Contacts of the helix formed by residues 159 - 172 (chain B) in PDB entry 1AOX
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 TRP 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B CYS* 4.3 5.8 - - - -
151B ASP 3.7 21.1 - - - -
152B GLU* 4.0 13.5 - - + -
156B ILE* 4.1 9.0 - - + -
157B TYR* 4.2 2.2 - - - +
158B PRO* 1.3 74.3 - - - +
160B ASP* 1.3 61.0 + - - +
162B VAL* 2.8 56.8 + - + +
163B LYS* 3.1 22.1 + - + +
166B LEU* 5.3 2.2 - - + -
186B GLN* 3.4 38.4 - - - -
213B THR* 3.2 41.6 + - + +
214B SER* 3.7 1.5 - - - +
215B GLN* 3.7 44.6 + - + +
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Residues in contact with ASP 160 (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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158B PRO* 3.1 10.2 - - + +
159B TRP* 1.3 79.9 + - - +
161B ALA* 1.3 56.0 + - - +
163B LYS* 3.3 29.8 + - - +
164B ASN* 2.8 46.9 + - - +
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Residues in contact with ALA 161 (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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158B PRO* 3.1 24.7 + - + +
159B TRP 2.9 0.8 + - - -
160B ASP* 1.3 79.4 - - - +
162B VAL* 1.3 56.0 + - - +
164B ASN* 3.8 6.4 + - - +
165B PHE* 3.2 24.1 + - - +
318B GLU* 3.6 41.1 - - + +
319B ALA* 4.2 5.8 - - - +
321B LEU* 4.7 1.1 - - - +
322B LEU* 5.2 3.3 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B CYS* 3.7 30.3 - - - -
156B ILE* 3.6 33.7 - - + -
158B PRO 4.5 1.3 - - - +
159B TRP* 2.8 32.5 + - + +
161B ALA* 1.3 71.7 - - - +
163B LYS* 1.3 61.3 + - - +
165B PHE* 3.1 13.9 + - + +
166B LEU* 2.9 35.2 + - + +
252B VAL* 5.7 1.6 - - + -
318B GLU* 5.0 4.7 - - + -
321B LEU* 4.3 16.6 - - + -
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Residues in contact with LYS 163 (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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159B TRP* 3.1 21.0 + - + +
160B ASP* 3.3 33.1 + - - +
162B VAL* 1.3 76.8 - - - +
164B ASN* 1.3 61.3 + - - +
166B LEU* 3.0 14.7 + - - +
167B GLU* 3.0 34.1 + - - +
210B THR* 3.7 6.4 - - - +
211B SER* 2.8 29.0 + - - +
212B GLN* 4.5 1.6 - - - +
213B THR* 3.1 40.5 + - + -
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Residues in contact with ASN 164 (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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160B ASP* 2.8 37.1 + - - +
161B ALA* 4.2 5.5 - - - +
163B LYS* 1.3 76.0 - - - +
165B PHE* 1.3 65.2 + - - +
167B GLU* 3.6 19.1 - - - +
168B LYS* 3.2 25.5 + - - +
322B LEU* 4.1 19.8 - - + +
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 5.6 1.6 - - + -
150B CYS* 6.1 0.4 - - - -
161B ALA 3.2 15.5 + - - +
162B VAL* 3.1 17.6 + - + +
164B ASN* 1.3 77.6 - - - +
166B LEU* 1.3 76.6 + - + +
168B LYS* 4.8 0.2 - - - -
169B PHE* 3.0 33.6 + + + +
250B VAL* 5.3 1.3 - - + -
252B VAL* 4.1 19.7 - - + -
280B ILE* 3.8 25.4 - - + -
321B LEU* 3.5 51.1 - - + -
322B LEU* 4.7 6.5 - - - +
324B LYS* 4.7 2.0 - - + -
325B ALA* 3.5 30.3 - - + +
328B LEU* 4.1 14.4 - - + -
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Residues in contact with LEU 166 (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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148B VAL* 4.2 29.8 - - + -
