Contacts of the helix formed by residues 210 - 222 (chain B) in PDB entry 4WFH
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 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B CYS* 2.7 36.7 + - - +
209B PHE* 1.3 79.9 - - + +
211B LEU* 1.3 77.9 + - + +
213B PRO* 3.3 3.9 - - - +
214B THR* 3.0 32.5 + - + +
229B ILE* 5.2 10.3 - - + -
232B VAL* 4.2 18.8 - - + +
233B ILE* 5.2 8.5 - - + -
236B LEU* 4.7 8.3 - - + -
272B PHE* 4.7 13.9 - - + -
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Residues in contact with LEU 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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206B CYS* 2.8 33.8 + - - -
207B LEU* 3.6 31.0 - - + +
210B VAL* 1.3 80.4 - - + +
212B THR* 1.3 64.0 + - - +
214B THR* 2.5 23.7 + - - +
215B PHE* 3.1 29.2 + - + -
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 2.3 40.8 + - - +
208B LEU* 3.5 18.4 - - + +
211B LEU* 1.3 74.3 - - - +
213B PRO* 1.3 65.8 - - + +
215B PHE* 3.3 5.6 + - - +
216B VAL* 2.9 39.8 + - + +
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Residues in contact with PRO 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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208B LEU 3.3 10.8 - - - +
209B PHE 3.2 19.5 - - - +
210B VAL 3.3 13.9 - - - +
212B THR* 1.3 96.1 - - + +
214B THR* 1.3 51.1 + - - +
216B VAL* 3.0 11.1 + - + +
217B PHE* 2.7 60.1 + - + -
232B VAL* 4.0 4.9 - - + -
264B TRP* 3.2 28.3 - - + +
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Residues in contact with THR 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* 3.0 17.2 + - + +
211B LEU* 2.5 29.2 + - - +
213B PRO* 1.3 75.9 - - - +
215B PHE* 1.3 64.7 + - - +
217B PHE* 4.4 0.4 - - - -
218B CYS* 3.0 29.3 + - - +
225B LYS* 5.1 1.7 - - - -
228B ALA* 3.4 16.7 - - - +
229B ILE* 3.4 40.9 - - + +
232B VAL* 3.5 22.7 - - + -
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Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.1 31.7 + - + +
212B THR* 3.6 9.4 - - - +
214B THR* 1.3 83.6 + - - +
216B VAL* 1.3 68.1 + - - +
218B CYS* 3.3 20.7 - - + +
219B TYR* 3.5 9.2 + - - +
225B LYS* 6.5 1.3 - - + -
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Residues in contact with VAL 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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212B THR* 2.9 36.0 + - + +
213B PRO* 3.2 11.4 - - + +
215B PHE* 1.3 77.7 - - + +
217B PHE* 1.3 68.5 + - + +
219B TYR* 3.2 6.9 + - - +
220B MET* 3.0 42.7 + - + +
257B TYR* 5.5 4.7 - - + -
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Residues in contact with PHE 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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213B PRO* 2.7 49.7 + - + +
214B THR* 4.0 2.9 - - - +
216B VAL* 1.3 78.0 - - + +
218B CYS* 1.3 66.7 + - - +
220B MET* 4.2 3.1 - - - +
221B GLU* 2.7 30.5 + - + +
222B ASP 3.9 0.2 + - - -
223B TRP* 3.9 22.6 + + + -
228B ALA* 4.3 3.8 - - + -
231B PHE* 3.8 24.2 - + - -
232B VAL* 4.2 6.1 - - + -
246B ALA* 3.5 23.3 - - + -
257B TYR* 3.5 20.4 - + - -
261B VAL* 4.0 17.9 - - + -
264B TRP* 3.8 26.2 - + - -
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Residues in contact with CYS 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 THR 3.0 19.7 + - - +
215B PHE* 3.3 15.7 - - + +
217B PHE* 1.3 78.5 - - - +
219B TYR* 1.3 61.1 + - + +
222B ASP* 3.4 15.8 + - - +
223B TRP 3.4 29.6 + - - +
224B SER* 4.2 0.4 - - - -
225B LYS* 3.9 26.9 - - - -
228B ALA* 4.2 5.0 - - + +
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Residues in contact with TYR 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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215B PHE 3.5 6.5 + - - +
216B VAL* 3.2 9.0 + - - +
217B PHE 3.2 0.6 - - - -
218B CYS* 1.3 80.4 - - + +
220B MET* 1.3 82.3 + - + +
221B GLU 3.6 0.2 - - - -
222B ASP* 4.1 4.9 + - - +
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Residues in contact with MET 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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216B VAL* 3.0 34.4 + - + +
217B PHE* 4.1 2.9 - - - +
219B TYR* 1.3 96.7 - - + +
221B GLU* 1.3 60.5 + - - +
222B ASP 3.5 0.2 - - - -
252B GLN* 3.0 21.2 + - - +
254B SER* 6.2 0.2 - - - -
257B TYR* 3.8 35.4 - - + +
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Residues in contact with GLU 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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217B PHE* 2.7 21.6 + - + +
220B MET* 1.3 73.7 - - - +
222B ASP* 1.3 69.7 + - - +
223B TRP* 3.4 50.1 + - + -
245B VAL 4.0 2.8 - - - +
246B ALA* 4.0 3.6 - - - -
247B GLY 2.8 30.6 + - - -
249B ASP* 4.3 12.1 + - - +
252B GLN* 3.5 16.5 + - - +
257B TYR* 3.0 26.0 + - - +
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Residues in contact with ASP 222 (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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218B CYS 3.4 10.8 + - - +
219B TYR 4.1 4.2 + - - +
220B MET 3.5 2.4 - - - -
221B GLU* 1.3 81.7 - - - +
223B TRP* 1.3 63.6 + - - +
227B GLU* 4.7 1.2 - - - +
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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