Contacts of the helix formed by residues 195 - 209 (chain E) in PDB entry 3ZXR
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 TYR 195 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ILE* 3.9 53.7 + - + -
140E ASP* 4.9 1.1 + - - -
157E ALA* 4.1 4.5 - - - +
158E ILE* 3.9 10.2 - - + +
159E SER* 2.7 45.1 + - - -
193E ASP* 3.2 2.4 + - - -
194E GLN* 1.3 90.6 - - + +
196E VAL* 1.3 58.4 + - - +
197E ASP 3.4 2.7 - - - -
198E LEU* 3.3 14.6 + - + +
199E ARG* 2.9 45.3 + - - +
218E HIS* 3.9 15.9 - + - -
223E GLY 4.0 1.7 - - - -
224E GLY* 3.4 22.8 + - - -
258E LYS* 4.4 18.4 - - - -
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Residues in contact with VAL 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D HIS* 4.1 12.8 - - + -
36D THR* 5.6 0.2 - - - +
84D ARG* 3.4 50.9 - - + +
190E ALA* 4.3 12.8 - - + -
193E ASP* 3.3 38.1 - - + +
194E GLN 3.6 1.8 - - - -
195E TYR* 1.3 78.2 - - - +
197E ASP* 1.3 60.5 + - - +
199E ARG* 3.9 9.4 - - - +
200E ASP* 3.0 29.2 + - - +
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Residues in contact with ASP 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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83D PHE 4.9 3.3 - - - +
84D ARG* 3.9 15.9 - - - +
85D ALA* 3.7 30.8 + - - +
86D ALA 5.2 0.3 + - - -
255D GLN* 5.4 4.3 + - - -
195E TYR 3.4 0.2 - - - -
196E VAL* 1.3 79.7 - - - +
198E LEU* 1.3 62.2 + - - +
200E ASP* 3.2 10.4 + - - +
201E LYS* 3.0 33.4 + - - +
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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
----------------------------------------------------------
138E ILE* 3.7 34.5 - - + -
195E TYR* 3.3 18.6 + - + +
196E VAL 3.3 0.4 - - - -
197E ASP* 1.3 79.4 - - - +
199E ARG* 1.3 57.4 + - - +
201E LYS* 3.0 11.8 + - + +
202E MET* 3.0 38.0 + - + +
252E THR* 4.1 14.4 - - + +
253E ALA* 4.4 1.3 - - - -
256E ASN* 3.8 37.5 - - + +
258E LYS* 3.8 21.3 - - + -
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Residues in contact with ARG 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D HIS* 4.2 8.9 - - - -
36D THR* 5.5 3.2 + - - -
138E ILE* 4.3 16.8 - - + -
193E ASP* 2.7 43.2 + - - -
195E TYR* 2.9 28.1 + - - +
196E VAL* 4.0 13.4 - - - +
198E LEU* 1.3 73.0 - - - +
200E ASP* 1.3 61.5 + - - +
202E MET* 3.2 14.7 + - - +
203E LEU* 2.8 39.0 + - + +
216E GLY* 4.5 3.5 + - - -
217E HIS* 3.4 32.4 - - - +
218E HIS* 3.4 25.9 - - - +
226E ALA* 3.7 16.2 - - + +
227E GLU 4.9 2.2 - - - -
228E ILE* 4.1 8.9 - - + +
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Residues in contact with ASP 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 3.5 14.6 + - + -
84D ARG* 2.8 49.1 + - - +
86D ALA* 3.9 23.2 + - + +
88D THR* 4.4 0.5 + - - -
196E VAL* 3.0 17.3 + - - +
197E ASP* 3.4 15.1 - - - +
198E LEU 3.2 0.2 - - - -
199E ARG* 1.3 76.6 - - - +
201E LYS* 1.3 56.6 + - + +
203E LEU* 3.2 16.6 + - - +
204E THR* 2.9 34.6 + - - -
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Residues in contact with LYS 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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85D ALA* 6.6 0.4 - - - -
197E ASP* 3.0 22.2 + - - +
198E LEU* 3.0 15.2 + - - +
200E ASP* 1.3 74.8 - - + +
202E MET* 1.3 64.0 + - - +
204E THR* 3.4 6.0 + - - -
205E ASN* 3.0 30.9 + - - +
252E THR* 3.9 12.8 - - + -
256E ASN* 3.1 34.9 + - - +
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Residues in contact with MET 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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136E PHE* 3.8 25.1 - - + -
