Contacts of the helix formed by residues 233 - 239 (chain A) in PDB entry 4EOZ
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 MET 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A MET 5.2 2.2 - - - +
231A HIS* 2.7 22.0 + - + +
232A GLU* 1.3 78.8 - - - +
234A GLU* 1.3 68.8 + - - +
235A GLU* 3.3 11.4 - - - +
236A SER* 2.8 14.7 + - - -
237A LYS* 3.1 10.6 + - - +
44B ILE* 4.2 9.6 - - + -
49B ASN* 4.2 9.9 - - + +
50B SER 4.4 4.7 - - - -
52B LEU* 3.7 21.1 - - + +
53B SER 4.3 3.6 - - - +
54B PHE* 3.8 37.7 - - + +
57B LEU* 4.6 1.3 - - + -
118B MSE 4.1 25.4 - - + +
122B ILE* 3.6 28.5 - - + -
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Residues in contact with GLU 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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233A MET* 1.3 69.3 - - - +
235A GLU* 1.3 68.8 + - + +
237A LYS* 2.9 9.7 + - - +
238A LYS* 2.8 69.7 + - + +
240A ARG 5.0 2.7 - - - +
242A GLU* 5.4 8.5 - - - +
50B SER 3.8 10.4 + - - +
51B GLY 4.3 10.7 - - - +
52B LEU 3.0 19.3 + - - +
53B SER* 4.0 17.2 - - - -
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET* 4.1 21.3 - - + +
229A PHE* 4.4 8.1 - - + -
233A MET* 4.2 4.9 - - - +
234A GLU* 1.3 75.7 - - + +
236A SER* 1.3 58.2 + - - +
239A ASN* 2.8 31.9 + - - +
240A ARG 3.3 24.6 + - - +
241A VAL* 3.8 24.0 - - + -
242A GLU 5.2 1.7 + - - -
53B SER* 2.4 29.7 + - - -
54B PHE* 2.9 28.9 + - - +
55B GLU* 3.2 17.0 + - - +
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Residues in contact with SER 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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215A LYS* 6.1 1.6 - - - -
228A MET 4.4 7.1 + - - -
229A PHE* 4.1 21.5 + - - +
230A GLU 5.3 0.2 - - - -
231A HIS 3.0 30.2 + - - -
232A GLU* 4.7 3.0 - - - -
233A MET 2.8 9.9 + - - -
235A GLU* 1.3 75.4 - - - +
237A LYS* 1.3 65.2 + - - +
238A LYS 3.6 0.2 + - - -
239A ASN* 3.9 15.0 + - - +
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Residues in contact with LYS 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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232A GLU* 3.0 44.2 + - + +
233A MET 3.1 15.6 + - - +
234A GLU* 2.9 13.1 + - - +
236A SER* 1.3 82.2 - - - +
238A LYS* 1.3 64.7 + - + +
239A ASN* 5.1 2.4 + - - -
50B SER* 4.4 15.4 - - - +
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Residues in contact with LYS 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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234A GLU* 2.8 54.0 + - + +
237A LYS* 1.3 84.4 - - + +
239A ASN* 1.3 71.2 + - - +
240A ARG* 3.3 23.9 + - + +
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Residues in contact with ASN 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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201A ASP 3.6 17.2 + - - +
202A CYS* 3.3 8.5 - - - +
203A CYS* 2.9 25.1 + - - +
215A LYS* 3.2 34.6 + - - +
229A PHE* 5.7 2.2 - - - -
235A GLU 2.8 12.3 + - - +
236A SER* 3.9 11.3 + - - +
237A LYS 3.5 3.4 + - - -
238A LYS* 1.3 80.4 - - - +
240A ARG* 1.3 58.0 + - - +
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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