Contacts of the helix formed by residues 296 - 302 (chain B) in PDB entry 1OI4
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 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLU* 3.5 3.4 + - - -
96A HIS* 3.1 61.4 + + + +
99A ASP* 3.9 21.0 + - - -
100A TYR* 2.9 28.2 + + - -
233B GLU* 2.9 33.6 + - + +
267B LYS* 3.7 19.9 + - + -
295B GLY* 1.3 74.9 + - - -
297B SER* 1.3 64.5 + - - +
298B PRO* 3.4 2.0 - - - -
299B ASP* 3.2 18.6 + - - +
300B TYR* 3.2 18.7 + - + -
326B HIS* 5.6 2.1 + + - -
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Residues in contact with SER 297 (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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229B LEU 4.3 1.2 + - - -
230B ILE* 3.7 4.7 - - - -
231B THR* 3.0 39.4 + - - +
232B ASP 4.0 1.8 - - - -
233B GLU 3.8 3.6 + - - -
234B PHE* 3.7 26.7 - - - -
293B PRO* 4.6 3.0 + - - -
294B GLY 3.8 1.6 - - - -
296B HIS* 1.3 78.2 - - - +
298B PRO* 1.3 71.8 - - - +
300B TYR* 3.1 3.8 + - - +
301B LEU* 3.0 32.3 + - - +
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Residues in contact with PRO 298 (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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293B PRO 3.3 18.8 - - - +
294B GLY* 3.4 11.4 - - - +
295B GLY 3.7 7.0 - - - +
296B HIS 3.6 2.9 - - - -
297B SER* 1.3 96.3 - - - +
299B ASP* 1.3 54.3 - - - +
301B LEU* 4.5 0.9 - - + +
302B ARG* 2.8 37.9 + - - +
326B HIS 3.6 27.6 - - - +
327B GLY* 3.7 8.5 - - - +
329B GLN* 3.7 12.8 - - + +
330B LEU* 4.3 21.4 - - + +
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Residues in contact with ASP 299 (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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96A HIS* 3.8 14.4 - - + -
126A HIS* 2.8 38.9 + - - -
129A GLN* 5.5 0.5 + - - -
147A PRO* 3.4 29.8 - - - +
148A ILE* 4.7 3.3 - - - +
296B HIS* 3.2 16.0 + - - +
297B SER 3.2 0.6 - - - -
298B PRO* 1.3 80.9 - - - +
300B TYR* 1.3 77.1 + - - +
302B ARG* 3.5 12.7 + - - +
303B GLY* 3.9 0.7 + - - -
329B GLN* 3.9 13.0 + - - +
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Residues in contact with TYR 300 (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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67A LYS* 3.3 26.6 + - - -
96A HIS* 3.1 22.3 + + - -
231B THR* 3.8 15.7 - - + +
232B ASP* 3.5 28.5 - - + -
233B GLU* 2.4 32.8 + - + -
258B LYS* 5.4 6.1 + - - -
296B HIS 3.2 8.7 + - - -
297B SER 3.1 6.1 + - - +
299B ASP* 1.3 97.7 - - - +
301B LEU* 1.3 62.1 + - + +
303B GLY* 3.5 9.9 + - - -
304B ASP* 4.5 3.8 + - - +
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Residues in contact with LEU 301 (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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229B LEU* 3.7 34.8 - - + +
230B ILE* 4.0 2.0 - - - +
231B THR* 3.9 20.2 - - + -
257B GLU* 4.7 6.1 - - + -
258B LYS* 5.7 3.1 - - - +
297B SER* 3.0 36.6 + - - +
298B PRO* 4.0 2.5 - - + +
300B TYR* 1.3 72.9 - - - +
302B ARG* 1.3 55.4 + - - +
303B GLY 3.0 11.2 + - - -
304B ASP* 3.0 25.2 + - - +
307B PHE* 3.7 45.4 - - + +
330B LEU* 4.0 18.8 - - + -
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Residues in contact with ARG 302 (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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129A GLN* 5.5 0.2 - - - +
146A LYS 5.1 0.9 - - - +
147A PRO* 3.3 29.0 + - + +
148A ILE* 4.5 5.3 - - - +
150A ILE* 3.3 11.5 - - - +
151A ASP* 2.8 38.4 + - - -
298B PRO 2.8 28.4 + - - +
299B ASP* 3.5 19.5 + - - +
301B LEU* 1.3 71.5 - - - +
303B GLY* 1.3 57.3 + - - +
304B ASP 3.2 3.2 + - - -
308B VAL* 3.7 15.6 - - - +
329B GLN* 3.3 48.2 + - - +
330B LEU* 3.6 20.1 - - + +
332B ILE* 3.8 8.1 - - - +
333B SER* 2.8 35.3 + - - +
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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