Contacts of the helix formed by residues 198 - 210 (chain E) in PDB entry 2ZU6
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 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195E GLU 4.1 7.1 + - - -
196E MSE 3.2 0.6 - - - -
197E LYS* 1.3 77.6 - - - +
199E GLY* 1.3 59.0 + - - +
200E VAL 3.1 1.8 + - - -
201E PRO* 3.3 4.7 - - - +
202E VAL* 3.3 7.6 - - - +
235E ASP* 3.3 29.7 + - - -
238E LYS* 3.6 36.9 + - - +
239E SER* 2.2 37.6 + - - -
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Residues in contact with GLY 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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164E PHE* 3.2 30.6 - - - -
196E MSE 3.0 13.9 + - - +
198E SER* 1.3 76.3 + - - +
200E VAL* 1.3 64.5 + - - +
202E VAL* 3.9 12.1 - - - +
203E LEU* 3.6 12.0 + - - +
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Residues in contact with VAL 200 (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 PHE* 4.7 2.0 - - + -
168E LEU* 3.3 35.7 - - + -
172E ILE* 4.4 12.7 - - + +
184E VAL* 6.0 1.3 - - + -
188E LEU* 4.3 20.4 - - + -
193E LEU* 4.1 19.1 - - + -
196E MSE 4.4 2.0 - - - +
197E LYS 2.9 14.2 + - - +
199E GLY* 1.3 77.5 - - - +
201E PRO* 1.4 77.4 - - + +
202E VAL 2.8 1.9 + - - -
203E LEU* 2.9 8.3 + - - +
204E ALA* 2.8 20.0 + - + -
222E LEU* 5.8 2.0 - - + -
223E LEU* 5.8 1.3 - - + -
226E LEU* 4.8 10.5 - - + -
231E MSE 5.2 2.9 - - - -
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Residues in contact with PRO 201 (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 LYS 3.4 7.4 - - - +
198E SER* 3.3 7.0 - - - +
200E VAL* 1.4 96.3 - - + +
202E VAL* 1.3 55.1 + - - +
204E ALA* 3.4 1.5 - - + +
205E VAL* 2.8 38.3 + - + +
223E LEU* 4.0 33.7 - - + -
231E MSE 4.1 20.0 - - + -
236E VAL* 4.8 11.0 - - + +
239E SER* 2.9 29.2 - - - +
240E PHE* 5.5 1.6 - - + -
243E LEU* 4.5 3.4 - - + -
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Residues in contact with VAL 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 SER 3.3 17.9 - - - +
199E GLY* 3.9 12.6 - - - +
200E VAL 2.8 0.6 + - - -
201E PRO* 1.3 76.0 - - - +
203E LEU* 1.3 60.6 + - - +
205E VAL* 4.1 1.0 - - - +
206E SER* 2.8 33.4 + - - +
239E SER* 3.6 24.9 - - - +
242E LYS* 3.7 35.4 - - + -
243E LEU* 3.7 16.0 - - + +
246E ASP* 4.7 6.7 - - - +
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Residues in contact with LEU 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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164E PHE* 4.5 7.0 - - + -
165E GLU* 4.2 30.1 - - + +
168E LEU* 3.7 30.7 - - + +
169E THR* 3.6 28.3 - - - +
172E ILE* 4.5 7.0 - - + -
199E GLY 3.6 9.0 + - - +
200E VAL* 2.9 8.2 + - - +
202E VAL* 1.3 79.8 - - - +
204E ALA* 1.3 68.8 + - - +
206E SER* 3.0 5.9 + - - -
207E LEU* 3.0 37.3 + - + +
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Residues in contact with ALA 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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172E ILE* 3.6 29.1 - - + +
176E PHE* 4.5 0.9 - - - -
200E VAL* 2.8 12.3 + - + +
201E PRO* 3.0 13.2 + - + +
203E LEU* 1.3 79.7 - - - +
205E VAL* 1.3 66.1 + - - +
207E LEU* 3.3 3.3 + - - +
208E ALA* 2.9 19.4 + - - +
219E THR* 4.1 18.3 + - + +
222E LEU* 4.6 9.6 - - + -
223E LEU* 4.4 9.0 - - + -
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Residues in contact with VAL 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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201E PRO 2.8 21.5 + - - +
204E ALA* 1.3 74.6 - - - +
206E SER* 1.3 55.9 + - - +
208E ALA* 3.3 3.6 + - - +
209E LEU* 2.9 33.3 + - + +
219E THR* 3.7 23.6 - - + -
223E LEU* 4.0 14.1 - - + -
240E PHE* 4.8 5.4 - - + -
243E LEU* 4.0 33.2 - - + -
261E VAL* 5.3 4.7 - - + -
264E PHE* 3.5 37.6 - - + -
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Residues in contact with SER 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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110D ARG* 5.6 5.3 + - - -
202E VAL* 2.8 25.8 + - - +
203E LEU* 3.0 12.8 + - - -
204E ALA 2.9 1.2 + - - -
205E VAL* 1.3 72.8 - - - +
207E LEU* 1.3 67.8 + - - +
209E LEU* 3.2 19.3 + - - +
210E GLU* 3.3 15.2 + - - +
243E LEU* 4.4 2.6 - - - +
250E LEU* 3.7 29.0 - - - +
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Residues in contact with LEU 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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169E THR* 4.2 27.8 - - + +
172E ILE* 3.8 28.5 - - + -
173E GLN* 4.3 16.2 - - + +
176E PHE* 4.0 14.4 - - + -
203E LEU* 3.0 28.7 + - + +
204E ALA 3.5 6.7 - - - +
206E SER* 1.3 75.2 - - - +
208E ALA* 1.3 58.2 + - - +
210E GLU* 2.7 29.1 + - + +
211E GLY* 3.3 5.2 + - - -
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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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176E PHE* 4.3 6.4 - - + -
204E ALA 2.9 11.5 + - - +
205E VAL 3.5 7.9 - - - +
207E LEU* 1.3 73.0 - - - +
209E LEU* 1.3 63.0 + - - +
211E GLY* 3.1 9.3 + - - +
212E LYS 4.7 0.2 - - - +
215E HIS* 3.8 10.1 - - - +
216E ARG* 3.1 31.6 + - + +
219E THR* 3.4 25.8 - - - +
264E PHE* 3.7 19.1 - - + -
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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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190D ARG* 3.1 16.0 + - - -
205E VAL* 2.9 24.9 + - + +
206E SER* 3.2 10.5 + - - +
208E ALA* 1.3 72.7 - - - +
210E GLU* 1.3 59.7 + - + +
211E GLY 3.3 3.8 + - - +
216E ARG* 3.5 11.2 + - - +
250E LEU* 4.2 28.0 - - + -
254E THR* 3.5 16.3 - - + +
257E ALA* 3.6 26.0 - - + +
260E LEU* 3.2 43.7 - - + -
261E VAL* 4.7 7.2 - - + +
264E PHE* 4.2 14.1 - - + -
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Residues in contact with GLU 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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109D THR* 3.5 26.1 - - + +
110D ARG* 2.9 70.4 + - - +
111D GLU 4.2 1.4 + - - -
190D ARG* 3.8 13.2 - - - +
206E SER 3.3 8.0 + - - +
207E LEU* 2.7 21.2 + - + +
209E LEU* 1.3 72.9 - - + +
211E GLY* 1.3 55.0 + - - -
253E ASP* 3.5 14.4 - - - +
254E THR* 3.5 18.1 + - - +
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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