Contacts of the helix formed by residues 202 - 219 (chain E) in PDB entry 4GOM
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 THR 202 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E SER* 4.3 9.9 - - - +
201E PHE* 1.3 78.1 - - - +
203E LEU* 1.3 53.6 + - - +
204E GLU* 3.2 17.2 + - - +
205E GLN* 2.8 54.9 + - - +
206E GLN* 2.8 21.2 + - - +
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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
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186E PRO* 4.0 32.5 - - + -
201E PHE 5.6 1.8 - - - +
202E THR* 1.3 73.0 - - - +
204E GLU* 1.3 66.5 + - - +
206E GLN* 3.3 11.9 - - + +
207E ALA* 3.0 27.9 + - - +
232E LEU* 4.7 11.9 - - + -
236E TRP* 3.9 19.3 + - + -
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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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202E THR* 3.2 23.9 - - - +
203E LEU* 1.3 84.6 + - - +
205E GLN* 1.3 58.3 + - + +
207E ALA* 3.4 5.8 + - - +
208E HIS* 3.0 27.2 + - - +
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Residues in contact with GLN 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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164E SER* 5.7 0.6 + - - -
165E TYR* 3.7 29.6 + - - +
200E SER 4.0 3.5 - - - +
201E PHE* 3.5 30.0 - - + -
202E THR* 2.8 40.9 + - - +
204E GLU* 1.3 74.3 - - + +
206E GLN* 1.3 65.9 + - - +
207E ALA 3.1 1.6 - - - -
208E HIS* 2.9 13.4 + - - +
209E LEU* 2.9 15.2 + - - +
301E 0Y0 4.4 9.3 + - - -
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Residues in contact with GLN 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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182E PRO* 4.3 4.3 - - - +
183E PRO 3.0 23.8 + - - +
184E TYR 3.7 3.2 + - - -
185E ALA* 3.5 20.0 - - - +
186E PRO* 5.1 1.4 - - - +
201E PHE* 3.6 27.5 + - + +
202E THR 2.8 21.9 + - - +
203E LEU* 3.3 15.7 - - + +
205E GLN* 1.3 71.6 - - - +
207E ALA* 1.3 61.1 + - - +
209E LEU* 3.6 17.1 - - - +
210E ALA* 3.6 8.0 + - - +
227E ASN* 3.4 19.1 + - - -
236E TRP* 3.4 35.7 - - + +
237E TYR* 4.2 6.6 + - - -
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Residues in contact with ALA 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 LEU 3.0 12.6 + - - +
204E GLU* 3.9 5.8 - - - +
205E GLN 3.1 0.2 - - - -
206E GLN* 1.3 75.3 - - - +
208E HIS* 1.3 66.7 - - - +
210E ALA* 3.1 6.3 + - - +
211E GLU* 2.9 22.3 + - - +
236E TRP* 3.5 33.4 - - + +
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Residues in contact with HIS 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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165E TYR* 2.7 25.2 + + - +
166E ALA* 4.5 10.1 - - + -
204E GLU 3.0 17.9 + - - +
205E GLN* 3.3 6.3 - - - +
207E ALA* 1.3 75.6 - - - +
209E LEU* 1.3 64.6 + - - +
211E GLU* 3.0 24.9 + - - +
212E ILE* 2.9 46.6 + - + +
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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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35E PHE* 4.0 17.3 - - + -
165E TYR* 4.2 15.8 - - + -
169E MET* 3.5 34.3 - - + -
180E CYS* 3.9 15.9 - - + -
182E PRO* 3.8 37.7 - - + -
201E PHE* 5.0 4.3 - - + -
205E GLN 2.9 11.1 + - - +
206E GLN* 3.6 13.2 - - - +
208E HIS* 1.3 75.8 - - - +
210E ALA* 1.3 57.9 + - - +
212E ILE* 3.2 5.7 + - - +
213E ALA* 3.0 24.6 + - - +
225E ILE* 4.4 15.5 - - + -
237E TYR* 4.9 3.6 - - + +
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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 GLN 3.6 3.0 + - - +
207E ALA 3.1 9.0 + - - +
209E LEU* 1.3 81.9 - - - +
211E GLU* 1.3 61.3 + - - +
213E ALA* 3.3 7.3 + - - +
214E GLU* 3.2 28.8 + - - +
225E ILE* 4.7 2.7 - - - -
236E TRP* 3.5 32.3 - - + +
237E TYR* 3.8 23.6 - - + -
