Contacts of the helix formed by residues 206 - 226 (chain E) in PDB entry 6V3O
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 THR 206 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204E ASP 4.0 1.9 + - - -
205E ILE* 1.3 78.8 - - - +
207E ASP* 1.3 62.1 + - - +
208E ASP* 3.1 25.8 - - + +
209E ASP* 3.6 25.9 + - - +
210E LYS* 2.9 28.3 + - - +
262F ARG* 5.1 3.8 - - - +
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Residues in contact with ASP 207 (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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205E ILE 4.2 5.7 - - - +
206E THR* 1.3 77.1 - - + +
208E ASP* 1.3 59.6 + - - +
210E LYS* 3.3 10.5 + - - +
211E GLN* 2.8 41.3 + - + +
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Residues in contact with ASP 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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206E THR* 3.1 11.9 - - + +
207E ASP* 1.3 75.9 - - - +
209E ASP* 1.3 65.3 + - - +
211E GLN* 3.3 13.1 + - - +
212E GLU* 3.0 28.8 + - - +
142F ASP* 5.4 3.6 - - - +
144F GLU* 2.8 34.5 - - - +
262F ARG* 3.5 42.8 + - - +
265F THR* 3.6 14.2 - - + +
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Residues in contact with ASP 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 ILE* 3.8 17.1 - - + +
206E THR* 3.4 26.5 + - - +
207E ASP 3.4 0.4 - - - -
208E ASP* 1.3 77.2 - - - +
210E LYS* 1.3 57.7 + - - +
212E GLU* 3.2 4.9 + - - +
213E LEU* 2.8 38.6 + - + +
258F LYS* 4.2 9.7 + - - -
262F ARG* 3.0 23.5 + - - +
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Residues in contact with LYS 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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200E LEU* 2.8 48.5 + - + +
205E ILE* 3.8 24.9 - - + +
206E THR 2.9 18.3 + - - +
207E ASP* 3.6 9.9 - - - +
208E ASP 3.2 0.2 - - - -
209E ASP* 1.3 73.7 - - - +
211E GLN* 1.3 66.8 + - + +
213E LEU* 4.6 0.2 - - - -
214E ASP* 2.9 26.6 + - + +
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Residues in contact with GLN 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 ASP* 2.8 27.7 + - + +
208E ASP* 3.6 16.1 - - - +
210E LYS* 1.3 73.3 - - + +
212E GLU* 1.3 57.8 + - - +
214E ASP* 3.4 6.8 + - - +
215E GLU* 3.1 42.0 + - - +
265F THR* 3.7 20.4 + - + +
268F LYS* 5.8 3.6 - - - +
269F ASN* 2.9 33.3 + - - +
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Residues in contact with GLU 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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208E ASP 3.0 17.6 + - - +
209E ASP* 3.9 4.8 - - - +
211E GLN* 1.3 74.1 - - - +
213E LEU* 1.3 62.8 + - + +
215E GLU* 3.4 14.7 + - - +
216E ALA* 3.0 26.3 + - - +
219E ARG* 5.2 1.6 + - - -
258F LYS* 4.3 12.3 + - - +
261F ARG* 4.6 23.4 - - + +
262F ARG* 3.0 47.4 + - - +
265F THR* 2.6 30.8 + - + +
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Residues in contact with LEU 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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196E CYS* 4.2 22.0 - - - +
199E GLN* 3.5 48.0 - - + +
200E LEU* 4.1 13.9 - - + +
205E ILE* 3.8 22.4 - - + -
209E ASP* 2.8 25.4 + - + +
210E LYS 4.0 2.7 - - - +
212E GLU* 1.3 74.3 - - + +
214E ASP* 1.3 60.4 + - - +
