 - - - +
330B PHE* 1.3 69.2 + - - +
333B ASN* 3.1 33.6 + - - +
334B ARG 6.0 0.2 - - - +
337B ASP* 3.7 40.2 - - + +
338B SER* 4.3 14.1 - - - +
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Residues in contact with PHE 330 (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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311B ALA* 6.2 5.2 - - + -
314B ALA* 4.4 12.1 - - + +
326B ALA 2.8 13.7 + - - +
327B ASP* 3.4 11.2 - - - +
329B ILE* 1.3 80.9 - - - +
331B THR* 1.3 71.9 + - - +
333B ASN* 3.9 11.5 + - - +
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Residues in contact with THR 331 (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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327B ASP* 2.7 31.6 + - - +
328B ARG* 4.5 0.4 - - - -
330B PHE* 1.3 84.7 - - - +
332B TYR* 1.4 93.1 + - + +
333B ASN* 4.3 4.3 + - - -
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ARG* 2.8 30.4 + - + +
331B THR* 1.4 97.5 - - + +
333B ASN* 1.3 73.3 + - - +
334B ARG* 3.1 50.4 + - + +
1002B SO4 4.9 1.6 + - - -
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Residues in contact with ASN 333 (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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310B GLU* 3.5 33.7 - - - +
328B ARG 3.9 1.8 + - - -
329B ILE* 3.1 28.7 + - - +
330B PHE* 3.9 14.2 + - - +
331B THR 4.3 3.2 + - - -
332B TYR* 1.3 80.5 + - - +
334B ARG* 1.3 64.2 + - - +
335B LEU 3.6 1.2 + - - -
338B SER* 5.2 2.0 + - - -
1002B SO4 3.8 7.6 + - - -
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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