Contacts of the helix formed by residues 326 - 334 (chain B) in PDB entry 1R9T
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 ASP 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ILE* 3.5 8.2 - - - +
324B ILE* 3.6 6.4 + - - +
325B GLN* 1.4 83.9 + - - +
327B ARG* 1.3 61.5 - - + +
328B GLU* 1.9 33.9 + - - +
329B THR* 2.3 53.2 + - - +
330B ALA* 4.0 4.9 - - - -
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Residues in contact with ARG 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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287B ARG* 4.2 11.1 - - - +
288B ALA* 2.5 27.4 + - - -
289B LEU* 4.3 4.0 - - - +
290B GLY* 3.5 31.1 - - - +
292B ILE* 2.9 23.6 - - + +
326B ASP* 1.3 76.2 - - + +
328B GLU* 1.4 63.1 + - + +
329B THR 3.5 0.2 - - - -
330B ALA* 3.4 4.9 + - - +
331B LEU* 3.3 52.3 + - - +
353B LYS* 3.7 32.6 - - - +
357B GLN* 5.6 4.6 - - - +
371B GLU* 5.3 10.7 - - - +
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Residues in contact with GLU 328 (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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326B ASP* 1.9 21.8 + - - +
327B ARG* 1.4 75.2 - - + +
329B THR* 1.3 59.9 - - + +
330B ALA 3.4 2.0 - - - -
331B LEU* 3.6 12.1 + - - +
332B ASP* 3.4 15.9 + - - +
345B LYS* 5.5 2.4 - - - -
349B ILE* 4.2 15.4 - - + +
353B LYS* 6.0 4.3 - - - +
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Residues in contact with THR 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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324B ILE* 2.9 26.3 - - - +
326B ASP* 2.3 61.2 + - - +
328B GLU* 1.3 76.1 - - + +
330B ALA* 1.3 61.6 + - - -
332B ASP* 2.8 41.4 - - - +
345B LYS* 4.0 19.3 - - - +
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Residues in contact with ALA 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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284B ILE* 3.5 24.0 - - + +
287B ARG* 3.6 12.8 - - + -
288B ALA* 3.0 44.9 - - + +
324B ILE* 4.0 4.2 - - + +
326B ASP 3.4 4.8 + - - -
327B ARG 3.7 4.9 - - - +
329B THR* 1.3 71.8 - - - +
331B LEU* 1.3 61.1 + - - +
332B ASP 2.4 15.0 + - - -
333B PHE* 2.6 18.9 + - - +
334B ILE* 3.8 5.7 + - - +
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Residues in contact with LEU 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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288B ALA* 3.4 24.5 - - + +
327B ARG* 3.3 43.5 + - - +
328B GLU* 3.6 10.7 - - - +
329B THR 3.2 0.4 - - - -
330B ALA* 1.3 74.6 - - - +
332B ASP* 1.3 72.6 - - - +
334B ILE* 3.4 6.9 + - + +
348B ARG 3.9 3.3 - - - +
349B ILE* 4.0 23.3 - - + -
352B ALA* 3.6 27.3 - - + +
353B LYS* 4.0 29.2 - - + +
356B LEU* 3.7 24.7 - - + -
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Residues in contact with ASP 332 (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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328B GLU 3.4 7.7 + - - +
329B THR* 2.8 48.0 - - - +
330B ALA 2.4 1.0 + - - -
331B LEU* 1.3 97.9 - - - +
333B PHE* 1.4 63.9 - - + +
334B ILE* 2.2 26.0 + - - +
335B GLY 3.7 0.3 + - - -
345B LYS* 3.8 19.1 + - - +
348B ARG* 3.2 38.0 + - - +
349B ILE* 4.9 5.2 - - - +
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Residues in contact with PHE 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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278B GLN* 4.9 14.4 - - - -
279B ASP 5.4 2.7 - - - -
280B ILE* 4.5 20.0 - - + +
281B PRO* 4.7 11.9 - - + -
284B ILE* 4.6 13.5 - - + -
324B ILE* 3.9 25.4 - - + -
329B THR 4.2 0.2 - - - +
330B ALA 2.6 10.9 + - - +
332B ASP* 1.4 75.5 - - + +
334B ILE* 1.3 64.6 + - + +
335B GLY 3.7 14.1 + - - +
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Residues in contact with ILE 334 (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 LEU* 5.4 2.2 - - + -
276B ILE* 4.1 33.9 - - + -
277B LYS* 5.0 1.1 - - - -
280B ILE* 4.2 20.9 - - + -
284B ILE* 5.1 5.2 - - + -
285B ILE* 4.5 15.7 - - + -
288B ALA* 5.3 1.1 - - + -
330B ALA 4.0 11.0 - - - +
331B LEU* 3.7 8.8 - - + +
332B ASP 2.2 16.3 + - - +
333B PHE* 1.3 81.0 - - + +
335B GLY* 1.4 55.7 - - - +
348B ARG 3.4 19.0 - - - +
351B TYR* 4.5 9.6 - - - -
352B ALA* 3.9 14.0 + - + +
355B ILE* 5.6 3.1 - - + +
356B LEU* 4.2 24.5 - - + -
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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