Contacts of the helix formed by residues 181 - 196 (chain B) in PDB entry 2BEX
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 ILE 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B LEU* 4.0 14.1 - - + +
154B SER 3.8 10.8 - - - +
155B ALA* 3.3 17.3 - - - +
158B CYS* 3.6 24.5 - - - -
176B VAL* 4.5 9.2 - - + -
179B ASN* 2.9 24.5 + - + +
180B ASP* 1.3 72.3 - - - +
182B ASN* 1.3 71.5 + - - +
184B ALA* 5.0 0.2 - - - +
185B GLY* 3.0 19.2 + - - -
186B VAL* 3.9 22.7 - - + +
189B LEU* 4.0 24.0 - - + -
205B LEU* 4.4 7.2 - - + -
208B CYS* 3.5 26.9 - - + +
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Residues in contact with ASN 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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180B ASP* 3.3 33.2 + - - +
181B ILE* 1.3 79.2 - - - +
183B GLU* 1.3 69.9 + - - +
184B ALA 3.4 1.8 - - - +
186B VAL* 2.8 26.7 + - - +
208B CYS 2.9 19.0 + - - +
209B GLY* 3.6 18.0 - - - +
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Residues in contact with GLU 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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182B ASN* 1.3 77.8 - - - +
184B ALA* 1.3 58.7 + - - +
187B ARG* 2.9 45.9 + - - +
209B GLY 3.5 5.2 + - - -
211B THR* 2.7 37.9 + - + +
213B ASP* 3.7 16.2 - - - +
214B ASN* 3.1 28.8 + - - +
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Residues in contact with ALA 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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155B ALA* 4.3 13.2 - - + -
181B ILE 5.0 0.2 - - - +
182B ASN* 3.4 1.4 - - + +
183B GLU* 1.3 80.6 - - - +
185B GLY* 1.3 63.2 + - - +
187B ARG* 3.4 9.6 + - - +
188B VAL* 3.1 30.5 + - + +
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA* 3.5 13.5 - - - +
158B CYS* 3.6 29.9 - - - +
181B ILE* 3.0 23.3 + - - -
184B ALA* 1.3 75.2 - - - +
186B VAL* 1.3 64.4 + - - +
188B VAL* 3.3 1.8 + - - -
189B LEU* 3.1 19.9 + - - +
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Residues in contact with VAL 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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181B ILE* 3.9 24.4 + - + +
182B ASN 2.8 26.8 + - - +
185B GLY* 1.3 72.0 - - - -
187B ARG* 1.3 63.9 + - - +
189B LEU* 3.3 4.9 + - - +
190B CYS* 2.9 39.0 + - - -
205B LEU* 4.5 12.3 - - + -
208B CYS* 4.3 1.6 - - + +
210B VAL* 3.8 31.0 - - + -
214B ASN* 3.6 30.7 - - + +
218B LEU* 5.1 2.0 - - + -
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Residues in contact with ARG 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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183B GLU* 2.9 36.2 + - - +
184B ALA* 3.4 11.0 - - - +
186B VAL* 1.3 78.0 - - - +
188B VAL* 1.3 66.9 + - + +
190B CYS* 3.4 2.8 + - - +
191B GLN* 3.0 41.6 + - + +
213B ASP* 4.0 11.3 + - - -
214B ASN* 3.7 10.0 - - - +
216B ARG* 3.3 25.7 - - - +
217B ASP* 4.1 17.5 - - - +
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Residues in contact with VAL 188 (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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155B ALA 5.8 1.6 - - - +
158B CYS* 3.8 7.6 - - + +
159B GLU* 3.0 54.7 - - + +
162B ALA* 3.6 6.3 - - + +
166B ARG* 5.0 0.4 + - - +
184B ALA* 3.1 18.6 + - + +
185B GLY* 3.8 4.3 - - - +
187B ARG* 1.3 78.5 - - + +
189B LEU* 1.3 66.5 + - - +
191B GLN* 3.2 10.9 + - + +
192B GLY 3.1 17.0 + - - -
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Residues in contact with LEU 189 (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 CYS* 3.4 32.3 - - + +
