Contacts of the helix formed by residues 201 - 221 (chain E) in PDB entry 3KDO
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 201 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLU* 5.5 2.0 + - - -
131D LYS* 6.0 0.4 - - - +
170E PRO* 4.6 4.2 - - - +
196E SER* 2.7 36.9 + - - -
197E PRO* 3.4 12.9 - - - +
198E TRP* 3.6 30.9 + - - +
200E ASN* 1.3 78.1 + - - +
202E PHE* 1.3 66.9 + - - +
203E GLU* 3.3 25.4 - - - +
204E GLU* 3.1 40.4 + - + +
205E ARG* 3.2 10.1 + - - -
97I GLU* 4.7 7.3 + - - +
98I GLU* 4.9 14.6 + - - +
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Residues in contact with PHE 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E THR 4.2 1.6 - - - +
196E SER* 2.8 25.6 + - - +
200E ASN 3.6 2.4 + - - -
201E ARG* 1.3 71.8 - - - +
203E GLU* 1.3 71.2 + - - +
204E GLU 3.2 0.3 + - - -
205E ARG* 3.3 23.7 + - - +
206E ALA* 3.0 25.3 + - + +
226E TRP* 4.5 2.4 - + - -
228E ALA* 3.6 20.2 - - + -
229E ASN 3.4 30.5 - - - -
230E ILE* 4.0 5.8 - - + -
240E ARG* 3.4 52.0 - - + +
243E VAL* 4.2 11.4 - - + -
244E LEU* 3.6 30.3 - - + -
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Residues in contact with GLU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E SER* 4.0 5.8 + - - -
201E ARG* 3.4 27.2 - - - +
202E PHE* 1.3 87.2 + - + +
204E GLU* 1.3 65.2 + - + +
206E ALA* 3.5 6.9 + - - +
207E GLU* 3.1 41.4 + - - +
240E ARG* 6.0 0.5 - - - +
243E VAL* 4.5 19.2 - - + +
247E LEU* 4.9 0.2 - - - +
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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
----------------------------------------------------------
134D ARG* 4.3 22.1 + - - +
358D SER* 5.6 0.3 + - - -
170E PRO* 3.8 25.3 - - + +
171E GLU* 4.8 2.8 - - - +
198E TRP 6.0 0.7 - - - -
201E ARG* 3.1 38.6 + - + +
203E GLU* 1.3 85.8 - - + +
205E ARG* 1.3 59.2 + - - +
207E GLU* 3.8 7.8 + - - +
208E ILE* 3.3 27.4 + - + +
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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
----------------------------------------------------------
170E PRO* 4.4 7.2 - - + +
173E PHE* 4.3 22.0 - - + -
190E ASP* 3.1 35.2 + - - -
194E LEU* 3.6 25.5 + - - +
195E THR 2.7 30.5 + - - -
200E ASN* 3.0 46.1 + - - +
201E ARG 3.2 1.4 + - - -
202E PHE* 3.6 29.7 - - - +
204E GLU* 1.3 76.8 - - - +
206E ALA* 1.3 62.7 + - - +
208E ILE* 3.6 6.8 - - - +
209E MET* 2.8 34.1 + - - +
226E TRP* 3.6 14.5 - - + -
229E ASN 3.9 2.0 + - - -
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Residues in contact with ALA 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E PHE* 3.0 22.5 + - + +
203E GLU 3.6 5.6 - - - +
205E ARG* 1.3 77.9 - - - +
207E GLU* 1.3 56.5 + - - +
209E MET* 3.3 2.1 + - - +
210E ALA* 2.9 30.5 + - - +
226E TRP* 3.4 23.8 - - + -
243E VAL* 3.9 15.3 - - + -
247E LEU* 3.5 17.5 - - + +
249E LEU* 3.9 6.4 - - + +
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Residues in contact with GLU 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 GLU* 3.1 24.2 + - - +
204E GLU* 4.0 7.1 - - - +
205E ARG 3.4 0.2 - - - -
206E ALA* 1.3 78.1 - - - +
208E ILE* 1.3 63.0 + - + +
210E ALA* 3.5 4.0 + - - +
211E LYS* 3.2 21.8 + - - +
243E VAL* 6.1 0.4 - - + -
247E LEU* 3.6 26.8 - - + +
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Residues in contact with ILE 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E PRO* 3.2 44.4 - - + +
171E GLU* 4.1 7.0 - - + +
173E PHE* 4.9 7.4 - - + -
174E GLU* 3.7 38.8 - - + +
204E GLU* 3.3 10.9 + - + +
205E ARG* 3.6 8.7 - - - +
206E ALA 3.2 0.2 - - - -
207E GLU* 1.3 79.3 - - + +
209E MET* 1.3 58.8 + - - +
211E LYS* 3.3 11.1 + - + +
212E ILE* 2.8 41.4 + - + +
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Residues in contact with MET 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E PHE* 3.3 35.2 - - + -
177E ALA* 3.9 12.8 - - - -
181E LEU* 4.0 25.8 - - + -
188E MET* 4.2 8.7 - - + -
205E ARG 2.8 23.5 + - - +
206E ALA 3.8 0.9 - - - +
208E ILE* 1.3 72.2 - - - +
210E ALA* 1.3 59.3 + - - +
212E ILE* 4.3 5.8 - - + +
213E ILE* 2.7 49.8 + - + +
225E THR 4.5 0.7 - - - +
226E TRP* 3.6 52.0 - - + -
249E LEU* 4.5 2.5 - - + -
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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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206E ALA 2.9 17.4 + - - +
207E GLU* 3.6 6.7 - - - +
208E ILE 3.4 0.2 - - - -
209E MET* 1.3 75.5 - - - +
211E LYS* 1.3 63.6 + - - +
