Contacts of the helix formed by residues 209 - 221 (chain B) in PDB entry 1WSQ
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 GLY 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B PRO* 2.9 18.1 + - - -
206B GLN 5.3 0.2 - - - -
207B THR 3.2 3.6 + - - -
208B GLU* 1.3 83.4 - - - +
210B VAL* 1.3 65.7 + - - +
211B ASN 3.3 3.3 + - - -
212B ALA 3.7 4.1 + - - -
213B VAL* 3.7 16.3 - - - +
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Residues in contact with VAL 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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205B PRO* 3.8 13.2 + - + +
209B GLY* 1.3 71.6 - - - -
211B ASN* 1.3 62.4 + - - +
213B VAL* 3.4 1.4 + - - -
214B GLU* 2.8 42.7 + - - +
233B LEU* 3.8 36.7 - - + +
234B TYR* 4.0 42.0 - - + +
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Residues in contact with ASN 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 GLY 3.3 1.0 - - - -
210B VAL* 1.3 79.3 - - - +
212B ALA* 1.3 64.1 + - - +
214B GLU* 3.8 14.6 - - - +
215B ASP* 3.0 34.9 + - - +
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Residues in contact with ALA 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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203B GLN* 4.6 3.4 + - - +
208B GLU* 4.0 23.6 - - + +
209B GLY 3.7 1.2 + - - -
210B VAL 3.4 0.4 - - - -
211B ASN* 1.3 79.7 - - - +
213B VAL* 1.3 68.7 + - + +
215B ASP* 3.6 4.8 + - - +
216B GLU* 3.4 19.4 + - - +
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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
----------------------------------------------------------
203B GLN* 3.9 36.8 - - + +
205B PRO* 4.1 18.6 - - + -
208B GLU* 4.2 13.5 - - + +
209B GLY 3.7 13.0 + - - +
210B VAL 3.4 6.0 + - - +
211B ASN 3.4 0.4 - - - -
212B ALA* 1.3 77.2 - - + +
214B GLU* 1.3 58.1 + - - +
216B GLU* 3.1 4.9 + - - +
217B ILE* 2.8 33.6 + - + +
233B LEU* 3.9 17.3 - - + -
239B ILE* 3.7 30.5 - - + -
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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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210B VAL* 2.8 31.2 + - + +
211B ASN* 3.8 11.5 - - - +
213B VAL* 1.3 74.8 - - - +
215B ASP* 1.3 71.5 + - - +
217B ILE* 3.2 4.5 + - - +
218B LYS* 3.0 51.7 + - + +
233B LEU* 3.7 19.3 - - + +
402B ZN 1.9 38.2 - - - -
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Residues in contact with ASP 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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211B ASN* 3.0 19.8 + - - +
212B ALA* 4.1 5.0 - - - +
214B GLU* 1.3 81.9 - - - +
216B GLU* 1.3 62.7 + - - +
218B LYS* 3.6 6.6 + - - +
219B LYS* 3.2 23.8 + - - +
401B ZN 2.0 37.3 - - - -
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Residues in contact with GLU 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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82B HIS* 5.2 9.0 + - - -
175B ARG* 3.1 37.1 + - - +
199B THR* 4.7 5.9 + - - -
201B LYS* 6.0 0.5 - - - +
203B GLN* 3.6 22.8 + - - +
212B ALA 3.4 10.3 + - - +
213B VAL 3.1 9.0 + - - +
215B ASP* 1.3 78.0 - - - +
217B ILE* 1.3 64.1 + - - +
219B LYS* 3.3 1.0 + - - -
220B TYR* 3.0 49.3 + - + +
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Residues in contact with ILE 217 (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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175B ARG* 4.7 6.5 - - - +
203B GLN* 4.3 10.8 - - - +
213B VAL* 2.8 35.1 + - + +
214B GLU* 3.8 6.5 - - - +
216B GLU* 1.3 72.3 - - - +
218B LYS* 1.3 60.3 + - + +
221B THR* 2.6 54.5 + - + +
226B ARG* 3.6 24.9 - - - +
230B MET* 3.9 49.4 - - + +
233B LEU* 4.9 0.7 - - + -
239B ILE* 4.2 14.1 - - + -
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Residues in contact with LYS 218 (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* 3.0 45.3 + - + +
215B ASP* 4.1 7.6 - - - +
217B ILE* 1.3 81.2 - - + +
219B LYS* 1.3 61.4 + - - +
221B THR 4.0 8.3 - - - +
226B ARG* 4.0 23.5 + - - +
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Residues in contact with LYS 219 (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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57B PHE* 5.6 10.7 - - + -
83B ASP* 4.4 20.5 + - - +
215B ASP 3.2 18.3 + - - +
216B GLU* 3.8 4.3 - - - +
217B ILE 3.2 0.2 - - - -
218B LYS* 1.3 80.3 - - - +
220B TYR* 1.3 100.1 + - + +
221B THR 3.7 1.0 - - - +
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Residues in contact with TYR 220 (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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82B HIS* 5.3 4.9 - + - -
83B ASP* 4.0 8.0 + - - -
86B VAL* 3.6 32.2 - - + +
175B ARG* 3.6 25.6 - - - +
176B ASP* 3.9 6.8 - - - +
196B GLY 3.6 20.9 - - - -
197B SER* 2.7 44.7 + - - +
216B GLU* 3.0 45.1 + - + +
219B LYS* 1.3 119.7 + - + +
221B THR* 1.3 62.1 + - + +
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Residues in contact with THR 221 (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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175B ARG* 3.5 27.6 - - + +
176B ASP* 4.4 0.9 - - - -
217B ILE* 2.6 34.9 + - + +
218B LYS 4.0 6.6 - - - +
219B LYS 4.9 0.7 - - - +
220B TYR* 1.3 82.0 - - + +
222B THR* 1.3 62.6 + - - +
226B ARG* 2.7 46.3 + - - -
230B MET* 4.0 28.0 - - + -
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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