161B LEU* 3.8 27.8 - - + -
162B ALA* 4.1 5.8 - - - +
165B LEU* 4.3 10.4 - - + +
174B LEU* 4.7 4.5 - - + -
176B VAL* 4.1 23.3 - - + -
181B ILE* 4.0 25.6 - - + -
185B GLY 3.1 17.2 + - - +
186B VAL* 3.3 5.4 + - - +
188B VAL* 1.3 75.6 - - - +
190B CYS* 1.3 61.5 + - - +
192B GLY* 3.2 2.8 + - - -
193B LEU* 2.9 36.4 + - + +
205B LEU* 4.6 10.1 - - + -
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Residues in contact with CYS 190 (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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186B VAL* 2.9 33.1 + - - +
187B ARG 3.7 2.5 - - - +
189B LEU* 1.3 74.7 - - - +
191B GLN* 1.3 60.5 + - - +
193B LEU* 3.3 2.2 + - - +
194B LYS* 2.8 36.8 + - + +
203B LEU* 5.5 0.4 - - - -
205B LEU* 5.1 4.5 - - - -
217B ASP* 3.6 28.3 - - + -
218B LEU* 3.8 24.9 - - - -
221B ILE* 3.7 27.8 - - + +
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Residues in contact with GLN 191 (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 ARG* 3.8 10.3 - - - +
187B ARG* 3.0 34.0 + - + +
188B VAL* 3.2 10.1 + - + +
190B CYS* 1.3 75.8 - - - +
192B GLY* 1.3 59.0 + - - +
194B LYS* 3.3 21.4 + - - +
195B ASP* 2.9 38.7 + - - +
217B ASP* 3.0 36.1 + - - -
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Residues in contact with GLY 192 (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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162B ALA* 3.8 21.5 - - - -
165B LEU* 4.3 6.3 - - - -
166B ARG* 3.5 22.1 + - - +
188B VAL 3.1 10.1 + - - -
189B LEU 3.2 3.8 + - - -
191B GLN* 1.3 78.4 - - - +
193B LEU* 1.3 55.6 + - - +
196B SER* 2.9 31.1 + - - -
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Residues in contact with LEU 193 (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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165B LEU* 3.5 33.8 - - + +
171B PHE* 5.3 0.2 - - + -
174B LEU* 4.6 5.6 - - + -
189B LEU* 2.9 24.1 + - + +
190B CYS* 3.8 4.9 - - - +
192B GLY* 1.3 74.2 - - - +
194B LYS* 1.3 64.3 + - - +
196B SER* 3.4 7.5 + - - +
198B CYS* 4.4 13.5 - - - -
200B LEU* 4.1 24.7 - - + -
203B LEU* 3.8 40.2 - - + -
205B LEU* 6.1 0.7 - - + -
221B ILE* 4.0 16.6 - - + -
225B LYS* 3.1 27.3 + - - -
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Residues in contact with LYS 194 (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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190B CYS 2.8 26.2 + - - +
191B GLN* 3.3 18.5 + - - +
193B LEU* 1.3 78.2 - - - +
195B ASP* 1.3 65.0 + - - +
196B SER 3.5 4.9 + - - +
217B ASP* 2.8 45.4 + - + +
220B GLY* 4.4 13.0 - - - +
221B ILE* 3.7 22.9 - - + +
224B SER* 4.9 8.5 + - - +
225B LYS* 4.5 6.7 + - - +
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Residues in contact with ASP 195 (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 ARG* 3.1 43.2 + - + +
191B GLN* 2.9 20.4 + - - +
194B LYS* 1.3 78.4 - - - +
196B SER* 1.3 63.8 + - - +
197B PRO* 3.6 5.2 - - - +
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Residues in contact with SER 196 (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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165B LEU 2.7 30.7 + - - -
166B ARG* 4.0 5.1 - - - +
168B LYS 3.7 1.0 + - - -
192B GLY 2.9 18.6 + - - -
193B LEU* 3.5 6.9 - - - +
194B LYS 3.3 3.0 - - - +
195B ASP* 1.3 79.1 - - - +
197B PRO* 1.3 64.1 - - - +
198B CYS* 3.0 29.4 + - - +
225B LYS* 2.7 24.1 + - - -
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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