Contacts of the helix formed by residues 233 - 239 (chain A) in PDB entry 6OE7
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 SER 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ARG* 4.2 0.2 - - - -
231A GLU 4.1 2.8 + - - -
232A VAL* 1.3 74.6 - - - +
234A THR* 1.3 54.6 + - - +
235A GLN* 4.1 8.0 + - - +
236A GLU* 3.2 29.3 + - - +
237A ALA* 2.8 31.7 + - - +
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Residues in contact with THR 234 (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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103A MET* 4.1 15.9 - - + -
112A LEU* 3.7 49.0 + - + -
113A GLY* 4.8 5.5 + - - +
117A ARG* 4.1 8.4 + - - +
232A VAL 3.9 0.2 + - - -
233A SER* 1.3 67.9 - - - +
235A GLN* 1.3 57.7 + - - +
237A ALA* 3.2 7.3 + - - +
238A LEU* 2.8 50.3 + - + +
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Residues in contact with GLN 235 (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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233A SER* 3.3 8.1 + - - +
234A THR* 1.3 80.2 - - - +
236A GLU* 1.3 75.1 + - - +
238A LEU* 3.4 14.8 + - - +
239A LYS* 3.7 26.7 + - - +
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Residues in contact with GLU 236 (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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232A VAL* 3.7 16.2 - - + -
233A SER* 3.2 24.3 + - - +
235A GLN* 1.3 84.7 - - + +
237A ALA* 1.3 62.5 + - - +
239A LYS* 3.2 52.1 + - - +
240A LEU* 4.2 6.4 + - - +
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Residues in contact with ALA 237 (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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112A LEU* 5.9 0.2 - - + -
117A ARG* 3.5 37.5 - - - +
226A TRP* 3.5 20.2 - - + -
232A VAL* 3.8 6.5 - - + +
233A SER 2.8 19.8 + - - +
234A THR* 3.2 6.5 + - + +
236A GLU* 1.3 73.8 - - - +
238A LEU* 1.3 61.9 + - + +
240A LEU* 3.1 30.3 + - + +
241A ILE* 4.0 0.3 - - - +
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Residues in contact with LEU 238 (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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99A SER* 5.5 3.6 - - - +
102A VAL* 4.2 19.7 - - + -
103A MET* 3.7 34.8 - - + -
112A LEU* 4.4 9.9 - - + -
198A ILE* 5.6 3.4 - - + -
226A TRP* 4.4 11.4 - - + -
234A THR* 2.8 30.2 + - + +
235A GLN* 3.9 8.7 - - - +
236A GLU 3.3 0.4 - - - -
237A ALA* 1.3 72.4 - - + +
239A LYS* 1.3 55.2 - - - +
241A ILE* 3.2 43.9 + - + +
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Residues in contact with LYS 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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235A GLN* 3.7 28.8 + - - +
236A GLU* 3.2 42.2 + - - +
237A ALA 3.1 0.8 - - - -
238A LEU* 1.3 75.3 - - - +
240A LEU* 1.3 58.0 + - + +
241A ILE 3.3 2.6 - - - +
242A HIS* 3.4 17.0 + - - -
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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