Contacts of the strand formed by residues 207 - 215 (chain B) in PDB entry 4OBZ
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 GLN 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B VAL* 3.1 11.2 - - - +
201B THR* 2.7 39.4 + - - +
202B ARG* 2.8 64.7 + - - +
205B TYR* 3.1 7.4 + - + +
206B TRP* 1.4 71.7 - - - +
208B VAL* 1.3 56.2 + - - +
227B GLU* 3.2 31.7 + - - +
228B ALA 3.3 15.3 - - - +
229B ILE* 3.8 14.1 - - + +
318B LEU* 3.9 12.9 - - + +
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Residues in contact with VAL 208 (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 LEU* 3.8 32.3 - - + +
199B ASN 3.9 9.9 - - - +
200B VAL* 4.4 0.9 - - - -
201B THR* 4.2 4.0 - - - -
206B TRP 4.6 1.1 - - - +
207B GLN* 1.3 79.5 - - - +
209B HIS* 1.3 57.4 + - - +
227B GLU* 3.6 7.7 - - - +
228B ALA* 2.8 44.2 + - + +
230B VAL* 4.1 18.8 - - + -
278B LEU* 4.1 21.8 - - + -
321B LEU* 4.9 2.2 - - + -
340B VAL* 4.1 25.1 - - + -
342B PHE* 5.3 2.5 - - + -
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Residues in contact with HIS 209 (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 LEU* 3.7 10.3 - - - +
199B ASN 4.9 1.2 + - - -
201B THR* 3.7 13.8 - - + +
208B VAL* 1.3 72.5 - - - +
210B LEU* 1.3 65.0 + - - +
211B ASP* 3.4 29.4 + - - +
224B GLU 5.0 3.0 + - - -
225B GLY* 4.1 11.8 - - - -
226B CYS 3.1 24.7 + - - -
227B GLU* 3.0 27.0 + - - +
278B LEU* 3.6 14.5 - - - +
279B GLY 4.8 0.7 + - - -
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Residues in contact with LEU 210 (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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208B VAL 3.7 0.8 + - - -
209B HIS* 1.3 72.6 + - - +
211B ASP* 1.3 63.2 + - - +
212B GLN 3.7 16.2 - - - +
213B VAL* 3.8 17.5 - - + -
222B CYS* 3.5 2.2 - - - -
225B GLY* 3.3 1.7 - - - -
226B CYS* 2.8 63.0 + - - +
228B ALA* 4.1 16.4 - - + -
276B LEU* 3.9 21.1 - - + -
277B LYS 3.6 18.2 - - - +
278B LEU* 3.7 20.6 - - + -
319B TRP* 4.0 22.2 - - + -
321B LEU* 4.9 1.6 - - + -
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Residues in contact with ASP 211 (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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209B HIS* 3.4 23.4 + - - +
210B LEU* 1.3 71.5 - - - +
212B GLN* 1.3 65.8 + - + +
222B CYS 3.0 12.5 - - - +
223B LYS 4.1 1.7 - - - +
224B GLU 4.6 0.2 - - - -
225B GLY* 3.6 13.4 + - - -
277B LYS* 2.9 34.5 + - + +
278B LEU* 4.7 0.2 - - - -
279B GLY* 3.6 6.3 + - - -
280B GLY* 3.4 27.4 + - - -
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Residues in contact with GLN 212 (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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210B LEU* 3.5 8.1 - - - +
211B ASP* 1.3 83.9 - - - +
213B VAL* 1.3 62.0 + - - +
214B GLU* 3.1 30.3 + - + +
220B THR* 3.8 20.0 - - + +
221B LEU 4.0 0.2 - - - +
222B CYS* 3.2 18.4 - - - +
223B LYS* 3.0 28.7 - - - +
275B THR 3.9 0.2 - - - +
276B LEU* 3.6 3.5 - - - -
277B LYS* 3.0 34.0 + - + +
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Residues in contact with VAL 213 (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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210B LEU* 3.8 24.9 - - + -
212B GLN* 1.3 75.0 - - - +
214B GLU* 1.3 60.5 + - - +
215B VAL* 5.5 0.2 - - + -
219B LEU 4.0 0.9 - - - +
220B THR* 3.6 3.6 - - - +
221B LEU* 3.0 62.9 + - + +
222B CYS* 4.1 4.7 - - + -
247B LEU* 4.6 3.6 - - + -
274B ILE* 4.2 20.4 - - + -
275B THR 3.7 3.8 - - - +
276B LEU* 4.7 9.4 - - + +
306B PHE* 5.1 2.0 - - + -
319B TRP* 3.8 35.7 - - + -
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Residues in contact with GLU 214 (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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212B GLN* 3.1 30.4 + - + +
213B VAL* 1.3 74.2 - - - +
215B VAL* 1.3 62.9 + - - +
216B ALA 4.0 0.8 + - - -
219B LEU 4.0 2.2 - - - -
220B THR* 4.8 7.6 - - + +
274B ILE* 3.2 8.4 - - - +
275B THR* 2.8 54.2 + - - +
277B LYS* 3.7 38.5 + - + +
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Residues in contact with VAL 215 (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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214B GLU* 1.3 75.1 - - - +
216B ALA* 1.3 58.0 + - - +
217B SER* 3.7 16.4 - - - +
218B GLY* 2.8 33.3 + - - -
219B LEU* 2.8 42.6 + - + +
221B LEU* 4.2 19.1 - - + -
247B LEU* 4.6 6.7 - - + -
250B ALA* 5.0 3.8 - - + -
251B ILE* 4.3 10.1 - - + -
272B PRO* 3.7 18.2 - - + -
273B ALA 3.7 2.0 - - - -
274B ILE* 3.9 21.8 - - + -
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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