Contacts of the helix formed by residues 201 - 216 (chain E) in PDB entry 2ZSU
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 PHE 201 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E GLU* 5.3 0.4 - - - -
10E TYR* 3.8 17.9 - + - -
11E PRO* 3.7 28.0 - - + -
164E ASP* 3.3 35.9 - - + -
195E ALA 4.3 0.3 - - - +
196E GLY* 3.6 6.3 - - - -
197E SER* 2.8 38.7 + - - +
200E LEU* 1.3 81.2 - - + +
202E THR* 1.3 63.9 + - - +
203E ASP* 3.3 3.4 - - - -
204E GLU* 3.0 39.5 + - + +
205E PHE* 3.1 11.6 + - - +
233E TRP* 3.7 10.3 - + - -
1003E AG3 3.8 3.6 - - - -
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Residues in contact with THR 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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197E SER 3.5 1.0 + - - -
198E VAL 2.7 25.8 + - - +
199E TYR* 3.4 15.5 + - - -
200E LEU 3.3 2.8 + - - -
201E PHE* 1.3 77.0 - - - +
203E ASP* 1.3 58.4 + - - +
205E PHE* 3.2 8.3 + - + +
206E LEU* 2.9 49.2 + - + +
275E TYR* 4.6 5.1 + - + -
276E ILE* 4.3 11.9 - - + +
279E MET* 3.9 17.0 - - + -
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Residues in contact with ASP 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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201E PHE 3.3 0.8 - - - -
202E THR* 1.3 75.3 - - - +
204E GLU* 1.3 60.1 + - - +
206E LEU* 4.6 6.7 - - - +
207E THR* 2.6 61.2 + - - +
210E ARG* 5.5 1.2 + - - -
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Residues in contact with GLU 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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164E ASP* 4.3 0.7 - - - +
165E PRO* 3.3 45.5 - - + +
173E PHE* 3.9 11.4 - - + -
194E GLN* 4.6 2.1 - - - +
195E ALA* 3.1 32.1 - - - +
196E GLY* 3.3 2.8 + - - -
201E PHE* 3.0 40.6 + - + +
203E ASP* 1.3 77.7 + - - +
205E PHE* 1.3 56.9 + - - +
207E THR* 3.0 17.5 + - - -
208E ALA* 3.0 20.8 + - - +
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Residues in contact with PHE 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E ALA* 3.7 18.3 + - + +
197E SER 5.4 2.0 - - - +
198E VAL* 5.8 3.6 - - - -
201E PHE 3.1 6.3 + - - +
202E THR* 3.4 11.4 - - + +
203E ASP 3.2 0.2 - - - -
204E GLU* 1.3 76.5 - - - +
206E LEU* 1.3 92.0 + - + +
208E ALA* 3.3 3.3 + - - +
209E TYR* 2.9 22.6 + + - +
221E TYR* 3.7 29.4 - + + -
234E ALA* 3.5 28.7 - - + -
235E PHE 4.3 1.3 - - - -
236E LEU* 3.5 30.0 - - + +
272E MET* 3.8 16.4 - - + -
276E ILE* 3.8 26.0 - - + -
280E LEU* 4.4 10.5 - - + -
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Residues in contact with LEU 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 THR* 2.9 39.7 + - + +
203E ASP* 4.1 5.6 - - - +
205E PHE* 1.3 90.5 - - + +
207E THR* 1.3 64.4 + - + +
209E TYR* 3.0 7.8 + - - +
210E ARG* 3.0 49.5 + - - +
276E ILE* 4.1 16.4 - - + +
279E MET* 3.9 30.5 - - + +
280E LEU* 3.8 24.9 - - + +
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Residues in contact with THR 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 ASP* 2.6 51.3 + - - +
204E GLU* 3.0 11.8 + - - -
206E LEU* 1.3 74.8 - - + +
208E ALA* 1.3 60.7 + - - +
210E ARG* 3.6 20.5 + - - +
211E LYS* 3.3 39.1 + - - +
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Residues in contact with ALA 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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173E PHE* 4.1 16.2 - - + -
178E TYR* 3.7 19.3 - - - +
195E ALA* 5.2 0.2 - - + -
204E GLU 3.0 16.3 + - - +
207E THR* 1.3 78.0 + - - +
209E TYR* 1.3 65.4 + - - +
211E LYS* 3.3 8.7 + - - +
212E MET* 2.9 28.4 + - - +
236E LEU* 3.3 23.3 - - + -
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Residues in contact with TYR 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 PHE* 2.9 15.2 + + + +
