Contacts of the helix formed by residues 194 - 213 (chain E) in PDB entry 2BQZ
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 SER 194 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192E ARG* 2.7 4.7 + - - +
193E LYS* 1.3 81.2 + - - +
195E LYS* 1.3 66.5 + - - +
196E ALA* 3.3 4.5 - - - -
197E GLU* 2.8 16.1 + - - +
198E LEU* 2.7 23.9 + - - +
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Residues in contact with LYS 195 (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 SER* 1.3 70.2 - - - +
196E ALA* 1.3 71.4 + - - +
198E LEU* 2.7 26.7 + - - +
199E GLN* 3.1 12.6 + - + +
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Residues in contact with ALA 196 (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 SER* 3.3 4.4 - - - -
195E LYS* 1.3 84.4 - - - +
197E GLU* 1.3 57.0 + - - +
199E GLN* 3.4 4.3 + - - +
200E SER* 2.8 31.5 + - - -
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Residues in contact with GLU 197 (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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193E LYS* 3.6 21.5 - - + -
194E SER* 2.8 32.6 + - - +
196E ALA* 1.3 79.7 - - - +
198E LEU* 1.3 58.8 + - - -
200E SER* 3.3 8.0 + - - -
201E GLU* 3.1 52.4 + - - +
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Residues in contact with LEU 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E ARG* 3.9 37.5 - - + +
193E LYS* 4.0 23.3 - - + +
194E SER 2.7 17.7 + - - +
195E LYS* 2.7 16.0 + - - +
197E GLU* 1.3 73.0 - - - +
199E GLN* 1.3 55.1 + - + +
201E GLU* 3.5 6.9 + - - +
202E GLU* 2.9 27.8 + - - +
205E ARG* 4.7 1.9 + - - -
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Residues in contact with GLN 199 (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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195E LYS* 3.1 13.0 + - + +
196E ALA* 3.7 4.7 - - - +
198E LEU* 1.3 74.5 - - + +
200E SER* 1.3 64.1 + - - +
201E GLU 3.3 0.4 - - - -
202E GLU* 3.6 25.7 - - - +
203E ARG* 3.1 48.8 + - - +
206E ILE* 5.6 0.3 - - - +
310E HIS* 5.6 2.6 - - - -
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Residues in contact with SER 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E ALA 2.8 18.4 + - - -
197E GLU* 3.6 14.9 + - - -
199E GLN* 1.3 77.9 - - - +
201E GLU* 1.3 57.6 + - - +
203E ARG* 4.0 2.0 - - - +
204E LYS* 3.0 51.3 + - - +
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Residues in contact with GLU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E LYS* 2.7 38.8 + - - +
197E GLU* 3.1 41.6 + - - +
198E LEU* 3.8 6.5 - - - +
200E SER* 1.3 81.7 - - - +
202E GLU* 1.3 55.7 + - - +
204E LYS* 3.8 6.9 - - - +
205E ARG* 2.9 47.3 + - - +
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Residues in contact with GLU 202 (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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198E LEU 2.9 19.1 + - - +
199E GLN* 3.6 25.4 - - - +
200E SER 3.3 0.2 - - - -
201E GLU* 1.3 75.4 - - - +
203E ARG* 1.3 65.7 + - - +
205E ARG* 3.0 36.8 + - - +
206E ILE* 3.0 46.8 + - + +
239E GLY 4.7 10.7 - - - +
321E ILE* 6.0 0.3 - - - +
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Residues in contact with ARG 203 (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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199E GLN* 3.1 41.2 + - - +
200E SER* 4.0 2.9 - - - +
202E GLU* 1.3 78.1 - - - +
204E LYS* 1.3 54.9 + - + +
206E ILE* 3.8 3.7 - - - +
207E ASP* 2.8 56.8 + - - +
310E HIS* 4.4 16.2 + - + +
311E ASP* 4.3 24.2 + - - -
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Residues in contact with LYS 204 (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 SER* 3.0 34.5 + - - +
