Contacts of the strand formed by residues 209 - 216 (chain B) in PDB entry 3O9Z
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 VAL 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LEU* 3.9 1.5 - - - +
204B ALA* 4.4 15.0 - - + -
205B ARG* 3.5 1.0 - - - -
206B THR* 2.8 34.4 + - + +
208B THR* 1.3 91.1 - - - +
210B ASN* 1.3 81.3 + - - +
224B PHE* 3.8 24.7 - - + -
225B LEU 3.3 5.2 - - - +
226B SER* 3.5 14.4 - - - +
231B PHE* 3.7 24.9 - - + -
309B LEU* 5.2 2.0 - - + -
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Residues in contact with ASN 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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178B LEU* 4.0 14.3 - - - +
179B ALA* 3.5 31.3 - - - +
202B VAL* 5.3 3.4 - - + +
204B ALA 3.3 9.6 - - - +
205B ARG* 3.8 21.4 - - - +
206B THR 3.7 9.9 - - - +
209B VAL* 1.3 92.2 - - - +
211B ALA* 1.3 61.2 + - - +
223B TRP* 3.4 18.9 - - + -
225B LEU* 2.8 40.8 + - + +
292B LEU* 5.9 1.8 - - - +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 3.5 6.4 - - - +
203B HIS* 2.7 23.8 + - - -
204B ALA* 3.1 14.2 + - + -
210B ASN* 1.3 76.9 - - - +
212B GLY* 1.3 59.2 + - - +
223B TRP* 3.3 21.5 - - - +
224B PHE* 4.0 11.0 - - + -
306B HIS* 5.0 0.9 - - + -
309B LEU* 3.9 37.2 - - + -
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Residues in contact with GLY 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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201B GLU 3.3 12.6 - - - -
203B HIS* 3.5 20.1 + - - -
211B ALA* 1.3 77.1 - - - +
213B TYR* 1.3 61.7 + - - +
222B ARG* 3.6 3.8 - - - +
223B TRP* 3.0 42.6 + - - +
304B ASN 4.2 1.6 - - - +
306B HIS* 4.9 2.3 - - - +
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Residues in contact with TYR 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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199B HIS* 4.4 10.1 - + - -
200B VAL* 3.6 2.4 - - - -
201B GLU* 2.9 48.8 + - + +
203B HIS* 3.7 18.1 - - + -
212B GLY* 1.3 75.1 - - - +
214B LEU* 1.3 85.0 + - - +
215B GLU* 4.0 13.6 - - + +
220B ARG* 3.3 33.2 - - + +
221B VAL 3.2 31.6 - - - -
222B ARG* 4.1 4.7 - - + -
223B TRP* 3.3 0.8 + - - +
303B GLU 5.1 1.1 - - - -
304B ASN* 3.4 50.0 + - + +
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Residues in contact with LEU 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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187B PHE* 4.0 14.1 - - + -
190B LEU* 3.7 30.5 - - + -
197B ALA* 4.7 0.7 - - + -
199B HIS 3.5 3.6 - - - +
200B VAL* 3.9 31.9 - - + -
213B TYR* 1.3 88.2 - - - +
215B GLU* 1.3 58.9 + - - +
216B LEU* 3.7 28.6 + - + -
220B ARG* 3.5 2.6 - - - -
221B VAL* 2.8 38.6 + - + +
223B TRP* 3.7 19.5 - - + +
288B VAL* 4.1 15.0 - - + -
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Residues in contact with GLU 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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197B ALA* 3.6 2.4 - - - -
198B LEU* 2.8 52.8 + - + +
199B HIS* 2.9 33.0 + - + +
213B TYR* 4.0 13.9 - - + +
214B LEU* 1.3 71.3 - - - +
216B LEU* 1.3 61.4 + - - +
219B ALA 3.9 3.8 - - - +
220B ARG* 4.7 12.8 - - + +
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Residues in contact with LEU 216 (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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149B ALA* 5.5 0.7 - - - +
190B LEU* 3.8 33.4 - - + +
191B ALA* 6.1 0.2 - - - -
194B PHE* 3.7 27.4 - - + +
195B GLY 4.2 4.9 - - - +
196B ARG 3.2 6.5 - - - +
197B ALA* 3.4 33.9 - - + +
198B LEU* 4.3 5.5 - - - +
214B LEU* 3.7 24.5 - - + -
215B GLU* 1.3 80.2 - - - +
217B GLU* 1.3 69.2 + - - +
218B GLY 3.1 1.2 + - - -
219B ALA 2.7 24.9 + - - +
221B VAL* 3.8 15.9 - - + -
288B VAL* 5.8 1.1 - - + -
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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