Contacts of the helix formed by residues 171 - 186 (chain A) in PDB entry 4O5A
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 ASP 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ASP* 4.9 0.8 - - - +
170A SER* 1.3 76.2 - - - +
172A ASP* 1.3 62.0 + - - +
173A ALA* 3.6 9.7 + - - +
174A ALA* 3.1 32.5 + - + +
175A ALA* 3.1 20.4 + - - +
326A GLU* 5.0 3.8 - - - +
329A TYR* 4.5 8.8 - - + -
401A GOL 3.3 33.4 + - - +
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP* 4.8 4.4 + - - +
170A SER* 3.8 17.7 + - - -
171A ASP* 1.3 75.3 + - - +
173A ALA* 1.3 57.1 + - - +
175A ALA* 3.7 4.3 - - - +
176A SER* 2.8 33.0 + - - -
202A HIS* 3.5 18.7 - - - +
205A ILE* 4.2 11.8 - - + +
206A ARG* 2.9 52.3 + - + -
209A ALA* 5.3 0.2 - - - -
281A TRP* 3.9 11.6 + - + -
299A ARG* 5.5 6.2 - - - -
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP* 5.7 0.4 + - - -
171A ASP* 3.2 7.7 + - - +
172A ASP* 1.3 78.1 - - - +
174A ALA* 1.3 62.9 + - - +
176A SER* 3.3 3.8 + - - -
177A GLY* 3.1 18.0 + - - -
205A ILE* 4.4 13.4 - - + +
209A ALA* 3.8 25.9 - - + +
213A ILE* 4.3 4.3 - - - +
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Residues in contact with ALA 174 (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 ASP* 3.1 36.2 + - + +
173A ALA* 1.3 75.9 - - - +
175A ALA* 1.3 62.5 + - - +
177A GLY* 3.1 5.3 + - - -
178A THR* 3.0 17.8 + - - -
181A ARG* 4.7 2.3 + - - -
329A TYR* 3.1 22.7 + - + +
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Residues in contact with ALA 175 (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 ASP 3.1 10.2 + - - +
172A ASP* 3.7 9.9 - - - +
174A ALA* 1.3 79.0 - - - +
176A SER* 1.3 63.0 + - - +
178A THR* 3.2 2.8 + - - -
179A MSE 3.1 29.5 + - - +
281A TRP* 4.2 13.2 - - + +
297A LEU* 4.0 28.1 - - + +
329A TYR* 3.5 21.0 + - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP 2.8 21.9 + - - -
173A ALA 3.4 9.6 - - - -
174A ALA 3.2 0.2 - - - -
175A ALA* 1.3 76.2 - - - +
177A GLY* 1.3 59.4 + - - +
179A MSE 3.3 6.0 + - - +
180A ILE* 2.9 36.5 + - - +
206A ARG* 4.4 2.4 + - - -
209A ALA* 3.8 16.5 - - - +
210A PHE* 3.4 36.5 - - - -
213A ILE* 4.5 3.1 - - - -
281A TRP* 3.4 9.2 - - - -
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Residues in contact with GLY 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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173A ALA 3.1 5.8 + - - -
174A ALA* 3.1 8.0 + - - -
176A SER* 1.3 79.6 - - - +
178A THR* 1.3 56.0 + - - +
180A ILE* 4.7 1.1 - - - -
181A ARG* 2.8 53.8 + - - +
213A ILE* 3.5 22.4 - - - +
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Residues in contact with THR 178 (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 ALA 3.0 4.7 + - - -
175A ALA 3.2 8.0 + - - -
177A GLY* 1.3 76.0 - - - +
179A MSE 1.3 61.8 + - - +
181A ARG* 3.5 20.6 + - - +
182A HIS* 3.2 22.3 + - - +
297A LEU* 4.6 2.0 - - + -
329A TYR* 2.6 38.6 + - + -
331A LEU* 3.9 28.9 - - + +
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Residues in contact with MSE 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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175A ALA 3.1 23.8 + - - +