206E LEU 3.3 9.2 - - - +
208E ALA* 1.3 76.4 - - - +
210E ARG* 1.3 68.2 + - + +
212E MET* 3.3 5.1 + - - +
213E ARG* 2.9 51.1 + - - +
219E VAL* 3.5 37.1 + - + +
220E TYR 4.9 0.7 - - - -
221E TYR* 3.9 25.7 - + + -
236E LEU* 3.7 28.0 - - + +
280E LEU* 3.5 44.5 - - + +
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Residues in contact with ARG 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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203E ASP* 5.5 1.4 + - - -
206E LEU* 3.0 42.9 + - - +
207E THR* 4.0 24.2 - - - +
209E TYR* 1.3 85.5 - - + +
211E LYS* 1.3 63.6 + - + +
213E ARG* 3.3 21.4 + - - +
214E LYS* 3.4 28.6 + - - +
279E MET* 3.3 23.0 + - - +
280E LEU* 4.2 15.5 + - - +
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Residues in contact with LYS 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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173E PHE 3.5 26.1 + - - +
174E SER* 4.4 7.1 - - - +
175E GLU* 4.1 25.0 - - + +
178E TYR* 4.0 14.1 - - + -
207E THR* 3.3 28.8 + - - +
208E ALA* 3.7 4.5 - - - +
209E TYR 3.3 0.6 - - - -
210E ARG* 1.3 78.4 - - + +
212E MET* 1.3 62.0 + - - +
213E ARG 3.3 0.3 + - - -
214E LYS* 3.3 17.5 + - - +
215E VAL* 3.5 18.2 - - - +
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Residues in contact with MET 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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178E TYR* 3.5 40.6 - - + -
191E TYR* 3.8 19.3 - - + -
193E THR* 4.5 2.9 - - - -
208E ALA 2.9 21.2 + - - +
209E TYR* 3.8 4.5 - - - +
211E LYS* 1.3 75.9 - - - +
213E ARG* 1.3 57.3 + - - +
215E VAL* 3.2 1.5 + - - +
216E PHE* 2.9 40.7 + - + -
219E VAL* 3.2 13.3 - - + +
236E LEU* 3.7 31.6 - - + -
237E VAL 3.6 9.6 - - - +
238E GLY* 3.6 29.8 - - - +
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Residues in contact with ARG 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 TYR* 2.9 34.1 + - + +
210E ARG* 3.3 16.3 - - - +
211E LYS 3.1 0.2 - - - -
212E MET* 1.3 77.5 - - - +
214E LYS* 1.3 63.6 + - + +
215E VAL 3.4 0.3 + - - -
216E PHE 3.7 12.0 - - - +
219E VAL* 3.5 23.9 - - + +
280E LEU 5.0 9.9 + - - -
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Residues in contact with LYS 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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175E GLU* 5.9 9.4 - - + +
210E ARG* 3.4 26.8 + - - +
211E LYS* 3.3 11.9 + - - +
212E MET 3.3 0.8 - - - -
213E ARG* 1.3 77.7 - - + +
215E VAL* 1.3 63.8 + - + +
216E PHE 4.9 0.7 - - - -
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Residues in contact with VAL 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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175E GLU* 4.4 9.9 - - + +
178E TYR* 3.5 33.4 - - + +
179E LYS* 3.8 30.3 - - + -
182E TYR* 3.5 31.9 - - + -
211E LYS 3.5 15.0 - - - +
212E MET 3.2 5.4 + - - +
214E LYS* 1.3 84.5 - - + +
216E PHE* 1.3 73.7 + - + +
217E ASP* 5.0 0.3 - - - +
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Residues in contact with PHE 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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178E TYR* 4.0 40.2 - + + -
181E ALA* 4.5 0.4 - - + -
182E TYR* 3.8 23.6 - + - -
185E LEU* 3.8 15.3 - - + -
191E TYR* 3.6 41.1 - + + -
212E MET* 2.9 44.2 + - + +
213E ARG 3.7 13.0 - - - +
214E LYS 4.9 0.3 - - - -
215E VAL* 1.3 79.2 - - + +
217E ASP* 1.3 68.0 + - - +
218E LYS* 3.3 8.0 - - - +
219E VAL* 4.2 2.0 - - + +
238E GLY* 3.5 19.5 - - - -
239E VAL 3.6 13.2 - - - +
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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