Contacts of the strand formed by residues 222 - 229 (chain B) in PDB entry 4OTZ
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 GLU 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B LYS* 2.8 20.1 + - + +
193B LYS* 3.8 24.3 - - - +
194B VAL* 2.8 34.7 + - - +
216B VAL* 4.2 2.0 - - - -
220B GLY 5.8 0.2 - - - +
221B LEU* 1.3 73.0 - - - +
223B LEU* 1.3 57.9 + - - +
224B VAL* 3.3 15.6 + - + +
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Residues in contact with LEU 223 (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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194B VAL 3.6 4.3 - - - +
196B VAL* 3.6 30.5 - - + -
213B GLN* 4.1 24.7 - - + +
216B VAL* 4.3 15.3 - - + -
217B LYS* 4.2 28.9 - - + +
221B LEU 3.8 3.2 + - - -
222B GLU* 1.3 68.5 - - - +
224B VAL* 1.3 62.4 + - - +
225B THR* 3.8 12.7 - - - +
226B VAL* 4.0 22.0 - - + -
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Residues in contact with VAL 224 (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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193B LYS* 3.6 39.9 - - + +
194B VAL 2.9 25.2 + - - +
195B ALA* 4.0 10.8 - - + +
222B GLU* 4.0 14.8 - - + +
223B LEU* 1.3 73.2 - - - +
225B THR* 1.3 64.6 + - - +
246B LEU* 3.4 40.7 - - + +
248B PRO* 4.4 8.1 - - + -
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Residues in contact with THR 225 (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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195B ALA* 3.7 23.7 - - + -
196B VAL 2.9 25.6 + - - +
223B LEU* 3.4 6.5 - - - +
224B VAL* 1.3 82.5 - - - +
226B VAL* 1.3 67.5 + - - +
227B GLN* 2.9 39.2 + - + +
243B ALA* 4.2 9.2 - - - -
246B LEU* 3.6 20.1 - - + +
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Residues in contact with VAL 226 (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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196B VAL* 3.2 8.7 - - + +
198B PHE* 3.6 31.2 - - + -
213B GLN* 3.7 35.2 - - + +
223B LEU* 4.0 20.2 - - + -
225B THR* 1.3 82.8 + - - +
227B GLN* 1.3 65.1 + - - +
228B LYS* 4.3 5.1 + - + +
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Residues in contact with GLN 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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196B VAL 2.7 9.6 + - - +
197B PHE* 3.2 30.3 - - + +
198B PHE* 2.9 27.4 + - - -
225B THR* 2.9 34.4 + - + +
226B VAL* 1.3 76.2 + - - +
228B LYS* 1.3 63.1 + - - +
239B GLN* 3.4 30.4 - - + +
242B ASN* 3.2 40.7 + - + +
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Residues in contact with LYS 228 (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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198B PHE* 3.4 43.2 - - + +
200B GLN* 3.7 37.1 - - + +
226B VAL* 5.1 4.3 - - - +
227B GLN* 1.3 75.4 + - - +
229B PHE* 1.3 62.1 + - - +
239B GLN* 2.9 25.0 + - - +
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Residues in contact with PHE 229 (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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197B PHE* 3.9 9.6 - + + -
198B PHE* 3.0 33.5 + - - -
199B ALA* 3.3 17.5 - - + -
200B GLN* 2.8 31.1 + - - +
228B LYS* 1.3 78.2 - - - +
230B GLN* 1.3 77.1 + - - +
233B ASP* 3.6 12.1 - - - +
236B PHE* 3.6 20.6 - + + -
239B GLN* 3.7 10.8 - - - +
253B ILE* 4.3 4.9 - - + -
254B SER 3.7 10.3 - - - -
255B GLY* 4.0 7.6 - - - -
259B ASP* 3.3 28.7 - - + -
260B GLY* 5.2 1.8 - - - -
263B LEU* 3.7 28.7 - - + -
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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