Contacts of the helix formed by residues 177 - 187 (chain B) in PDB entry 2AOT
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 SER 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B VAL* 3.9 2.1 - - - +
174B SER 2.8 20.2 + - - -
176B SER* 1.3 84.0 + - - +
178B GLY* 1.3 64.0 + - - +
179B TRP* 3.1 28.3 + - - +
180B ASP* 3.2 9.9 + - - +
181B LYS* 3.4 14.1 - - - +
270B GLU 4.6 0.9 - - - -
282B ASN* 3.5 21.8 - - - -
284B THR* 3.6 22.7 - - - -
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Residues in contact with GLY 178 (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 SER* 1.3 72.2 - - - +
179B TRP* 1.3 53.4 + - - +
181B LYS* 3.1 4.5 + - - +
182B LEU* 2.7 35.9 + - - +
270B GLU 4.0 10.1 - - - -
271B PHE* 4.0 12.4 - - - -
281B PHE* 3.2 27.7 - - - -
282B ASN* 2.9 16.4 + - - +
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Residues in contact with TRP 179 (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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22B PHE* 4.5 2.0 - + - -
173B VAL* 3.5 25.4 - - + +
177B SER* 3.1 13.4 - - - +
178B GLY* 1.3 76.7 - - - +
180B ASP* 1.3 55.8 + - - +
182B LEU* 3.6 8.9 - - + +
183B TRP* 2.8 73.9 + + + -
224B MET* 4.3 10.8 - - - -
243B PHE* 3.7 28.9 - + - -
244B LEU* 3.9 34.8 - - + -
281B PHE* 3.5 17.1 - + - -
282B ASN 4.0 7.9 - - - -
283B ASN* 2.7 27.4 + - - -
401B 2PM 3.5 30.5 - - - -
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Residues in contact with ASP 180 (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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174B SER 4.0 5.2 - - - +
175B GLY* 3.0 35.7 - - - +
177B SER* 3.2 10.0 + - - +
179B TRP* 1.3 78.6 - - - +
181B LYS* 1.3 79.2 + - - +
183B TRP* 4.1 1.9 - - - +
184B LYS* 3.0 68.7 + - - +
200B THR* 4.0 21.5 + - + +
202B ASP* 5.2 1.4 - - - +
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Residues in contact with LYS 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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175B GLY 2.9 28.3 + - - -
176B SER* 3.6 14.5 + - - +
177B SER 3.4 11.0 - - - +
178B GLY 3.1 6.0 + - - +
180B ASP* 1.3 81.5 + - - +
182B LEU* 1.3 66.0 + - - +
184B LYS* 4.1 4.6 - - - +
185B LYS* 3.1 28.8 + - - +
270B GLU* 3.8 34.5 - - + +
271B PHE* 3.5 26.8 - - + -
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Residues in contact with LEU 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 GLY 2.7 20.8 + - - +
179B TRP* 3.6 24.0 - - + +
181B LYS* 1.3 73.2 - - - +
183B TRP* 1.3 62.1 + - + +
186B TYR* 2.8 34.5 + - + +
187B GLY 3.6 0.2 + - - -
190B PHE* 3.9 18.6 - - + -
244B LEU* 3.3 37.9 - - + +
245B THR* 5.9 0.4 - - + +
262B LEU* 3.9 28.9 - - + -
266B LEU* 4.8 11.2 - - + -
271B PHE* 3.7 14.3 - - + -
281B PHE* 4.6 6.5 - - + -
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Residues in contact with TRP 183 (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 TYR* 4.2 2.7 - + - -
173B VAL* 3.7 24.7 - - + -
179B TRP* 2.8 46.8 + + + +
180B ASP* 4.2 1.6 - - - +
182B LEU* 1.3 84.8 - - + +
184B LYS* 1.3 63.1 + - + +
187B GLY* 2.7 29.8 + - - +
190B PHE* 4.9 5.6 - + - -
198B TYR* 3.3 54.1 - + + -
199B ILE 3.4 28.3 - - - -
200B THR* 3.9 15.0 - - + -
244B LEU 4.9 2.8 + - - -
246B GLU* 6.3 0.4 - - - +
401B 2PM 3.5 46.6 - + - -
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Residues in contact with LYS 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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175B GLY 5.2 0.6 + - - -
180B ASP* 3.0 50.7 + - - +
181B LYS* 4.1 4.2 - - - +
183B TRP* 1.3 78.4 - - + +
185B LYS* 1.3 60.0 + - + +
187B GLY 4.9 0.2 + - - -
202B ASP* 5.2 11.3 + - - -
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Residues in contact with LYS 185 (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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181B LYS 3.1 17.2 + - - +
184B LYS* 1.3 79.6 - - + +
186B TYR* 1.3 82.5 + - + +
187B GLY 3.8 0.4 - - - -
188B SER* 5.5 1.4 + - - -
189B ARG* 3.0 25.6 + - - +
261B GLU* 4.1 10.3 - - - +
264B LYS* 6.2 0.6 - - - +
265B ASP* 3.0 33.7 + - - +
271B PHE* 4.8 5.2 - - + -
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Residues in contact with TYR 186 (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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182B LEU* 2.8 26.1 + - + +
185B LYS* 1.3 98.6 - - + +
187B GLY* 1.3 67.2 + - - +
188B SER* 3.3 2.9 - - - -
189B ARG* 3.0 50.2 + - - +
190B PHE* 3.4 31.5 + - + -
258B LEU* 3.8 11.0 - - + -
261B GLU* 3.3 28.2 + - + +
262B LEU* 3.3 35.7 - - + -
265B ASP* 2.4 35.7 + - + -
271B PHE* 4.5 7.6 - + - -
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Residues in contact with GLY 187 (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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182B LEU 3.6 0.6 + - - -
183B TRP* 2.7 30.3 + - - -
184B LYS 4.7 0.4 + - - -
185B LYS 3.8 0.8 - - - -
186B TYR* 1.3 73.2 - - - +
188B SER* 1.3 58.9 + - - +
190B PHE* 3.4 13.1 + - - +
198B TYR* 3.3 41.9 + - - -
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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