Contacts of the strand formed by residues 225 - 229 (chain B) in PDB entry 3KDO
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 THR 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B MET* 3.1 18.6 - - - +
150B LEU* 3.9 15.5 - - + -
181B LEU* 4.5 4.0 - - - +
186B ASP 3.3 4.3 + - - +
187B TYR* 3.1 41.7 - - + -
188B MET* 3.1 4.0 + - - +
209B MET* 4.8 1.2 - - - +
213B ILE* 3.9 10.4 - - - +
224B LYS* 1.3 75.9 - - - +
226B TRP* 1.3 68.9 + - - +
227B PHE* 3.8 9.6 - - + -
250B LYS* 4.0 5.9 + - - +
251B HIS* 2.8 36.5 + - + +
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Residues in contact with TRP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 4.4 4.9 - + - -
188B MET* 3.0 39.3 - - + +
189B KCX 4.8 0.2 - - - -
190B ASP* 2.7 35.0 + - - -
202B PHE* 4.5 4.5 - + - -
205B ARG* 3.6 20.2 - - + -
206B ALA* 3.5 38.1 - - + -
209B MET* 3.6 40.5 - - + +
213B ILE* 4.1 6.3 - - + +
225B THR* 1.3 83.3 + - - +
227B PHE* 1.3 64.3 + - - +
228B ALA* 3.0 40.2 + - + -
244B LEU* 3.8 1.3 - - + -
249B LEU* 3.7 25.2 - - + +
251B HIS* 3.5 17.7 + - - +
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Residues in contact with PHE 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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150B LEU* 6.3 0.7 - - + -
157B ILE* 5.7 1.6 - - + -
187B TYR* 3.3 42.6 - + - -
188B MET 2.8 9.4 + - - -
189B KCX 3.7 31.0 - - + -
190B ASP* 3.1 24.9 + - - +
225B THR* 3.8 15.7 - - + -
226B TRP* 1.3 73.0 - - - +
228B ALA* 1.3 62.2 + - - +
229B ASN 3.5 1.2 + - - -
251B HIS* 3.7 35.0 - + + -
253B MET* 3.9 18.3 - - + +
279B HIS* 3.8 30.5 - + + -
312B GLN* 3.5 17.9 - - - -
387B VAL* 4.6 4.5 - - + -
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Residues in contact with ALA 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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190B ASP* 3.4 6.5 - - - -
202B PHE* 3.7 6.3 - - + -
226B TRP* 3.0 46.8 + - + -
227B PHE* 1.3 69.4 - - - +
229B ASN* 1.3 62.1 + - - +
230B ILE* 3.2 8.1 + - - +
244B LEU* 3.7 21.5 - - + -
251B HIS 4.1 3.2 + - - +
252B ALA* 3.7 0.7 - - - -
253B MET* 2.7 27.5 + - - +
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Residues in contact with ASN 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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190B ASP* 3.0 22.8 + - + +
191B ASP 3.3 6.7 + - - -
192B GLU* 3.1 27.5 + - - +
194B LEU 3.2 27.0 + - - +
195B THR* 4.6 7.7 - - - +
202B PHE* 3.4 17.3 - - - -
205B ARG* 4.0 4.7 + - - -
227B PHE 3.5 2.4 + - - -
228B ALA* 1.3 68.3 - - - +
230B ILE* 1.3 59.3 + - - +
231B THR* 2.5 34.0 + - - -
240B ARG* 5.0 1.0 + - - -
253B MET* 3.5 23.7 - - - +
255B ASP* 3.7 2.3 - - - +
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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
------------------------------------------------------------
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