Contacts of the helix formed by residues 176 - 186 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLY 4.0 7.2 - - - +
175A THR* 1.3 83.4 - - - +
177A LEU* 1.3 66.1 + - - +
178A LYS* 2.9 7.8 + - - +
179A ASP* 2.6 45.3 + - - +
180A LEU* 3.1 8.8 + - - +
224A TRP* 4.2 2.5 - - - -
225A ARG* 5.8 2.9 - - + +
227A GLU* 3.6 17.7 - - + +
240B ARG* 4.1 31.4 - - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A THR* 1.3 70.1 - - - +
178A LYS* 1.3 66.1 + - + +
180A LEU* 3.2 27.1 + - + +
181A ILE* 3.1 37.2 + - + +
193A LEU* 6.0 0.7 - - + -
201A ILE* 4.6 4.7 - - + -
224A TRP* 3.8 17.6 - - + -
227A GLU* 2.6 46.8 + - + +
228A GLU 4.2 2.7 - - - +
229A VAL* 3.7 29.2 - - + -
263A ILE* 3.7 30.7 - - + -
281A ASP* 5.2 3.6 - - - +
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A THR* 2.9 9.4 + - - +
177A LEU* 1.3 82.1 - - + +
179A ASP* 1.3 62.6 + - - +
180A LEU 3.1 0.3 + - - -
181A ILE* 3.7 11.0 - - + +
182A TYR* 2.8 32.4 + - - +
227A GLU* 3.1 26.8 + - + +
281A ASP* 5.7 2.2 + - - -
366B ASP* 5.4 9.4 - - - +
367B ILE* 5.6 10.5 - - + +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLY 4.7 0.3 - - - +
175A THR* 4.3 2.7 - - + -
176A THR* 2.6 31.6 + - - +
178A LYS* 1.3 76.7 - - - +
180A LEU* 1.3 56.5 + - - +
182A TYR* 4.4 5.4 - - - -
183A ASP* 2.5 46.8 + - - +
240B ARG* 6.2 0.2 - - - +
243B PHE* 3.2 30.4 - - + -
244B ARG* 3.0 30.6 + - - +
247B GLU* 3.2 13.6 - - - +
357B ARG* 4.4 3.0 + - - +
366B ASP* 4.9 6.5 - - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 4.7 8.3 - - + -
175A THR* 3.9 18.4 - - + -
176A THR 3.1 13.0 + - - +
177A LEU* 3.3 25.8 - - + +
178A LYS 3.1 0.8 - - - -
179A ASP* 1.3 78.3 - - - +
181A ILE* 1.3 65.7 + - - +
183A ASP* 3.2 6.1 + - - +
184A MET* 2.8 21.7 + - - +
193A LEU* 4.1 19.4 - - + +
197A VAL* 4.5 17.0 - - + -
201A ILE* 3.6 34.3 - - + -
224A TRP* 4.3 12.8 - - + -
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 3.1 31.3 + - + +
178A LYS* 3.7 12.6 - - + +
180A LEU* 1.3 80.3 - - + +
182A TYR* 1.3 67.0 + - - +
184A MET* 3.0 22.5 + - + +
185A THR* 2.9 38.7 + - + +
193A LEU* 5.9 2.2 - - + -
263A ILE* 4.7 11.2 - - + -
281A ASP* 4.0 24.5 - - - +
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Residues in contact with TYR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LYS 2.8 22.0 + - - +
179A ASP* 3.8 4.5 - - - +
181A ILE* 1.3 75.0 - - - +
183A ASP* 1.3 79.8 + - - +
184A MET 2.6 12.1 + - - -
185A THR* 3.0 15.0 + - - -
186A THR* 3.1 43.8 + - + +
327B PRO* 4.5 7.1 - - - +
357B ARG* 3.7 42.6 - - + +
359B ASP* 4.1 14.7 + - + +
364B THR* 4.4 18.4 - - - -
365B ILE 4.5 1.3 - - - -
366B ASP* 3.4 48.0 - - + -
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 2.5 34.4 + - - +
180A LEU* 3.5 6.1 - - - +
182A TYR* 1.3 86.7 - - - +
184A MET* 1.3 56.3 + - - +
186A THR* 3.6 4.6 + - - -
187A SER* 2.9 28.6 + - - -
243B PHE* 5.1 1.6 - - - -
247B GLU* 2.7 28.5 - - - +
357B ARG* 4.0 11.3 + - - -
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Residues in contact with MET 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU 2.8 12.0 + - - +
181A ILE* 3.0 23.8 - - + +
182A TYR 2.6 4.6 + - - -
183A ASP* 1.3 71.9 - - - +
185A THR* 1.3 63.9 + - - +
187A SER* 2.6 36.0 + - - +
189A SER 4.2 4.5 - - - +
191A SER 3.3 17.4 - - - +
192A GLY* 4.1 7.2 - - - +
193A LEU* 3.4 47.8 - - + +
255A ARG* 3.1 37.9 + - - +
262A PHE 4.5 14.6 - - - +
263A ILE* 5.1 2.0 - - + +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 2.9 30.5 + - + +
182A TYR* 3.2 9.8 + - - -
184A MET* 1.3 82.2 - - + +
186A THR* 1.3 76.8 + - - +
187A SER 3.1 8.8 + - - +
189A SER 4.8 2.3 - - - +
190A GLY* 5.1 5.0 - - - -
255A ARG* 4.9 17.5 - - + +
362B THR* 4.9 16.7 + - - +
364B THR* 5.0 2.8 + - - -
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.1 44.7 + - + +
183A ASP* 3.6 5.2 + - - -
185A THR* 1.3 89.0 + - - +
187A SER* 1.3 62.3 + - - +
359B ASP* 3.6 41.7 - - + +
362B THR* 4.9 2.0 - - + -
364B THR* 4.9 3.6 - - - +
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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