Contacts of the helix formed by residues 176 - 187 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C GLY 3.6 13.9 - - - +
175C THR* 1.3 74.6 - - - +
177C LEU* 1.3 66.5 + - - +
178C LYS* 3.8 6.1 + - - +
179C ASP* 2.4 49.7 + - - +
180C LEU* 3.2 13.0 + - - +
224C TRP* 3.7 7.0 - - - -
225C ARG* 5.9 2.0 - - + +
227C GLU* 3.5 17.5 - - - +
240E ARG* 4.3 24.5 - - + +
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C THR* 1.3 70.1 - - - +
178C LYS* 1.3 66.0 + - + +
180C LEU* 2.9 25.9 + - + +
181C ILE* 3.0 34.6 + - + +
201C ILE* 5.2 4.7 - - + -
224C TRP* 3.5 26.9 - - + -
227C GLU* 2.5 36.3 + - + +
228C GLU 3.8 22.2 - - - +
229C VAL* 4.1 15.3 - - + -
263C ILE* 4.3 24.7 - - + -
281C ASP* 5.7 0.9 - - - +
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Residues in contact with LYS 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C THR* 3.2 7.6 - - - +
177C LEU* 1.3 80.7 - - + +
179C ASP* 1.3 57.9 + - - +
181C ILE* 3.3 9.9 + - + +
182C TYR* 2.8 33.7 + - - +
227C GLU* 2.9 37.7 + - - +
366E ASP* 5.4 4.7 - - - +
367E ILE* 4.5 31.0 - - + +
370E ASN* 6.1 0.7 - - - +
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Residues in contact with ASP 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLY 4.4 0.2 - - - +
175C THR* 4.4 3.6 - - + -
176C THR* 2.4 41.5 + - - +
178C LYS* 1.3 78.8 - - - +
180C LEU* 1.3 64.2 + - - +
182C TYR* 3.6 6.0 - - - +
183C ASP* 2.9 30.5 + - - +
243E PHE* 3.6 32.8 - - + -
244E ARG* 3.5 25.9 + - - +
247E GLU* 4.1 11.6 - - - +
357E ARG* 4.4 3.7 + - - +
366E ASP* 4.6 3.9 - - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ILE* 4.5 7.2 - - + -
175C THR* 4.0 15.0 - - + -
176C THR 3.7 7.0 - - - +
177C LEU* 2.9 14.9 + - + +
179C ASP* 1.3 79.2 - - - +
181C ILE* 1.3 64.6 + - + +
183C ASP* 3.0 19.3 + - + +
184C MET* 3.1 12.9 + - - +
193C LEU* 4.1 23.8 - - + +
197C VAL* 4.4 15.5 - - + -
201C ILE* 3.7 29.8 - - + -
224C TRP* 4.1 28.7 - - + -
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Residues in contact with ILE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LEU* 3.0 40.6 + - + +
178C LYS* 3.7 10.8 - - + +
180C LEU* 1.3 74.4 - - + +
182C TYR* 1.3 66.1 + - - +
184C MET* 3.1 15.8 - - + +
185C THR* 2.9 38.4 + - - +
255C ARG* 4.4 16.8 - - - +
263C ILE* 4.8 9.9 - - + -
281C ASP* 3.9 21.3 - - - +
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Residues in contact with TYR 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LYS 2.8 22.3 + - - +
179C ASP* 3.6 5.8 - - - +
181C ILE* 1.3 74.0 - - - +
183C ASP* 1.3 64.2 + - - +
185C THR* 3.6 6.2 - - + -
186C THR* 2.7 67.4 + - + +
327E PRO* 4.3 10.6 - - - +
357E ARG* 3.5 51.6 - - + +
359E ASP* 4.2 20.5 + - + +
364E THR* 4.8 11.0 - - - -
366E ASP* 3.1 43.5 - - + +
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Residues in contact with ASP 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASP* 2.9 19.6 + - - +
180C LEU* 3.0 12.3 + - + +
182C TYR* 1.3 80.4 - - - +
184C MET* 1.3 60.8 + - - +
186C THR* 3.4 7.6 - - - +
187C SER* 2.8 31.1 + - - -
193C LEU* 6.0 1.3 - - + -
243E PHE* 5.8 0.9 - - - -
247E GLU* 2.9 28.8 - - - +
251E THR* 4.0 20.3 + - - +
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Residues in contact with MET 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C LEU 3.1 8.1 + - - +
181C ILE* 3.1 22.7 - - - +
183C ASP* 1.3 75.5 - - - +
185C THR* 1.3 71.8 + - - +
187C SER* 3.0 24.4 + - - +
189C SER 4.9 0.2 - - - +
190C GLY* 5.8 0.5 - - - -
191C SER 3.7 17.6 + - - +
192C GLY* 3.7 27.1 - - - -
193C LEU* 4.1 26.4 - - + +
255C ARG* 3.6 42.0 - - + +
262C PHE* 4.1 11.7 - - + +
263C ILE* 5.5 5.2 - - - +
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Residues in contact with THR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ILE* 2.9 34.4 + - - +
182C TYR* 3.6 7.0 - - + -
184C MET* 1.3 81.5 - - - +
186C THR* 1.3 62.6 + - - +
187C SER 3.1 4.0 + - - +
255C ARG* 3.8 20.7 + - - +
359E ASP* 5.8 0.2 - - - +
362E THR* 4.4 27.4 + - + +
364E THR* 5.2 6.1 - - + +
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Residues in contact with THR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C TYR* 2.7 60.9 + - + +
183C ASP* 3.4 14.1 - - - +
185C THR* 1.3 74.3 - - - +
187C SER* 1.3 66.3 + - - +
188C GLY* 3.1 4.9 + - - -
251E THR* 5.8 3.8 - - + -
359E ASP* 3.6 26.8 + - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ASP 2.8 20.4 + - - -
184C MET* 3.0 19.3 + - - +
185C THR 4.1 3.6 - - - +
186C THR* 1.3 75.7 - - - +
188C GLY* 1.3 67.0 + - - +
189C SER* 2.9 38.0 + - - +
190C GLY* 4.1 2.8 + - - -
191C SER* 4.6 4.3 + - - -
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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