Contacts of the helix formed by residues 322 - 328 (chain B) in PDB entry 4OBZ
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 GLY 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B ASP 3.3 9.6 - - - -
234B THR* 3.2 16.8 - - - -
236B LEU 3.4 20.4 + - - -
237B MET* 4.1 4.8 - - - -
320B ILE 3.5 1.6 + - - -
321B LEU* 1.3 76.8 - - - +
323B ASP* 1.3 60.2 + - - -
324B VAL 3.3 2.9 - - - -
325B PHE 3.0 17.0 + - - -
326B ILE* 3.1 13.7 + - - +
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP 4.7 0.2 - - - +
13A ALA 4.1 6.2 - - - +
15A TYR* 3.2 40.2 + - + -
169B LEU* 3.4 18.4 - - + +
171B ARG* 3.5 10.3 + - - +
232B THR* 2.8 31.7 - - - +
233B GLY 5.1 0.3 - - - -
234B THR 2.8 19.2 + - - +
235B SER* 3.5 17.3 + - - +
322B GLY* 1.3 67.0 - - - -
324B VAL* 1.4 55.8 + - - +
326B ILE* 4.4 2.7 - - - +
327B GLY* 2.7 32.6 + - - -
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 4.0 17.7 - - - +
235B SER 3.0 21.5 + - - +
236B LEU* 4.0 13.9 - - + -
237B MET* 3.8 24.9 - - + -
285B LEU* 4.3 9.1 - - + +
289B ASP* 3.6 20.4 - - - +
290B TYR* 4.0 13.7 - - + -
292B LEU* 4.0 27.1 - - + -
305B GLY* 4.2 6.7 - - - +
322B GLY 3.3 0.6 - - - -
323B ASP* 1.4 75.0 - - - +
325B PHE* 1.4 63.3 + - - +
327B GLY* 4.2 0.9 - - - -
328B ARG* 3.8 14.4 + - - +
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Residues in contact with PHE 325 (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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237B MET* 3.7 30.9 - - + -
276B LEU* 4.3 13.2 - - + -
278B LEU* 3.8 19.5 - - + -
283B TYR* 3.7 37.2 - + + -
285B LEU* 4.5 8.1 - - + -
321B LEU* 4.0 21.1 - - + +
322B GLY 3.0 10.0 + - - +
324B VAL* 1.4 75.5 - - - +
326B ILE* 1.4 55.4 + - + +
327B GLY 3.1 3.1 - - - -
328B ARG* 3.0 11.8 + - - +
329B TYR* 2.9 46.7 + + + -
342B PHE* 3.4 41.3 - + - -
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Residues in contact with ILE 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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167B PHE* 4.2 21.3 - - + +
168B TYR* 5.5 0.2 - - - -
169B LEU* 3.6 34.5 + - + -
230B VAL* 4.0 23.8 - - + -
231B ASP 4.1 8.1 - - - +
232B THR* 3.6 28.9 - - + -
321B LEU 4.1 7.4 - - - +
322B GLY 3.1 15.2 + - - +
323B ASP* 4.7 0.9 - - - +
325B PHE* 1.4 76.2 - - + +
327B GLY* 1.3 61.5 + - - +
329B TYR 3.0 24.1 - - - +
330B TYR* 3.9 2.8 + - - -
331B THR* 3.4 21.1 - - - +
333B PHE* 4.8 1.8 - - + -
345B ALA* 4.9 0.9 - - - +
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 5.6 0.3 - - - -
169B LEU* 3.6 19.8 - - - +
171B ARG* 3.6 28.1 - - - +
323B ASP 2.7 23.2 + - - -
325B PHE 3.0 0.4 + - - -
326B ILE* 1.3 73.1 - - - +
328B ARG* 1.4 55.8 + - - +
345B ALA* 3.4 17.8 - - - +
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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
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171B ARG* 4.7 0.8 - - - +
284B LYS* 3.7 30.2 + - - +
285B LEU* 4.2 9.6 - - + -
286B SER* 4.1 12.5 - - - +
289B ASP* 2.9 40.2 + - + +
324B VAL 3.8 9.5 + - - +
325B PHE 3.0 8.1 + - - +
327B GLY* 1.4 74.5 - - - +
329B TYR* 1.4 90.8 + - + +
344B GLU* 3.5 30.1 + - - +
345B ALA* 3.1 22.7 + - - +
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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