Contacts of the helix formed by residues 238 - 248 (chain A) in PDB entry 1O94
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 VAL 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLU* 3.1 30.4 + - + +
237A GLU* 1.3 84.3 - - - +
239A ASP* 1.3 74.7 + - - +
242A LYS* 3.5 38.2 + - - +
619B PRO* 3.7 24.5 - - + -
620B GLY* 5.3 0.4 - - - +
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 5.4 2.7 - - + -
182A PRO* 4.8 3.6 - - - +
195A LEU* 3.7 22.3 - - + +
198A ARG* 2.8 43.3 + - - +
223A PHE* 5.1 0.2 - - - -
233A GLN 5.0 4.2 - - - +
234A ILE* 4.1 25.6 - - + +
235A GLU 3.2 4.5 + - - +
238A VAL* 1.3 89.8 - - - +
240A GLY* 1.3 55.8 + - - +
241A GLN 3.5 0.2 - - - -
242A LYS* 3.4 1.6 + - - +
243A PHE* 2.8 38.0 + - - +
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.4 25.0 - - - -
225A VAL* 3.8 21.8 - - - -
234A ILE* 4.3 1.0 - - - +
235A GLU 3.0 12.9 + - - -
236A ALA 3.3 6.9 + - - -
239A ASP* 1.3 78.0 - - - +
241A GLN* 1.3 63.2 + - - +
243A PHE 3.2 0.3 + - - -
244A VAL* 3.1 19.4 + - - +
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A VAL* 5.5 2.5 - - + -
236A ALA* 2.7 19.1 + - + +
237A GLU* 3.8 26.6 - - - +
238A VAL 4.5 0.8 + - - +
239A ASP 3.5 0.2 - - - -
240A GLY* 1.3 73.2 - - - +
242A LYS* 1.3 65.7 + - + +
244A VAL* 3.2 7.9 + - - +
245A GLU* 3.2 28.5 + - - +
285A LEU* 2.9 41.3 + - + +
286A VAL* 5.4 0.7 - - + -
288A GLN* 3.1 28.7 - - - +
289A VAL* 3.6 24.3 - - + +
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Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 3.4 25.1 - - + -
237A GLU 5.3 3.8 + - - -
238A VAL* 3.5 29.0 + - - +
239A ASP* 3.4 3.3 + - - +
240A GLY 3.2 0.8 - - - -
241A GLN* 1.3 76.3 - - + +
243A PHE* 1.3 65.3 + - - +
245A GLU* 3.4 18.0 + - - +
246A MET* 3.2 28.1 + - + +
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Residues in contact with PHE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.9 16.6 - - + -
195A LEU* 4.3 3.5 - - + +
199A ALA* 3.7 32.8 - - + -
202A TRP* 3.4 54.7 - + + -
203A LEU* 4.1 15.0 - - + -
223A PHE* 3.7 25.8 - + + -
239A ASP 2.8 22.4 + - - +
240A GLY 3.6 3.1 - - - +
242A LYS* 1.3 73.9 - - - +
244A VAL* 1.3 64.6 + - - +
246A MET* 3.0 9.4 + - - +
247A ALA* 3.0 31.2 + - + +
254A TRP* 3.8 19.7 - + - -
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 4.0 15.0 - - + -
240A GLY 3.1 15.8 + - - +
241A GLN* 3.2 8.3 + - - +
243A PHE* 1.3 73.9 - - - +
245A GLU* 1.3 54.1 + - - +
248A ASP* 2.8 37.8 + - - +
254A TRP* 3.5 33.5 - - + -
286A VAL* 4.1 22.4 - - + -
289A VAL* 3.6 21.5 - - + -
290A SER* 3.7 26.2 - - - -
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Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLN* 3.2 16.5 + - - +
242A LYS* 3.7 20.2 - - - +
243A PHE 3.1 0.6 - - - -
244A VAL* 1.3 75.9 - - - +
246A MET* 1.3 65.0 + - + +
247A ALA 3.4 0.3 + - - -
248A ASP* 3.6 13.6 + - - +
249A SER 5.0 1.0 + - - -
289A VAL* 3.8 37.6 - - + +
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Residues in contact with MET 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 3.7 32.5 - - + -
196A GLU* 3.8 36.8 - - + +
199A ALA* 4.0 24.0 - - - -
203A LEU* 3.8 24.1 - - + +
242A LYS* 3.2 15.5 + - + +
243A PHE* 3.0 10.6 + - + +
245A GLU* 1.3 78.9 - - + +
247A ALA* 1.3 58.5 + - - +
249A SER* 4.9 6.4 + - - -
250A LEU* 5.2 2.3 - - - +
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.6 20.9 - - + -
206A LEU* 4.3 10.5 - - + -
243A PHE* 3.0 25.4 + - + +
244A VAL 3.6 0.2 - - - -
246A MET* 1.3 76.9 - - - +
248A ASP* 1.3 60.0 + - - +
249A SER 3.3 2.5 - - - -
250A LEU* 2.8 25.6 + - - +
251A VAL* 3.3 12.0 - - - +
254A TRP* 3.7 20.9 - - + -
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Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A VAL 2.8 16.2 + - - +
245A GLU* 3.6 11.8 + - - +
246A MET 3.5 2.2 - - - -
247A ALA* 1.3 76.3 - - - +
249A SER* 1.3 59.4 - - - +
250A LEU 3.3 0.9 + - - -
251A VAL* 3.3 7.8 + - - +
254A TRP* 2.9 21.5 + - - +
289A VAL 4.4 2.0 - - - +
290A SER* 2.7 30.3 + - - -
291A LYS* 2.8 34.8 + - - +
292A LYS* 2.8 36.0 + - - +
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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