Contacts of the helix formed by residues 176 - 186 (chain B) in PDB entry 1IAS
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B GLY 3.6 13.9 - - - +
175B THR* 1.3 80.9 - - - +
177B LEU* 1.3 66.4 + - - +
178B LYS* 3.8 6.6 + - - +
179B ASP* 2.5 43.2 + - - +
180B LEU* 3.2 8.5 + - - +
224B TRP* 3.7 5.6 - - - -
225B ARG* 6.0 0.7 - - - +
227B GLU* 3.3 19.7 - - - +
240C ARG* 3.9 29.2 - - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B THR* 1.3 70.5 - - - +
178B LYS* 1.3 65.5 + - + +
180B LEU* 2.9 26.5 + - + +
181B ILE* 2.9 31.6 + - + +
201B ILE* 5.0 5.2 - - + -
224B TRP* 3.5 26.5 - - + -
227B GLU* 2.4 33.8 + - + +
228B GLU 3.8 22.2 - - - +
229B VAL* 3.8 19.1 - - + -
263B ILE* 4.1 29.2 - - + -
281B ASP* 5.4 1.6 - - - +
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B THR* 3.2 8.2 - - - +
177B LEU* 1.3 82.7 - - + +
179B ASP* 1.3 53.9 + - - +
181B ILE* 3.3 10.3 + - + +
182B TYR* 2.8 38.0 + - - +
227B GLU* 3.0 36.0 + - - +
366C ASP 4.3 9.9 - - - +
367C ILE* 5.4 2.0 - - - -
368C ALA* 3.9 25.4 - - + +
369C PRO* 3.1 39.5 - - + +
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Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLY 4.3 0.3 - - - +
175B THR* 4.4 3.8 - - + -
176B THR* 2.5 41.6 + - - +
178B LYS* 1.3 78.4 - - - +
180B LEU* 1.3 63.6 + - + +
182B TYR* 3.4 6.6 + - - +
183B ASP* 2.9 35.8 + - - +
240C ARG* 6.1 0.2 - - - +
243C PHE* 3.8 29.5 - - + -
244C ARG* 3.6 24.5 + - - +
247C GLU* 4.4 7.1 - - - +
357C ARG* 4.6 4.2 + - - +
366C ASP* 5.6 1.2 - - - -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 4.5 7.0 - - + -
175B THR* 4.0 15.0 - - + -
176B THR 3.7 7.6 - - - +
177B LEU* 2.9 14.5 + - + +
179B ASP* 1.3 78.4 - - - +
181B ILE* 1.3 65.9 + - + +
183B ASP* 3.1 17.6 + - + +
184B MET* 3.1 12.3 + - - +
193B LEU* 4.0 28.2 - - + +
197B VAL* 4.5 11.4 - - + -
201B ILE* 3.7 30.5 - - + -
224B TRP* 4.2 27.1 - - + -
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU* 2.9 41.9 + - + +
178B LYS* 3.7 11.0 - - + +
180B LEU* 1.3 74.5 - - + +
182B TYR* 1.3 65.9 + - - +
184B MET* 3.1 14.5 - - - +
185B THR* 2.9 31.3 + - - +
193B LEU* 6.3 0.7 - - + -
255B ARG* 3.3 28.3 - - - +
263B ILE* 4.4 11.4 - - + -
281B ASP* 3.5 24.5 - - - +
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LYS 2.8 22.1 + - - +
179B ASP* 3.6 6.1 - - - +
181B ILE* 1.3 74.0 - - - +
183B ASP* 1.3 69.5 + - - +
185B THR* 3.4 6.9 + - + -
186B THR* 3.0 51.9 + - + +
327C PRO* 4.6 6.1 - - - +
357C ARG* 3.9 41.6 + - + +
358C HIS 4.5 0.7 - - - -
359C ASP* 3.9 16.9 + - + +
364C THR* 4.4 16.4 - - - -
365C ILE 3.3 26.9 - - - -
366C ASP* 3.0 31.4 - - - +
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Residues in contact with ASP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 2.9 22.8 + - - +
180B LEU* 3.1 11.6 + - + +
182B TYR* 1.3 86.5 - - - +
184B MET* 1.3 60.5 + - - +
186B THR* 5.2 0.2 - - - -
187B SER* 3.3 14.3 + - - +
188B GLY* 2.9 21.7 + - - -
193B LEU* 6.0 1.1 - - + -
243C PHE* 5.9 0.7 - - - -
247C GLU* 3.3 24.5 - - - +
251C THR* 4.8 9.2 - - - +
357C ARG* 4.8 2.6 + - - -
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Residues in contact with MET 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU 3.1 7.5 + - - +
181B ILE* 3.1 22.9 - - - +
183B ASP* 1.3 74.9 - - - +
185B THR* 1.3 70.7 + - - +
188B GLY* 3.0 28.8 - - - -
189B SER 4.0 0.9 + - - -
190B GLY 4.9 4.1 + - - +
191B SER 4.1 13.4 - - - +
192B GLY* 3.5 32.5 - - - -
193B LEU* 3.9 32.5 - - + +
255B ARG* 3.7 32.3 - - - +
262B PHE* 4.0 13.2 - - + +
263B ILE* 5.3 4.7 - - - +
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 2.9 35.5 + - - +
182B TYR* 3.5 9.0 - - + -
184B MET* 1.3 80.2 - - - +
186B THR* 1.3 63.7 + - - +
190B GLY 5.9 0.7 + - - -
255B ARG* 4.1 19.8 + - + +
362C THR* 4.0 29.9 + - + +
364C THR* 4.7 9.6 - - + +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 3.0 43.0 + - + +
183B ASP* 4.4 0.7 - - - -
184B MET 3.3 0.2 - - - -
185B THR* 1.3 82.6 - - - +
187B SER* 1.3 73.2 + - - +
188B GLY 3.2 0.8 + - - -
189B SER* 3.8 6.2 + - - -
359C ASP* 3.4 39.3 + - + +
362C THR* 4.8 1.3 + - - -
364C THR* 4.5 4.2 + - - -
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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