Contacts of the strand formed by residues 233 - 239 (chain A) in PDB entry 2WO6
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASN* 3.8 0.6 + - - -
141A ASP* 2.8 24.9 + - - -
145A TYR 3.4 19.3 - - - -
146A ASP* 4.3 0.2 - - - -
147A TYR* 3.3 44.6 + + - +
189A ILE* 3.5 22.3 - - + +
190A ILE 2.7 25.4 + - - +
191A LYS 5.5 0.2 - - - -
192A ASN* 3.4 12.6 + - + +
229A MET* 3.5 4.6 - - - -
230A PHE 2.9 32.2 + - - +
231A ARG 3.3 23.1 - - - -
232A ASN* 1.3 79.3 - - - +
234A LEU* 1.3 61.9 + - - +
235A CYS* 3.5 3.2 + - - -
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Residues in contact with LEU 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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189A ILE* 3.7 1.4 - - - -
190A ILE* 2.8 40.2 + - + +
191A LYS 5.6 0.2 + - - -
197A LEU* 3.4 35.1 - - + +
200A ALA* 3.8 26.2 - - + +
201A GLN* 4.0 16.2 - - + -
204A VAL* 4.6 3.8 - - + -
227A HIS* 4.5 14.6 - - + +
228A PHE 3.8 12.3 - - - +
229A MET* 3.6 19.3 - - + +
233A HIS* 1.3 71.7 - - - +
235A CYS* 1.3 66.1 + - - +
236A LEU* 3.7 19.1 - - + -
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Residues in contact with CYS 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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155A TRP* 3.8 27.1 - - - -
187A ILE* 3.8 12.8 - - + -
188A LYS 3.2 3.8 - - - -
189A ILE* 3.9 19.1 - - - -
227A HIS* 3.2 7.1 - - - +
228A PHE* 2.8 58.1 + - + +
230A PHE* 4.0 8.7 - - - -
233A HIS* 3.8 13.5 - - - -
234A LEU* 1.3 75.3 - - - +
236A LEU* 1.3 63.1 + - - +
237A VAL 4.0 0.3 + - - -
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Residues in contact with LEU 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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187A ILE* 3.4 3.8 - - - -
188A LYS* 2.9 42.5 + - + +
190A ILE* 4.9 4.7 - - + -
200A ALA* 4.4 6.7 - - + +
203A GLU* 3.4 32.1 - - + +
204A VAL* 3.8 29.2 - - + +
207A LEU* 4.7 1.3 - - + -
224A LEU* 3.5 14.6 - - + -
226A ARG 3.8 4.3 - - - -
227A HIS* 4.0 4.9 - - + -
234A LEU* 3.7 25.1 - - + +
235A CYS* 1.3 80.9 - - - +
237A VAL* 1.3 63.8 + - - +
238A PHE* 3.6 21.1 + - + -
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Residues in contact with VAL 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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159A TYR* 3.9 13.2 - - + +
185A VAL* 3.7 35.7 - - + -
186A ALA 3.8 2.5 - - - +
187A ILE* 4.4 9.0 - - + +
224A LEU* 3.6 3.5 - - - +
225A LYS* 2.8 31.6 + - + -
226A ARG* 2.8 46.5 + - + +
228A PHE* 3.4 33.0 - - + -
236A LEU* 1.3 74.4 - - - +
238A PHE* 1.3 62.0 + - - +
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Residues in contact with PHE 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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173A VAL* 6.5 0.2 - - + -
185A VAL* 3.4 10.4 - - - +
186A ALA 2.8 33.3 + - - +
188A LYS* 4.0 25.1 - - + -
203A GLU* 3.8 16.6 - - - -
207A LEU* 3.6 32.1 - - + -
222A VAL* 3.8 24.9 - - + -
223A HIS 3.5 15.7 - - - +
224A LEU* 3.9 10.5 - - + -
225A LYS* 4.1 4.5 - - - -
236A LEU* 3.6 32.1 - - + -
237A VAL* 1.3 74.0 - - - +
239A GLU* 1.3 71.6 + - - +
600A D15 3.9 25.4 - + + +
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Residues in contact with GLU 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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184A TRP 5.4 0.2 - - - -
222A VAL* 3.6 7.2 - - + +
223A HIS* 2.8 44.8 + - + +
225A LYS* 3.6 23.9 - - - +
238A PHE* 1.3 74.6 - - - +
240A MET* 1.3 62.1 + - - +
241A LEU* 3.5 10.8 + - + +
304A LYS* 2.7 42.5 + - - +
600A D15 2.8 22.5 + - - -
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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