201E GLU* 3.8 6.5 - - - +
203E ARG* 1.3 76.9 - - + +
205E ARG* 1.3 56.5 + - - +
207E ASP* 4.0 5.7 - - - +
208E GLU* 2.9 43.4 + - + +
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Residues in contact with ARG 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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198E LEU 4.7 1.4 + - - -
201E GLU* 2.9 38.6 + - - +
202E GLU* 3.0 42.7 + - - +
204E LYS* 1.3 78.0 - - - +
206E ILE* 1.3 61.7 + - + +
208E GLU* 3.6 12.0 - - - +
209E LEU* 3.2 39.1 + - + +
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Residues in contact with ILE 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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199E GLN* 5.6 0.4 - - - +
202E GLU* 3.0 47.0 + - + +
203E ARG* 3.9 2.2 - - - +
205E ARG* 1.3 75.7 - - + +
207E ASP* 1.3 67.4 + - - +
209E LEU* 3.1 9.4 + - - +
210E ILE* 2.9 43.1 + - + +
241E PHE* 4.3 18.2 - - + -
310E HIS* 3.6 31.9 - - + +
319E ILE* 4.0 17.5 - - + -
321E ILE* 5.0 6.7 - - + -
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Residues in contact with ASP 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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203E ARG* 2.8 38.0 + - - +
204E LYS* 4.0 6.1 + - - +
206E ILE* 1.3 71.8 - - - +
208E GLU* 1.3 57.4 + - + +
210E ILE* 3.2 1.2 + - - +
211E GLU* 2.9 50.0 + - - +
310E HIS* 2.9 31.4 + - - -
311E ASP 5.6 0.3 - - - +
312E ILE* 3.9 26.3 - - + +
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Residues in contact with GLU 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 LYS* 2.9 31.3 + - + +
205E ARG* 3.6 12.9 - - - +
207E ASP* 1.3 77.8 - - + +
209E LEU* 1.3 62.0 + - + +
211E GLU* 4.0 11.4 + - - +
212E SER* 2.9 30.1 + - - -
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Residues in contact with LEU 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 ARG* 3.2 28.4 + - + +
206E ILE* 3.1 7.6 + - - +
208E GLU* 1.3 76.1 - - + +
210E ILE* 1.3 66.4 + - - +
212E SER* 3.4 3.6 + - - +
213E GLY* 3.1 21.7 + - - -
214E LYS* 3.8 28.7 + - + +
241E PHE* 3.6 49.3 - - + -
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Residues in contact with ILE 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 ILE* 2.9 36.4 + - + +
207E ASP 3.7 3.4 - - - +
209E LEU* 1.3 80.3 - - - +
211E GLU* 1.3 63.9 + - + +
213E GLY* 3.4 8.7 + - - -
241E PHE* 4.2 10.5 - - + -
244E GLU* 3.5 27.3 - - - +
292E ARG* 5.0 3.3 + - - -
310E HIS* 3.7 20.0 - - + -
312E ILE* 3.8 15.9 - - + -
317E HIS* 3.7 29.2 - - + +
319E ILE* 3.9 24.2 - - + -
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Residues in contact with GLU 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* 2.9 37.1 + - - +
208E GLU* 4.0 10.0 - - - +
210E ILE* 1.3 79.0 - - + +
212E SER* 1.3 59.3 + - - +
213E GLY 3.7 0.2 + - - -
312E ILE* 4.7 18.4 - - + +
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Residues in contact with SER 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 GLU 2.9 22.2 + - - -
209E LEU* 3.4 6.4 + - - +
211E GLU* 1.3 76.3 - - - +
213E GLY* 1.3 63.6 + - - +
214E LYS* 3.2 35.9 + - - +
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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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209E LEU 3.1 11.3 + - - -
210E ILE* 3.4 5.6 + - - -
211E GLU 3.4 3.0 - - - -
212E SER* 1.3 77.1 - - - +
214E LYS* 1.3 65.2 + - - +
215E GLU* 3.2 17.1 + - - +
292E ARG* 3.9 29.5 + - - -
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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