Contacts of the strand formed by residues 193 - 199 (chain B) in PDB entry 4OG2
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 LYS 193 (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* 1.3 83.7 - - + +
194B VAL* 1.3 63.9 + - - +
222B GLU* 3.8 26.5 - - + +
224B VAL* 3.6 22.4 - - + -
246B LEU 4.1 10.6 + - - +
247B LYS* 4.1 15.4 - - - +
248B PRO* 3.6 11.1 - - + +
249B ASP* 2.8 38.8 + - - +
250B LEU 3.1 6.9 + - - -
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Residues in contact with VAL 194 (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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191B ILE* 4.4 3.1 - - + -
193B LYS* 1.3 79.0 - - - +
195B ALA* 1.3 64.0 + - - +
196B VAL* 4.1 4.5 - - + -
216B VAL* 3.9 17.5 - - + -
221B LEU* 3.9 30.3 - - + -
222B GLU 2.8 17.7 + - - +
223B LEU* 3.6 5.9 - - - +
224B VAL* 2.9 31.2 + - - +
225B THR 3.9 0.5 + - - -
250B LEU* 3.3 24.2 - - + +
252B ILE* 3.8 34.3 - - + -
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Residues in contact with ALA 195 (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* 1.3 73.5 - - - +
196B VAL* 1.3 62.0 + - - +
197B PHE* 4.4 3.1 - - + -
224B VAL* 4.1 2.7 - - + -
225B THR* 3.7 26.0 - - + -
243B ALA* 3.9 19.1 - - + -
248B PRO* 4.0 18.7 - - + +
250B LEU 2.9 6.5 + - - -
251B VAL* 3.2 11.0 - - + +
252B ILE 2.9 24.8 + - - +
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Residues in contact with VAL 196 (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* 4.1 13.2 - - + -
195B ALA* 1.3 77.7 - - - +
197B PHE* 1.3 63.3 + - - +
209B THR* 3.2 27.1 - - - +
212B PHE* 5.1 2.5 - - + -
213B GLN* 4.0 20.2 - - + +
216B VAL* 4.8 3.6 - - + -
223B LEU* 3.6 23.6 - - + -
225B THR 3.0 11.3 + - - +
226B VAL* 3.3 7.8 - - + +
227B GLN* 2.8 32.4 + - - +
252B ILE* 3.5 23.3 - - + +
254B SER* 6.0 0.4 - - - +
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Residues in contact with PHE 197 (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* 4.4 6.3 - - + -
196B VAL* 1.3 83.4 - - - +
198B PHE* 1.3 64.1 + - - +
227B GLN* 3.2 20.6 - - + +
229B PHE* 3.9 8.1 - + + -
239B GLN* 3.7 32.3 - - + -
240B ALA 4.0 1.3 - - - -
243B ALA* 3.5 33.2 - - + -
251B VAL* 3.7 32.1 - - + -
252B ILE 2.8 10.8 + - - +
253B ILE* 4.3 4.3 - - + -
254B SER* 2.9 24.9 + - - -
263B LEU* 3.7 37.2 - - + -
267B LEU* 4.1 15.7 - - + -
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Residues in contact with PHE 198 (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* 1.3 76.6 - - - +
199B ALA* 1.3 67.4 + - - +
200B GLN* 3.4 24.4 + - + -
205B SER 4.1 3.6 - - - +
206B LYS* 3.8 21.5 - - + -
209B THR* 3.5 37.7 - - + -
210B GLU* 6.1 0.7 - - - -
213B GLN* 4.6 1.3 - - - -
226B VAL* 3.6 25.6 - - + -
227B GLN 3.0 13.3 + - - -
228B LYS* 3.4 44.8 - - + -
229B PHE* 3.0 28.8 + - - -
254B SER* 3.2 10.3 - - - +
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Residues in contact with ALA 199 (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* 1.3 73.6 - - - +
200B GLN* 1.3 65.4 + - - +
201B ASN* 3.2 5.9 + - - +
202B ASP* 3.3 11.6 + - + +
205B SER* 3.4 25.0 - - - +
206B LYS* 4.0 0.7 - - - +
229B PHE* 3.2 25.1 - - + +
231B THR* 3.7 30.1 - - + -
254B SER 2.9 9.1 + - - +
255B GLY* 4.1 2.2 - - - -
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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