216E ALA* 3.3 6.1 + - + +
217E LEU* 2.9 29.1 + - - +
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Residues in contact with ASP 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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44E ARG* 2.5 42.7 + - - -
200E LEU* 4.2 11.6 - - + +
210E LYS* 2.9 21.6 + - + +
211E GLN* 3.4 8.3 - - - +
213E LEU* 1.3 76.6 - - - +
215E GLU* 1.3 61.7 + - + +
217E LEU* 3.1 6.1 + - - +
218E GLN* 2.8 49.9 + - - +
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Residues in contact with GLU 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 GLN* 3.1 34.9 + - - +
212E GLU* 3.8 14.8 - - - +
214E ASP* 1.3 77.3 - - + +
216E ALA* 1.3 57.6 + - - +
218E GLN* 3.6 15.3 + - - +
219E ARG* 3.0 43.6 + - - +
261F ARG* 5.1 2.4 + - - +
265F THR* 5.4 4.6 + - - +
268F LYS* 5.9 2.0 + - - -
275F ARG* 3.2 26.3 + - - +
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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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196E CYS* 3.8 17.9 - - - -
212E GLU 3.0 16.5 + - - +
213E LEU* 3.6 9.9 - - + +
214E ASP 3.1 0.2 - - - -
215E GLU* 1.3 76.0 - - - +
217E LEU* 1.3 59.0 + - - +
219E ARG* 3.1 23.3 + - - +
220E GLU* 2.9 34.7 + - + +
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Residues in contact with LEU 217 (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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40E LEU* 5.0 2.9 - - + -
41E LEU* 3.7 26.9 - - + -
44E ARG* 3.9 22.7 - - - +
193E ILE* 3.7 33.9 - - + +
196E CYS* 4.0 15.4 - - + -
197E LEU* 4.5 9.6 - - + +
200E LEU* 3.8 23.8 - - + -
213E LEU 2.9 13.6 + - - +
214E ASP* 3.5 8.1 - - - +
216E ALA* 1.3 77.2 - - - +
218E GLN* 1.3 62.9 + - - +
220E GLU* 3.3 4.0 + - - +
221E ILE* 3.0 35.3 + - + +
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Residues in contact with GLN 218 (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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44E ARG* 4.4 22.7 - - + +
48E ILE* 3.3 24.8 - - + +
214E ASP* 2.8 42.7 + - - +
215E GLU* 3.9 13.8 - - - +
217E LEU* 1.3 75.0 - - - +
219E ARG* 1.3 62.7 + - - +
221E ILE* 3.3 4.3 + - - -
222E GLN* 3.0 22.7 + - - +
430F ALA* 6.0 1.1 - - + -
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Residues in contact with ARG 219 (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 GLU 5.2 1.4 + - - -
215E GLU* 3.0 40.9 + - - +
216E ALA* 3.1 29.4 + - - +
218E GLN* 1.3 77.4 - - - +
220E GLU* 1.3 65.1 + - + +
222E GLN* 3.6 5.4 + - - +
223E ALA* 3.1 23.0 + - - +
261F ARG* 3.2 34.3 - - - +
275F ARG* 4.2 6.5 - - - +
430F ALA* 3.1 38.4 + - + +
431F ILE* 4.0 8.8 - - + +
433F ASP* 3.9 5.2 + - - +
434F GLY* 3.4 26.1 - - - +
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Residues in contact with GLU 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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189E LYS* 4.0 22.2 - - - +
192E ARG* 3.2 52.6 + - + +
193E ILE* 3.7 23.1 - - + +
196E CYS* 5.3 2.0 - - - -
216E ALA* 2.9 22.1 + - + +
217E LEU* 3.3 5.1 + - - +
219E ARG* 1.3 77.9 - - + +
221E ILE* 1.3 66.2 + - - +
223E ALA* 3.2 8.3 + - - +
224E ALA* 3.0 23.9 + - - +
329F GLU* 5.7 2.6 - - - -