213E ILE* 4.0 2.5 - - - +
214E ASP* 3.3 28.1 + - - +
247E LEU* 4.1 34.5 - - + +
249E LEU* 3.8 16.5 - - + +
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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
----------------------------------------------------------
174E GLU* 3.8 22.9 + - - +
207E GLU 3.2 9.8 + - - +
208E ILE* 3.4 12.3 - - + +
209E MET 3.1 0.6 - - - -
210E ALA* 1.3 76.4 - - - +
212E ILE* 1.3 74.0 + - + +
214E ASP* 3.2 8.7 + - - +
215E LYS* 3.0 32.6 + - + +
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Residues in contact with ILE 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E GLU* 3.8 33.4 - - + +
177E ALA* 4.4 2.7 - - + -
178E TYR* 3.8 42.6 - - + +
181E LEU* 4.2 12.6 - - + -
208E ILE* 2.8 36.7 + - + +
209E MET* 3.8 10.3 - - - +
211E LYS* 1.3 82.0 - - + +
213E ILE* 1.3 57.6 + - - +
215E LYS* 3.2 10.0 + - + +
216E VAL* 2.8 38.2 + - + +
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Residues in contact with ILE 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E LEU* 4.7 2.5 - - + -
209E MET* 2.7 35.7 + - + +
210E ALA* 4.0 4.3 - - - +
212E ILE* 1.3 72.9 - - - +
214E ASP* 1.3 62.4 + - - +
216E VAL* 3.9 3.7 - - - +
217E GLU* 2.9 62.1 + - + +
224E LYS* 3.8 17.5 - - + +
225E THR* 3.6 33.4 - - - +
226E TRP* 4.2 6.7 - - + +
249E LEU* 4.2 20.2 - - + -
250E LYS* 4.7 9.4 - - + +
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Residues in contact with ASP 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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210E ALA* 3.3 15.1 + - - +
211E LYS* 3.2 9.3 + - - +
213E ILE* 1.3 82.1 - - - +
215E LYS* 1.3 62.1 + - - +
217E GLU* 3.8 12.1 - - - +
218E ASN* 2.9 27.3 + - - +
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Residues in contact with LYS 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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178E TYR* 3.5 31.6 + - + -
211E LYS* 3.0 23.3 + - + +
212E ILE* 3.5 16.8 - - + +
214E ASP* 1.3 77.1 - - - +
216E VAL* 1.3 63.4 + - - +
218E ASN* 3.2 8.0 + - - +
219E GLU* 2.8 58.1 + - + +
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Residues in contact with VAL 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E TYR* 3.5 22.9 - - + +
181E LEU* 3.9 16.8 - - + +
182E SER* 3.4 20.0 - - - +
212E ILE* 2.8 29.6 + - + +
213E ILE* 4.1 2.7 - - - +
215E LYS* 1.3 73.4 - - - +
217E GLU* 1.3 57.6 + - - +
219E GLU* 3.2 7.2 + - - +
220E THR* 2.8 43.6 + - + +
224E LYS* 3.7 37.0 - - + -
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Residues in contact with GLU 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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213E ILE* 2.9 38.8 + - + +
214E ASP* 3.8 10.6 - - - +
216E VAL* 1.3 75.7 - - - +
218E ASN* 1.3 57.4 + - - +
221E GLY* 2.6 33.3 + - - -
222E GLU 3.0 22.7 - - - +
223E LYS* 3.2 19.7 + - + +
224E LYS* 2.9 19.2 + - + +
250E LYS* 2.8 29.2 + - - -
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Residues in contact with ASN 218 (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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214E ASP 2.9 18.6 + - - +
215E LYS* 3.6 6.7 + - - +
217E GLU* 1.3 77.1 - - - +
219E GLU* 1.3 65.1 + - - +
221E GLY* 4.5 1.9 + - - -
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Residues in contact with GLU 219 (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* 2.6 31.4 + - - -
182E SER* 4.6 2.6 + - - -
215E LYS* 2.8 51.5 + - + +
216E VAL* 3.9 4.5 - - - +
218E ASN* 1.3 86.8 - - + +
220E THR* 1.3 64.9 + - + +
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Residues in contact with THR 220 (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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181E LEU 5.2 1.3 - - - +
182E SER* 4.6 20.6 - - - +
216E VAL* 2.8 35.5 + - + +
219E GLU* 1.3 84.5 - - + +
221E GLY* 1.3 61.7 + - - +
222E GLU* 3.0 40.9 + - - +
224E LYS* 4.4 0.5 - - - -
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Residues in contact with GLY 221 (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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151E GLU* 4.8 8.1 - - - +
217E GLU* 2.6 23.8 + - - -
218E ASN 4.4 2.3 + - - -
219E GLU 3.7 0.8 - - - -
220E THR* 1.3 73.3 - - - +
222E GLU* 1.3 58.6 + - - +
223E LYS* 4.2 1.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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