Contacts of the strand formed by residues 224 - 230 (chain B) 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 LEU 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 4.2 28.7 - - + +
207B LEU* 4.1 34.2 - - + +
208B GLU* 4.5 9.6 - - + -
211B ASN* 5.4 1.4 + - - +
222B VAL 3.7 3.8 + - - -
223B HIS* 1.3 89.7 + - - +
225B LYS* 1.3 60.9 + - - +
226B ARG* 3.4 24.7 - - - +
227B HIS* 4.5 9.2 - - + -
236B LEU* 3.5 25.4 - - + -
237B VAL 3.5 9.0 - - - +
238B PHE* 3.8 19.0 - - + -
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Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 2.6 36.8 + - - +
184B TRP 5.5 0.7 - - - -
185B VAL* 4.0 18.6 - - + -
223B HIS* 3.6 23.9 + - + +
224B LEU* 1.3 74.7 - - - +
226B ARG* 1.3 88.7 + - - +
237B VAL* 2.8 16.7 + - + +
238B PHE 4.2 1.3 - - - -
239B GLU* 3.6 37.2 - - - +
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Residues in contact with ARG 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ARG* 3.2 33.3 - - - +
159B TYR* 3.0 29.9 + - - +
178B ASP* 3.6 7.1 + - - -
181B GLU* 4.2 15.0 + - - +
183B GLU* 5.1 1.8 + - - -
185B VAL* 5.3 0.6 - - - +
224B LEU* 3.4 11.2 - - - +
225B LYS* 1.3 105.0 + - - +
227B HIS* 1.3 71.6 + - - +
228B PHE* 4.8 5.6 - - + -
237B VAL* 2.8 49.2 + - + +
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Residues in contact with HIS 227 (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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204B VAL* 3.6 24.6 - - + +
208B GLU* 3.2 27.6 + - - -
224B LEU* 4.5 5.6 - - + -
226B ARG* 1.3 83.7 - - - +
228B PHE* 1.3 70.8 + - - +
234B LEU* 4.5 10.9 - - + +
235B CYS 3.1 14.6 - - - +
236B LEU* 4.0 16.8 - - + -
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Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TRP* 4.1 15.0 - + - -
156B MET* 3.7 32.5 - - + -
159B TYR* 3.4 40.4 - + - -
187B ILE* 4.5 3.1 - - + -
226B ARG* 4.8 4.7 - - + -
227B HIS* 1.3 80.1 - - - +
229B MET* 1.3 66.2 + - - +
230B PHE* 3.8 16.6 - - + -
234B LEU* 3.7 4.5 - - - +
235B CYS* 2.8 54.1 + - + +
237B VAL* 3.5 24.2 - - + -
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Residues in contact with MET 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B MET* 3.8 15.9 - - - +
197B LEU* 4.5 19.1 - - + -
201B GLN* 6.2 0.7 - - - -
228B PHE* 1.3 74.5 - - - +
230B PHE* 1.3 61.0 - - - +
232B ASN* 4.0 21.8 - - - +
233B HIS 3.4 21.5 - - - -
234B LEU* 3.9 30.3 - - + +
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Residues in contact with PHE 230 (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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147B TYR* 4.0 9.6 - + - -
154B LYS 5.3 0.4 - - - -
155B TRP* 3.4 69.8 - + + -
156B MET* 4.4 23.1 - - + -
189B ILE* 6.4 0.7 - - + -
228B PHE* 3.8 18.8 + - + -
229B MET* 1.3 75.1 - - - +
231B ARG* 1.3 115.7 + - + +
232B ASN 3.1 1.1 - - - -
233B HIS* 2.9 30.1 + - - +
235B CYS* 4.2 6.7 - - - -
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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