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Residues in contact with ILE 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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41E LEU* 4.0 32.1 - - + +
44E ARG* 4.4 12.3 - - + -
45E PHE* 4.0 27.8 - - + -
48E ILE* 3.6 14.6 - - + -
108E LEU* 4.2 19.7 - - + -
193E ILE* 4.4 14.8 - - + -
217E LEU* 3.0 38.5 + - + +
218E GLN* 3.8 4.7 - - - +
220E GLU* 1.3 75.0 - - - +
222E GLN* 1.3 64.0 + - - +
224E ALA* 3.4 4.4 + - - +
225E PHE* 3.1 21.1 + - - +
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Residues in contact with GLN 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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48E ILE* 3.8 32.7 - - + +
51E ASP* 5.0 6.5 + - - +
52E LEU* 3.9 11.0 - - + +
218E GLN 3.0 16.9 + - - +
219E ARG* 3.9 4.5 - - - +
221E ILE* 1.3 77.4 - - - +
223E ALA* 1.3 62.4 + - - +
225E PHE* 3.1 6.7 + - + +
226E ARG* 3.0 38.4 + - + +
427F GLY 3.6 15.4 + - - -
428F ASP* 3.1 27.7 + - - +
430F ALA* 3.5 25.3 - - - +
431F ILE* 4.1 7.5 - - + +
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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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189E LYS* 3.8 15.0 - - + -
219E ARG 3.1 17.8 + - - +
220E GLU* 3.2 11.8 + - - +
222E GLN* 1.3 76.6 - - - +
224E ALA* 1.3 61.8 + - - +
226E ARG* 3.2 6.8 + - - -
227E THR* 3.1 23.7 - - - +
329F GLU 5.5 0.2 - - - +
332F MET* 3.7 23.2 - - + +
431F ILE* 3.9 12.5 - - + +
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Residues in contact with ALA 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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104E HIS* 3.5 20.2 - - + +
108E LEU* 6.5 0.7 - - + -
186E LEU* 3.9 23.4 - - + +
189E LYS* 4.0 13.1 - - + +
190E ASN* 5.7 0.7 - - - +
193E ILE* 4.7 14.1 - - + -
220E GLU 3.0 15.6 + - - +
221E ILE* 3.8 4.9 - - - +
222E GLN 3.3 0.2 - - - -
223E ALA* 1.3 76.9 - - - +
225E PHE* 1.3 58.9 + - - +
227E THR* 3.5 14.6 + - - -
228E ASP* 4.9 1.0 + - - -
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Residues in contact with PHE 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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45E PHE* 3.7 31.0 - + + -
48E ILE* 4.9 6.7 - - + -
49E LEU* 4.6 13.7 - - + -
52E LEU* 4.0 22.0 - - + -
53E HIS* 4.2 12.3 - + - -
97E LEU* 3.6 30.7 - - + -
100E SER* 4.8 2.2 - - - -
101E SER* 4.4 6.7 - - - -
104E HIS* 3.5 31.6 + + + -
221E ILE 3.1 12.1 + - - +
222E GLN* 3.1 10.4 + - - +
224E ALA* 1.3 79.1 - - - +
226E ARG* 1.3 71.6 + - + +
227E THR 3.5 0.2 - - - -
228E ASP* 2.9 34.1 - - - +
334F ARG* 6.2 0.4 - - - -
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Residues in contact with ARG 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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52E LEU* 3.8 30.2 - - - +
53E HIS* 4.7 15.0 + - - -
222E GLN* 3.0 25.6 + - + +
223E ALA 3.2 3.3 + - - +
225E PHE* 1.3 85.9 - - + +
227E THR* 1.3 60.2 + - - +
228E ASP* 3.3 6.0 + - - -
332F MET* 4.1 21.4 - - + +
333F TRP* 4.0 6.4 - - - -
334F ARG* 3.0 60.0 + - - +
426F CYS 2.8 29.7 + - - -
428F ASP* 2.9 31.2 + - - +
431F ILE* 4.6 2.5 - - + -
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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