150B CYS* 5.3 4.3 - - - -
159B TRP* 5.3 1.3 - - + -
162B VAL* 2.9 27.8 + - + +
163B LYS* 3.0 8.9 + - - +
165B PHE* 1.3 90.3 - - + +
167B GLU* 1.3 65.7 + - - +
169B PHE* 3.2 10.4 + - + +
170B VAL* 3.0 28.1 + - + +
184B LEU* 4.1 28.9 - - + -
186B GLN* 5.2 2.0 - - - +
210B THR* 3.7 17.0 - - + +
213B THR* 4.4 18.6 - - + -
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Residues in contact with GLU 167 (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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163B LYS* 3.0 16.3 + - - +
164B ASN* 3.6 24.1 - - - +
166B LEU* 1.3 72.7 - - - +
168B LYS* 1.3 53.2 + - - +
170B VAL 3.1 2.8 + - - -
171B GLN* 2.8 37.2 + - - +
207B ILE* 3.3 27.6 - - + +
210B THR* 3.0 29.1 - - + +
211B SER* 3.0 36.5 + - - -
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Residues in contact with LYS 168 (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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164B ASN 3.2 14.9 + - - +
165B PHE 3.9 2.7 - - - +
167B GLU* 1.3 77.1 - - - +
169B PHE* 1.3 66.5 + - - +
171B GLN* 3.7 33.9 + - + +
172B GLY* 3.8 5.5 + - - -
322B LEU* 3.9 21.5 - - + -
325B ALA* 3.6 19.4 - - + +
326B GLY* 4.2 20.7 - - - +
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Residues in contact with PHE 169 (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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146B VAL* 4.2 11.0 - - + -
148B VAL* 3.9 28.5 - - + -
165B PHE* 3.0 25.5 + + + +
166B LEU* 3.2 13.6 + - + +
168B LYS* 1.3 75.3 - - - +
170B VAL* 1.3 74.0 + - + +
172B GLY* 3.3 11.6 + - - -
173B LEU* 3.8 31.2 - - + +
182B VAL* 5.2 2.7 - - + -
250B VAL* 4.5 2.9 - - + -
325B ALA* 4.2 11.9 - - + -
328B LEU* 3.8 28.7 - - + -
329B GLY* 4.0 23.5 - - - -
332B ILE* 3.7 26.9 - - + -
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Residues in contact with VAL 170 (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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166B LEU* 3.0 19.9 + - + +
167B GLU* 3.5 3.4 - - - +
169B PHE* 1.3 84.1 - - + +
171B GLN* 1.3 56.6 + - - +
172B GLY 2.9 10.7 + - - -
173B LEU* 3.2 23.7 + - - +
175B ILE* 4.4 4.1 - - + +
182B VAL* 4.7 13.2 - - + -
195B PHE* 5.9 0.4 - - + -
203B LYS* 4.0 9.8 + - + +
206B MET* 3.8 39.0 - - + -
207B ILE* 3.5 25.4 - - + +
210B THR* 4.4 12.1 - - - +
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Residues in contact with GLN 171 (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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167B GLU* 2.8 23.1 + - - +
168B LYS* 3.7 36.0 - - + +
170B VAL* 1.3 71.0 - - - +
172B GLY* 1.3 56.8 + - - +
173B LEU 3.5 0.7 - - - -
203B LYS* 3.2 31.4 + - + +
207B ILE* 3.9 18.1 - - + +
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Residues in contact with GLY 172 (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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168B LYS 3.8 5.3 + - - -
169B PHE 3.3 8.1 + - - -
170B VAL 2.9 2.2 + - - -
171B GLN* 1.3 78.9 - - - +
173B LEU* 1.3 68.3 + - - +
329B GLY* 4.4 11.1 - - - +
330B GLU* 5.4 0.7 - - - -
333B PHE* 4.3 11.4 - - - +
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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