268E TYR* 4.0 6.1 + - - +
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Residues in contact with GLU 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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207E ALA 2.9 12.1 + - - +
208E HIS* 3.0 26.0 + - + +
210E ALA* 1.3 78.3 - - - +
212E ILE* 1.3 63.3 + - + +
214E GLU* 3.3 18.5 + - - +
215E GLY* 3.2 16.3 + - - -
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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
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165E TYR* 3.9 21.1 - - + -
166E ALA* 3.9 19.3 - - + +
169E MET* 4.0 30.3 - - + -
170E ALA 5.8 0.4 - - - +
208E HIS* 2.9 49.6 + - + +
209E LEU* 3.2 6.0 + - - +
211E GLU* 1.3 70.6 - - + +
213E ALA* 1.3 65.7 + - - +
215E GLY* 2.9 14.7 + - - +
216E LEU* 3.0 18.8 + - + +
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Residues in contact with ALA 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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169E MET* 4.2 5.4 - - + +
209E LEU 3.0 13.3 + - - +
210E ALA 3.5 9.6 - - - +
211E GLU 3.3 0.2 - - - -
212E ILE* 1.3 72.7 - - - +
214E GLU* 1.3 54.6 + - - +
216E LEU* 2.9 23.0 + - - +
217E VAL* 2.9 15.2 + - - +
223E VAL* 4.0 27.3 - - + +
225E ILE* 4.2 6.3 - - + -
268E TYR* 3.7 33.4 - - + -
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Residues in contact with GLU 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 3.2 14.6 + - - +
211E GLU* 3.5 17.9 - - - +
212E ILE 3.2 0.2 - - - -
213E ALA* 1.3 75.0 - - - +
215E GLY* 1.3 61.8 + - - +
217E VAL* 3.4 11.9 - - + +
218E GLU* 3.1 23.9 + - - +
236E TRP 4.1 14.7 - - - +
238E GLN* 5.3 1.9 - - - +
239E ARG* 3.7 36.9 + - + +
268E TYR* 3.7 17.3 + - + -
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Residues in contact with GLY 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 GLU 3.2 8.3 + - - -
212E ILE* 2.9 9.9 + - - -
214E GLU* 1.3 74.7 - - - +
216E LEU* 1.3 66.6 + - - +
218E GLU* 3.8 5.7 + - - +
219E ARG* 3.3 27.6 + - - +
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Residues in contact with LEU 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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169E MET* 3.9 45.3 - - + +
170E ALA* 5.7 0.2 - - - -
172E ALA* 4.6 1.8 - - + -
178E VAL* 4.0 16.8 - - + -
212E ILE* 3.0 16.1 + - + +
213E ALA 2.9 7.4 + - - +
215E GLY* 1.3 75.9 - - - +
217E VAL* 1.3 59.8 + - - +
219E ARG* 2.9 51.0 + - - +
220E HIS 3.2 0.2 + - - -
221E ILE* 3.0 43.9 + - + +
223E VAL* 3.8 18.4 - - + -
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Residues in contact with VAL 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 ALA 2.9 6.4 + - - +
214E GLU* 3.4 22.4 - - + +
216E LEU* 1.3 76.3 - - - +
218E GLU* 1.3 65.7 + - - +
220E HIS* 2.8 18.9 + - - -
221E ILE 3.3 7.5 + - - +
268E TYR* 3.3 47.1 - - + +
269E LYS 3.5 24.7 - - - +
270E PRO* 3.7 10.0 - - + +
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Residues in contact with GLU 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 GLU 3.1 18.4 + - - +
215E GLY* 4.1 6.1 - - - +
216E LEU 3.4 0.2 - - - -
217E VAL* 1.3 78.4 - - + +
219E ARG* 1.3 57.4 + - + +
220E HIS* 3.4 16.1 + - - -
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Residues in contact with ARG 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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169E MET 5.0 1.2 + - - -
170E ALA* 4.9 11.1 + - - +
172E ALA 4.1 18.2 + - - -
173E ASP* 5.4 2.0 - - - +
174E ASP* 5.7 1.7 - - - -
215E GLY 3.3 14.5 + - - +
216E LEU* 2.9 38.9 + - - +
218E GLU* 1.3 75.8 - - + +
220E HIS* 1.3 75.3 + - - +
221E ILE* 3.4 19.1 + - + +
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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