Contacts of the helix formed by residues 204 - 216 (chain E) in PDB entry 1WOH
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 MET 204 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180E GLY* 3.7 17.9 - - - +
181E LEU 2.8 19.0 + - - +
182E ARG* 4.2 7.0 - - + -
203E PRO* 1.3 71.7 - - - +
205E ASP* 1.3 62.6 + - - +
207E VAL* 2.9 29.5 + - + +
208E THR* 3.1 32.3 + - - +
247E ASP 3.3 24.7 - - - +
248E GLY* 3.5 13.2 - - - +
249E LEU* 3.5 33.4 - - + -
253E GLN* 3.4 26.7 - - - +
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Residues in contact with ASP 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D LYS* 5.9 1.2 + - - -
181E LEU 4.7 0.5 + - - +
203E PRO* 3.0 9.0 - - + +
204E MET* 1.3 79.6 - - - +
206E ASP* 1.3 62.2 - - - +
208E THR* 3.6 8.5 - - - -
209E ALA* 2.8 30.1 + - - +
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Residues in contact with ASP 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E ILE* 3.8 15.6 - - + +
203E PRO* 2.9 38.0 + - - +
205E ASP* 1.3 81.5 - - - +
207E VAL* 1.3 59.2 + - - +
209E ALA* 3.9 5.6 - - - +
210E ASP* 2.9 33.1 + - - +
214E VAL* 3.6 5.1 - - + +
217E GLN* 5.2 5.9 + - - +
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Residues in contact with VAL 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E VAL* 3.6 30.7 - - + -
202E ILE* 4.7 0.2 - - + -
203E PRO 3.6 6.5 + - - +
204E MET* 2.9 23.1 + - + +
206E ASP* 1.3 75.6 - - - +
208E THR* 1.3 65.9 + - - +
211E LEU* 3.2 39.0 + - + +
214E VAL* 3.8 17.3 - - + -
249E LEU* 4.0 16.8 - - + -
253E GLN* 3.6 25.2 + - + +
257E ILE* 4.6 2.2 - - + -
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Residues in contact with THR 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E MET* 3.1 27.4 + - - +
205E ASP* 3.6 11.1 - - - -
207E VAL* 1.3 81.1 - - - +
209E ALA* 1.3 63.5 + - - +
210E ASP* 4.5 0.2 - - - -
211E LEU 5.0 0.2 + - - -
253E GLN* 4.8 6.4 + - - +
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Residues in contact with ALA 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E ASP 2.8 22.6 + - - +
206E ASP* 3.9 7.4 - - - +
208E THR* 1.3 78.0 - - - +
210E ASP* 1.3 64.0 + - + +
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Residues in contact with ASP 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E ASP 2.9 21.0 + - - +
208E THR 4.5 0.2 - - - -
209E ALA* 1.3 79.8 - - + +
211E LEU* 1.3 63.9 + - - +
212E ALA* 3.5 13.0 + - - +
213E GLY* 3.0 33.9 + - - -
214E VAL* 3.3 8.1 + - - +
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E VAL* 3.2 37.0 + - + +
210E ASP* 1.3 71.6 + - - +
212E ALA* 1.3 65.7 + - + +
214E VAL* 2.9 23.0 + - + +
215E LEU* 3.0 48.8 + - + +
253E GLN* 5.0 11.0 - - + +
256E LYS* 4.4 22.2 - - + -
257E ILE* 4.3 14.8 - - + -
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Residues in contact with ALA 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ASP* 3.3 11.3 + - - +
211E LEU* 1.3 85.4 - - + +
213E GLY* 1.3 61.3 + - - +
215E LEU* 3.4 9.2 + - - +
216E ALA* 3.2 21.5 + - - +
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Residues in contact with GLY 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ASP* 3.0 26.9 + - - -
211E LEU 3.1 0.8 - - - -
212E ALA* 1.3 75.8 - - - +
214E VAL* 1.3 64.9 + - - +
216E ALA* 3.2 15.1 + - - +
217E GLN* 3.3 22.0 + - - +
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Residues in contact with VAL 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E VAL* 4.0 19.5 - - + -
202E ILE* 3.8 34.6 - - + +
206E ASP* 3.6 20.6 - - + +
207E VAL* 3.8 15.9 - - + -
210E ASP 3.3 15.0 + - - +
211E LEU* 2.9 12.5 + - + +
213E GLY* 1.3 77.6 - - - +
215E LEU* 1.3 56.8 + - + +
217E GLN* 2.9 32.6 + - - +
218E LEU* 3.6 9.3 + - + +
257E ILE* 4.9 8.7 - - + -
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Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E LEU* 3.0 41.9 + - + +
212E ALA* 3.8 10.5 - - - +
214E VAL* 1.3 72.0 - - + +
216E ALA* 1.3 61.9 + - - +
217E GLN 3.0 5.6 - - - -
218E LEU* 3.1 34.8 + - + +
220E ARG* 4.0 9.4 + - - -
256E LYS* 4.0 7.2 - - + +
257E ILE* 3.8 38.8 - - + +
260E ALA* 3.9 15.6 - - + +
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Residues in contact with ALA 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E ALA 3.2 12.9 + - - +
213E GLY* 3.4 13.9 - - - +
214E VAL 3.2 0.4 - - - -
215E LEU* 1.3 76.4 - - - +
217E GLN* 1.3 59.4 - - + +
218E LEU 3.4 0.9 + - - +
220E ARG* 3.7 23.5 + - - +
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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