Contacts of the helix formed by residues 219 - 231 (chain E) in PDB entry 2OX4
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 ASP 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E LEU 4.0 0.6 + - - -
182E GLU* 3.6 14.6 - - + +
183E GLY* 2.9 27.5 + - - -
218E THR* 1.3 75.3 - - - +
220E LEU* 1.3 67.0 + - - +
221E VAL* 3.0 17.3 + - - +
222E SER* 3.1 13.3 + - - -
223E ALA* 2.9 21.8 + - - +
241E ILE 3.7 5.2 - - - -
242E ASN* 3.8 4.0 - - - -
309G GLU* 3.5 38.6 - - + +
311G THR* 4.8 5.0 - - - +
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Residues in contact with LEU 220 (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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219E ASP* 1.3 73.0 - - - +
221E VAL* 1.3 67.3 + - + +
223E ALA* 3.7 5.9 - - - +
224E ILE* 3.0 46.4 + - + +
241E ILE* 5.7 0.2 - - - -
242E ASN* 3.9 5.8 - - - +
249E LEU* 3.7 45.3 - - + +
252E GLU* 4.6 6.3 - - + -
253E ALA* 4.2 21.3 - - + +
254G LYS* 6.3 0.4 - - - +
280G ARG* 3.7 39.0 - - + +
283G ASP* 4.6 2.0 - - - +
308G PHE 4.1 2.2 - - - +
309G GLU* 2.9 19.8 + - + +
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Residues in contact with VAL 221 (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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183E GLY* 4.5 4.3 - - - -
184E PRO* 3.9 35.2 - - + -
219E ASP* 3.0 8.8 + - - +
220E LEU* 1.3 79.6 - - + +
222E SER* 1.3 63.4 + - - +
224E ILE* 3.8 5.9 - - - +
225E GLN* 3.1 21.8 + - + +
260G PRO* 4.5 18.6 - - + -
280G ARG* 3.3 29.6 - - - +
283G ASP* 3.5 21.5 - - + +
309G GLU 4.0 7.9 - - - +
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Residues in contact with SER 222 (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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181E LEU 2.7 29.3 + - - -
183E GLY 3.3 17.9 + - - -
185E LEU* 3.6 18.6 - - - +
218E THR* 3.3 6.6 - - - +
219E ASP* 3.1 22.8 + - - -
221E VAL* 1.3 79.9 - - - +
223E ALA* 1.3 56.7 + - - +
225E GLN* 3.4 10.2 + - - +
226E PHE* 2.9 30.5 + - - +
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Residues in contact with ALA 223 (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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218E THR* 4.1 6.0 - - - +
219E ASP 2.9 19.8 + - - +
220E LEU* 3.7 4.7 - - - +
222E SER* 1.3 78.6 + - - +
224E ILE* 1.3 56.4 + - - +
227E ALA* 3.0 21.7 + - - +
238E TYR* 2.9 24.9 + - - +
241E ILE* 3.5 45.3 - - + +
257E ILE* 4.1 3.1 - - + -
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Residues in contact with ILE 224 (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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220E LEU* 3.0 41.0 + - + +
221E VAL* 3.8 5.6 - - - +
223E ALA* 1.3 77.2 - - - +
225E GLN* 1.3 62.6 + - - +
227E ALA* 3.3 3.1 + - - +
228E LYS* 3.1 40.4 + - + +
252E GLU 4.6 0.9 - - - +
253E ALA* 4.1 13.5 - - - +
256E LYS* 3.7 38.7 - - + +
257E ILE* 3.9 26.0 - - + -
254G LYS* 6.3 1.1 - - - +
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Residues in contact with GLN 225 (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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184E PRO* 3.7 9.3 - - - +
185E LEU* 2.8 51.2 + - - +
186E PRO 5.1 0.2 - - - -
187E SER* 5.5 1.0 - - - +
190E ILE* 3.7 25.2 - - + +