138E ILE* 3.9 23.1 - - + -
198E LEU* 3.0 28.9 + - + +
199E ARG* 3.5 15.9 - - - +
201E LYS* 1.3 77.4 - - - +
203E LEU* 1.3 62.7 + - - +
205E ASN* 3.3 2.4 + - - +
206E LEU* 3.0 30.2 + - - +
228E ILE* 3.7 12.8 - - + -
248E ILE* 4.4 0.6 - - - +
249E ILE* 3.7 38.4 - - + +
252E THR* 3.6 21.3 - - + -
253E ALA* 4.0 17.0 - - + +
260E VAL* 4.3 0.2 - - + -
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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
----------------------------------------------------------
20D TYR* 3.3 35.4 - - + +
36D THR* 4.4 15.0 - - + +
37D ILE 6.3 0.2 - - - -
38D PRO* 5.9 2.2 - - + -
199E ARG* 2.8 28.1 + - + +
200E ASP* 3.5 17.0 - - - +
202E MET* 1.3 71.7 - - - +
204E THR* 1.3 56.5 + - - +
206E LEU* 3.4 6.0 + - - +
207E ILE* 3.0 33.8 + - + +
213E LEU* 3.8 18.2 - - + +
215E LYS* 4.4 9.6 - - - +
216E GLY* 4.4 9.2 - - - +
228E ILE* 3.7 33.0 - - + -
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Residues in contact with THR 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLU* 4.3 12.3 + - - +
20D TYR* 2.8 24.4 + - - +
86D ALA* 5.1 2.4 - - - +
200E ASP 2.9 15.1 + - - -
201E LYS* 3.8 6.7 - - - -
203E LEU* 1.3 74.1 - - - +
205E ASN* 1.3 62.7 + - - +
207E ILE* 3.3 6.9 + - + +
208E ASN* 2.8 53.5 + - - +
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Residues in contact with ASN 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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82E PRO* 4.5 20.5 + - + +
83E PHE* 3.7 13.7 - - - -
201E LYS* 3.0 21.1 + - - +
202E MET 3.8 1.1 - - - +
204E THR* 1.3 79.9 - - - +
206E LEU* 1.3 61.9 + - - +
208E ASN* 3.5 9.0 + - - +
209E SER* 3.0 27.2 + - - -
248E ILE* 3.8 19.3 - - + -
252E THR* 2.9 28.3 + - - +
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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 MET 3.0 23.2 + - - +
203E LEU* 3.7 4.0 - - - +
204E THR 3.3 0.2 - - - -
205E ASN* 1.3 73.6 - - - +
207E ILE* 1.3 66.2 + - - +
209E SER 2.9 10.7 + - - -
211E PHE* 3.1 52.3 + - + -
213E LEU* 3.9 16.8 - - + -
228E ILE* 3.7 29.6 - - + -
230E TYR* 5.5 1.1 - - + -
245E TYR* 3.9 28.0 - - + +
248E ILE* 3.8 24.0 - - + -
249E ILE* 4.1 9.2 - - + -
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Residues in contact with ILE 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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19D GLU 5.6 0.9 - - - +
20D TYR* 3.8 28.7 - - + +
38D PRO* 4.4 15.5 - - + -
40D SER* 5.7 1.1 - - - +
203E LEU 3.0 21.4 + - - +
204E THR* 3.6 6.7 - - + +
206E LEU* 1.3 74.6 - - - +
208E ASN* 1.3 67.2 + - - +
210E GLY* 2.9 22.5 + - - -
211E PHE 3.8 11.3 + - - +
213E LEU* 3.5 19.5 - - + +
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Residues in contact with ASN 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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80E ILE* 5.4 4.0 - - - +
82E PRO* 6.0 4.0 - - + -
204E THR* 2.8 42.8 + - - +
205E ASN* 4.0 9.8 + - - +
207E ILE* 1.3 80.5 - - - +
209E SER* 1.3 57.9 + - - +
210E GLY 3.3 1.7 + - - -
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Residues in contact with SER 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ARG* 3.3 30.9 + - - +
80E ILE 4.3 9.4 + - - +
82E PRO* 3.9 15.9 - - - +
205E ASN 3.0 15.5 + - - -
206E LEU 2.9 6.8 + - - -
208E ASN* 1.3 77.0 + - - +
210E GLY* 1.3 61.6 + - - +
211E PHE* 3.3 12.8 + - - -
244E LEU* 4.5 8.0 - - - +
248E ILE* 3.3 22.7 - - - +
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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