Contacts of the helix formed by residues 205 - 217 (chain E) in PDB entry 2ZHX
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 ARG 205 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E GLU* 2.9 28.1 + - - -
103E ALA* 3.8 29.9 + - - +
104E ASP* 3.1 39.6 - - - +
203E GLY* 3.4 23.5 - - - +
204E SER* 1.3 76.9 - - - +
206E PRO* 1.4 66.1 - - - +
208E SER* 4.0 3.8 - - - +
209E ARG* 3.0 34.8 + - + +
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Residues in contact with PRO 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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100E GLU* 3.8 17.0 - - + +
104E ASP* 3.9 2.2 - - - +
166E ILE* 4.6 7.3 - - + +
168E TRP* 4.3 28.0 - - + +
187E ILE* 3.6 26.1 - - + +
201E PHE* 4.5 2.5 - - + -
204E SER* 3.3 18.2 - - - +
205E ARG* 1.4 90.6 - - - +
207E PHE* 1.3 79.2 + - + +
209E ARG* 4.3 0.2 - - + -
210E ALA* 2.8 30.5 + - - +
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Residues in contact with PHE 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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64E ILE* 5.4 0.4 - - + -
97E ILE* 3.7 27.8 - - + -
100E GLU* 4.3 2.5 - - + -
101E TYR* 3.1 47.1 - + + -
104E ASP* 2.9 14.0 + - + +
105E LEU* 4.0 11.4 - - + -
118E TRP* 3.7 25.6 - + - -
166E ILE* 5.4 3.6 - - + -
168E TRP* 4.5 12.8 - + - -
201E PHE* 5.5 0.7 - + - -
206E PRO* 1.3 91.4 - - + +
208E SER* 1.3 64.8 + - - +
210E ALA* 3.4 2.8 + - - +
211E ASN* 3.2 15.6 + - - -
224E TRP* 3.1 59.2 + + + +
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Residues in contact with SER 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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104E ASP* 2.5 31.8 + - - -
105E LEU* 4.1 12.9 - - - +
205E ARG* 3.5 8.0 + - - +
207E PHE* 1.3 73.8 - - - +
209E ARG* 1.3 64.7 + - - +
211E ASN* 2.8 9.9 + - - +
212E GLU* 2.8 48.4 + - - +
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Residues in contact with ARG 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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187E ILE* 3.8 41.3 - - + +
188E GLU 4.4 9.9 + - - -
204E SER* 2.8 34.2 + - - +
205E ARG* 3.0 27.5 + - + +
206E PRO* 4.0 4.5 - - + +
208E SER* 1.3 80.4 + - - +
210E ALA* 1.3 61.6 + - - +
212E GLU* 3.9 14.4 - - - +
213E LEU* 2.9 31.9 + - + +
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Residues in contact with ALA 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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62E VAL* 4.4 12.8 - - + -
164E VAL* 3.7 26.8 - - + +
166E ILE* 4.8 3.6 - - + -
187E ILE* 4.6 1.3 - - - +
206E PRO 2.8 21.8 + - - +
207E PHE 3.4 6.7 - - - +
208E SER 3.1 0.2 - - - -
209E ARG* 1.3 76.1 - - - +
211E ASN* 1.3 59.4 + - - +
213E LEU* 3.2 3.9 + - - +
214E LEU* 2.9 32.6 + - - +
224E TRP* 4.3 15.3 - - + -
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Residues in contact with ASN 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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105E LEU* 5.6 1.8 - - - +
207E PHE 3.2 8.2 + - - +
208E SER* 2.8 11.7 + - - +
210E ALA* 1.3 75.8 - - - +
212E GLU* 1.3 58.9 + - + +
213E LEU 3.0 1.1 - - - -
214E LEU* 2.7 10.3 + - - +
215E VAL* 2.7 39.4 + - + +
221E PRO* 3.4 17.1 - - + +
222E ILE* 2.6 50.9 + - - +
223E ASP 5.2 0.2 + - - -
224E TRP* 3.4 16.7 + - - +
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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 SER* 2.8 31.3 + - - +
209E ARG* 3.9 18.5 + - - +
211E ASN* 1.3 72.5 - - + +
213E LEU* 1.3 55.6 + - - +
215E VAL* 3.4 7.9 + - - +
216E GLY* 2.8 27.7 + - - -
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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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164E VAL* 3.7 18.8 - - + -
185E VAL* 3.9 37.2 - - + -
187E ILE* 3.7 29.2 - - + -
209E ARG* 2.9 23.5 + - + +
210E ALA 3.3 4.9 - - - +
211E ASN 3.0 0.2 - - - -
212E GLU* 1.3 74.5 - - + +
214E LEU* 1.3 65.5 + - - +
216E GLY* 3.3 3.3 + - - -
217E MET* 3.1 30.8 + - + +
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Residues in contact with LEU 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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61E ARG* 3.5 33.0 - - + +
62E VAL* 3.7 24.0 - - + -
162E PRO* 4.8 6.3 - - + +
164E VAL* 3.8 13.9 - - + +
210E ALA 2.9 15.7 + - - +
211E ASN* 2.7 26.3 + - - +
213E LEU* 1.3 69.5 - - - +
215E VAL* 1.3 66.5 + - - +
217E MET* 2.7 22.0 + - + +
218E GLY 3.1 7.6 + - - -
219E ALA* 3.1 23.9 + - + +
220E GLU 3.7 23.6 - - - +
221E PRO* 4.6 0.4 - - + -
222E ILE* 4.1 4.9 - - + -
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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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211E ASN* 2.7 24.5 + - + +
212E GLU* 3.8 7.2 - - - +
214E LEU* 1.3 72.6 - - - +
216E GLY* 1.3 55.8 + - - +
218E GLY* 2.6 25.8 + - - -
219E ALA 3.7 8.1 - - - +
221E PRO* 4.1 32.1 - - + -
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Residues in contact with GLY 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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212E GLU 2.8 17.7 + - - -
213E LEU* 3.6 4.0 - - - -
214E LEU 3.1 0.4 - - - -
215E VAL* 1.3 78.6 - - - +
217E MET* 1.3 58.5 + - - +
218E GLY 3.3 0.8 + - - -
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Residues in contact with MET 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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162E PRO* 3.6 33.2 - - + +
163E LEU 4.5 2.5 - - - +
164E VAL* 3.9 20.9 - - + -
183E ASN* 3.5 27.4 - - - +
185E VAL* 4.0 22.7 - - + -
213E LEU* 3.1 30.0 + - + +
214E LEU* 2.7 10.4 + - + +
216E GLY* 1.3 80.1 - - - +
218E GLY* 1.3 60.5 + - - +
219E ALA 3.3 1.0 + - - -
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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