221E VAL* 3.1 12.1 + - + +
222E SER* 3.5 8.5 - - - +
223E ALA 3.4 0.2 - - - -
224E ILE* 1.3 82.1 - - - +
226E PHE* 1.3 61.0 + - - +
228E LYS* 3.5 16.9 - - - +
229E ALA* 3.5 17.0 + - - +
234G ASN* 4.7 17.1 + - - +
236G PHE* 6.0 1.2 - - - -
260G PRO* 6.5 1.3 - - + -
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Residues in contact with PHE 226 (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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167E VAL* 3.5 33.7 - - + -
168E LEU* 3.7 32.1 - - + -
185E LEU* 5.0 0.7 - - + -
190E ILE* 3.8 27.8 - - + +
193E GLY* 3.6 23.6 - - - -
194E VAL* 3.8 4.5 - - + -
212E VAL* 4.2 5.8 - - + -
222E SER 2.9 16.7 + - - +
223E ALA* 4.9 0.2 - - - -
225E GLN* 1.3 74.6 - - - +
227E ALA* 1.3 66.1 + - - +
229E ALA* 2.9 15.3 + - + +
230E ILE* 3.1 52.8 + - + +
238E TYR* 3.7 19.1 - + - +
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Residues in contact with ALA 227 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223E ALA 3.0 18.5 + - - +
224E ILE 3.3 5.4 + - - +
226E PHE* 1.3 74.9 - - - +
228E LYS* 1.3 57.6 + - - +
230E ILE* 3.1 10.0 + - - +
231E GLU* 2.9 37.4 + - - +
238E TYR* 3.8 18.2 + - + -
256E LYS 5.2 0.7 - - - +
257E ILE* 3.9 26.5 - - + -
258E ASP 5.7 0.2 - - - +
259E ILE* 4.1 8.3 - - + +
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Residues in contact with LYS 228 (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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224E ILE* 3.1 33.6 + - + +
225E GLN* 3.5 18.2 - - - +
226E PHE 3.2 0.2 - - - -
227E ALA* 1.3 77.3 - - - +
229E ALA* 1.3 62.8 + - - +
231E GLU* 4.0 17.2 + - - +
232E GLU* 4.9 3.6 + - - +
256E LYS 5.3 4.9 - - - +
231G GLU* 6.1 2.0 - - - +
258G ASP* 2.9 41.5 + - + +
260G PRO* 5.8 2.6 - - - +
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Residues in contact with ALA 229 (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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190E ILE* 3.5 31.9 - - + -
194E VAL* 3.6 20.2 - - + +
225E GLN 3.5 6.4 + - - +
226E PHE* 2.9 11.0 + - + +
228E LYS* 1.3 80.9 - - - +
230E ILE* 1.3 58.7 + - - +
232E GLU* 3.6 16.9 - - - +
233E PHE* 3.9 5.2 - - - -
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Residues in contact with ILE 230 (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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194E VAL* 4.1 8.5 - - + -
197E VAL* 4.1 17.3 - - + -
212E VAL* 3.9 20.4 - - + -
226E PHE* 3.1 58.3 + - + +
227E ALA* 3.1 7.8 + - - +
229E ALA* 1.3 79.7 - - - +
231E GLU* 1.3 67.4 + - - +
232E GLU 3.2 3.1 - - - -
233E PHE* 3.0 27.7 + - + +
235E ILE* 3.6 28.5 - - + +
238E TYR* 4.6 6.1 - - + -
259E ILE* 4.1 8.1 - - + -
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Residues in contact with GLU 231 (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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227E ALA* 2.9 17.4 + - + +
228E LYS* 4.0 14.4 + - - +
229E ALA 3.7 1.2 - - - -
230E ILE* 1.3 76.6 - - - +
232E GLU* 1.3 61.1 + - - +
233E PHE 3.1 1.6 + - - -
234E ASN* 3.4 12.0 + - - -
235E ILE* 4.8 1.1 + - - -
258E ASP* 3.5 27.8 + - + +
259E ILE* 4.3 23.0 - - + +
228H LYS* 3.4 25.1 + - - +
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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