176A SER* 3.8 6.7 - - - +
178A THR* 1.3 75.0 - - - +
180A ILE* 1.3 64.5 + - - +
182A HIS* 3.3 8.8 + - - +
183A LEU* 3.1 26.4 + - - +
210A PHE* 4.3 4.5 - - + -
251A ILE* 3.9 26.5 - - + -
279A ILE* 3.8 31.7 - - + +
281A TRP* 3.5 51.8 - - + +
297A LEU* 3.9 26.7 - - + -
331A LEU* 4.3 8.5 - - + -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER 2.9 24.7 + - - +
177A GLY 4.1 0.4 - - - +
179A MSE 1.3 75.7 - - - +
181A ARG* 1.3 58.3 + - - +
183A LEU* 3.1 9.2 + - - +
184A ALA* 2.8 25.8 + - - +
191A ILE* 4.5 5.6 - - + -
210A PHE* 3.6 48.2 - - + -
213A ILE* 3.7 40.8 - - + -
214A THR* 4.1 9.4 - - + -
217A LEU* 4.2 2.5 - - + -
219A MSE 3.8 29.1 - - + +
251A ILE* 4.9 0.7 - - + -
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Residues in contact with ARG 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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174A ALA 4.7 2.0 + - - -
177A GLY* 2.8 37.7 + - - +
178A THR* 3.5 30.6 + - - +
180A ILE* 1.3 77.4 - - + +
182A HIS* 1.3 57.8 + - - +
184A ALA* 3.2 7.7 + - + +
185A LEU* 2.9 30.8 + - - +
213A ILE* 5.6 4.3 - - + +
217A LEU* 5.0 11.7 - - + -
329A TYR* 5.1 0.4 + - - -
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR 3.2 14.6 + - - +
179A MSE 3.4 8.3 - - - +
180A ILE 3.2 0.2 - - - -
181A ARG* 1.3 75.7 - - - +
183A LEU* 1.3 62.8 + - + +
185A LEU* 3.5 13.7 + - + +
186A PHE* 3.3 45.4 + + - +
279A ILE* 4.1 11.2 - - + -
295A THR* 4.3 2.7 - - + +
331A LEU* 3.6 22.1 - - + +
333A GLU* 3.5 39.5 + - + +
337A THR* 2.8 40.6 + - + -
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A MSE 3.1 12.6 + - - +
180A ILE* 3.6 6.7 - - - +
182A HIS* 1.3 77.3 - - + +
184A ALA* 1.3 63.7 + - - +
186A PHE* 3.1 7.4 + - + -
188A HIS* 3.1 45.1 + - + -
191A ILE* 4.0 17.3 - - + -
219A MSE 4.4 5.6 - - + -
249A ALA* 3.8 31.6 - - + -
251A ILE* 3.9 32.5 - - + -
277A SER* 4.4 1.8 - - - -
279A ILE* 3.7 19.1 - - + -
337A THR* 4.4 14.8 - - + -
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Residues in contact with ALA 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 ILE 2.8 16.1 + - - +
181A ARG* 3.6 9.2 - - - +
183A LEU* 1.3 76.3 - - - +
185A LEU* 1.3 59.0 + - - +
187A GLY* 2.8 20.6 + - - -
188A HIS 4.3 10.3 - - - -
217A LEU* 4.3 14.1 - - + -
219A MSE 4.1 16.5 - - + +
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Residues in contact with LEU 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 ARG 2.9 17.2 + - - +
182A HIS* 3.6 14.6 - - - +
184A ALA* 1.3 76.5 - - - +
186A PHE* 1.3 71.7 + - + +
187A GLY 3.1 2.3 + - - -
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Residues in contact with PHE 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 HIS* 3.3 46.4 + + - +
183A LEU* 3.1 10.0 + - - +
184A ALA 3.1 1.0 - - - -
185A LEU* 1.3 92.2 - - + +
187A GLY* 1.3 57.5 + - - +
188A HIS* 3.4 7.7 + + + -
333A GLU* 4.9 4.9 - - - -
337A THR* 3.8 9.0 - - - -
338A ALA* 3.6 39.5 - - - +
339A PRO* 3.2 28.0 - - + +
340A ALA 2.8 29.6 + - - -
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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