Contacts of the helix formed by residues 176 - 187 (chain E) in PDB entry 3FAA
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 176 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D ARG* 4.3 24.9 - - + +
174E GLY 3.5 10.5 - - - +
175E THR* 1.3 81.4 - - - +
177E LEU* 1.3 58.6 + - - +
178E LYS* 4.0 5.5 + - - +
179E ASP* 2.5 62.0 + - - +
180E LEU* 3.2 11.9 + - - +
224E TRP* 4.1 2.9 - - - -
225E ARG* 6.0 1.6 - - + +
227E GLU* 3.4 21.1 - - - +
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Residues in contact with LEU 177 (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 THR* 1.3 69.2 - - - +
178E LYS* 1.3 59.9 + - - +
180E LEU* 3.3 9.5 + - + +
181E ILE* 3.2 29.7 + - + +
193E LEU* 6.0 0.4 - - + -
201E ILE* 4.4 24.0 - - + -
224E TRP* 3.5 30.1 - - + -
227E GLU* 2.9 40.1 + - + +
228E GLU 4.8 3.4 - - - +
229E VAL* 4.4 15.7 - - + -
263E ILE* 3.8 35.9 - - + -
281E ASP* 5.8 0.9 - - - +
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Residues in contact with LYS 178 (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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365D ILE 5.0 3.4 - - - +
366D ASP 3.7 13.7 - - - +
367D ILE* 3.4 23.1 - - - +
368D ALA* 3.2 29.7 - - - +
176E THR* 2.8 10.0 + - - +
177E LEU* 1.3 79.7 - - - +
179E ASP* 1.3 57.5 + - - +
181E ILE* 3.4 8.3 + - + +
182E TYR* 2.9 28.0 + - + +
227E GLU* 3.3 10.8 + - - +
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Residues in contact with ASP 179 (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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243D PHE* 3.4 24.1 - - + -
244D ARG* 3.2 26.8 + - - +
247D GLU* 3.9 6.3 - - - +
366D ASP* 3.7 12.4 - - - +
174E GLY 4.3 0.5 - - - +
175E THR* 4.5 2.5 - - + -
176E THR* 2.5 46.1 + - - +
178E LYS* 1.3 70.1 - - - +
180E LEU* 1.3 67.6 + - - +
182E TYR* 3.1 5.7 + - - +
183E ASP* 2.8 39.8 + - - +
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Residues in contact with LEU 180 (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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171E ILE* 4.4 15.3 - - + -
175E THR* 4.0 20.2 - - + -
176E THR 3.2 8.4 + - - +
177E LEU* 3.5 12.6 - - + +
179E ASP* 1.3 80.3 - - - +
181E ILE* 1.3 59.4 - - + +
183E ASP* 3.8 4.9 - - - +
184E MET* 3.0 26.2 + - - +
193E LEU* 3.7 19.2 - - + +
197E VAL* 3.8 19.5 - - + -
201E ILE* 3.6 32.5 - - + -
224E TRP* 4.5 11.9 - - + -
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Residues in contact with ILE 181 (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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177E LEU* 3.2 18.0 + - + +
178E LYS* 3.7 9.0 - - + +
179E ASP 3.1 0.4 - - - -
180E LEU* 1.3 77.8 - - + +
182E TYR* 1.3 69.5 + - - +
184E MET* 2.9 23.7 + - + +
185E THR* 2.8 35.4 + - - +
193E LEU* 5.4 5.6 - - + -
255E ARG* 3.6 25.6 - - - +
262E PHE 5.2 0.4 - - - +
263E ILE* 4.2 23.8 - - + -
281E ASP* 4.4 9.6 - - - +
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Residues in contact with TYR 182 (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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327D PRO* 3.8 15.5 - - + +
357D ARG* 3.6 58.5 - - + +
359D ASP* 3.7 19.6 + - + +
364D THR* 4.1 21.3 - - - -
365D ILE 4.1 7.0 - - - +
366D ASP* 3.7 38.4 - - - +
178E LYS* 2.9 20.5 + - + +
179E ASP 3.7 2.2 - - - +
181E ILE* 1.3 76.2 - - - +
183E ASP* 1.3 62.7 + - - +
185E THR* 3.4 7.0 + - + -
186E THR* 2.8 57.6 + - + +
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Residues in contact with ASP 183 (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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243D PHE* 5.6 0.3 - - - -
247D GLU* 2.9 34.7 - - - +
357D ARG* 3.6 21.3 + - - -
179E ASP* 2.8 31.6 + - - +
180E LEU* 3.8 4.6 - - - +
182E TYR* 1.3 77.4 - - - +
184E MET* 1.3 57.2 + - - +
186E THR* 4.4 2.7 - - - -
187E SER* 2.8 38.6 + - - +
188E GLY 3.9 0.2 + - - -
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Residues in contact with MET 184 (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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180E LEU 3.0 12.7 + - - +
181E ILE* 2.9 40.4 + - + +
183E ASP* 1.3 73.9 - - - +
185E THR* 1.3 75.6 + - - +
186E THR 3.0 10.2 + - - -
187E SER 3.5 3.5 + - - -
188E GLY* 3.0 29.9 + - - +
190E GLY 4.3 6.5 - - - +
191E SER 3.9 18.4 - - - +
192E GLY* 3.0 31.6 - - - +
193E LEU* 3.8 22.4 - - + -
194E PRO* 6.0 0.2 - - + -
255E ARG* 4.4 17.7 - - - +
262E PHE 5.3 1.6 - - - +
263E ILE* 6.5 0.2 - - - -
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Residues in contact with THR 185 (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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359D ASP* 4.7 3.5 - - - +
362D THR* 4.1 33.0 - - + +
364D THR* 5.1 9.4 - - + +
181E ILE* 2.8 32.6 + - - +
182E TYR* 3.6 7.6 - - + +
184E MET* 1.3 82.7 - - - +
186E THR* 1.3 59.5 + - - +
255E ARG* 4.2 15.0 - - - -
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Residues in contact with THR 186 (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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327D PRO* 6.2 2.2 - - + -
359D ASP* 4.2 21.2 + - + +
364D THR* 5.5 0.3 + - - -
182E TYR* 2.8 50.7 + - + +
183E ASP* 3.8 3.6 - - - -
184E MET 3.0 0.6 - - - -
185E THR* 1.3 81.3 - - - +
187E SER* 1.3 72.1 + - - +
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Residues in contact with SER 187 (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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183E ASP* 2.8 22.4 + - - +
186E THR* 1.3 81.7 - - - +
188E GLY* 1.3 70.4 + - - -
189E SER* 2.7 10.4 + - - -
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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
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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