Contacts of the helix formed by residues 178 - 194 (chain B) in PDB entry 2B9R
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 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B TYR* 4.4 9.4 + - - -
15B ARG* 4.8 3.1 - - - +
18B GLU* 3.0 18.1 + - - +
138B PRO* 5.0 0.2 - - - +
141B PHE* 3.0 55.1 - - - +
177B PRO* 1.3 76.0 - - - +
179B GLN* 1.3 53.6 + - - -
180B ILE 3.3 1.4 - - - +
181B ALA* 3.6 5.9 - - - +
182B ALA* 2.7 36.9 + - - +
207B TYR* 3.3 18.6 - - - -
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Residues in contact with GLN 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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175B PHE* 3.5 23.6 - - + -
176B PRO* 3.2 30.6 - - + +
177B PRO 2.9 2.4 + - - -
178B SER* 1.3 78.3 - - - +
180B ILE* 1.3 69.0 + - - +
182B ALA* 3.8 1.5 - - - +
183B GLY* 2.9 20.4 + - - -
207B TYR* 3.4 34.6 - - + +
211B SER* 3.1 27.3 + - - -
212B LEU* 3.8 6.8 - - + +
214B PRO* 5.4 0.8 - - - +
215B VAL* 3.7 19.3 - - + +
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Residues in contact with ILE 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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138B PRO* 5.2 8.3 - - + -
163B MET* 3.7 17.9 - - + -
166B THR* 3.7 31.6 - - + +
172B MET* 3.8 29.2 - - + +
175B PHE* 3.4 31.6 - - + +
176B PRO 3.2 17.6 + - - +
177B PRO* 4.4 7.0 - - + -
178B SER 3.3 0.4 - - - -
179B GLN* 1.3 80.4 - - - +
181B ALA* 1.3 57.0 + - - +
183B GLY* 3.6 0.5 - - - -
184B ALA* 2.8 29.2 + - + +
215B VAL* 4.4 5.1 - - + +
219B LEU* 5.2 0.8 - - + +
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Residues in contact with ALA 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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138B PRO* 4.2 6.9 - - + +
141B PHE* 3.8 26.7 - - + +
142B LEU* 3.9 21.4 - - + +
145B ALA* 5.9 1.8 - - + -
163B MET* 4.2 13.6 - - - -
177B PRO* 5.1 0.2 - - - +
178B SER* 3.5 11.7 + - - +
180B ILE* 1.3 76.5 - - - +
182B ALA* 1.3 69.2 + - - +
183B GLY 2.8 0.7 + - - -
184B ALA* 3.0 1.8 + - - +
185B PHE* 2.8 27.9 + - - +
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Residues in contact with ALA 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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145B ALA* 5.9 1.1 - - - -
178B SER 2.7 22.8 + - - +
179B GLN 3.8 0.4 - - - +
181B ALA* 1.3 71.1 - - - +
183B GLY* 1.3 57.5 + - - +
185B PHE* 3.5 2.6 - - - +
186B SER* 2.9 29.3 + - - -
197B TRP* 3.5 26.0 - - + -
205B LEU* 5.1 8.1 - - + -
207B TYR* 3.8 16.6 - - + -
212B LEU* 3.3 22.9 - - + -
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Residues in contact with GLY 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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179B GLN 2.9 15.2 + - - -
180B ILE 3.6 2.5 - - - -
181B ALA 2.8 3.6 + - - -
182B ALA* 1.3 70.4 - - - +
184B ALA* 1.3 65.8 + - - +
185B PHE 3.1 0.9 - - - -
186B SER* 2.8 17.6 + - - -
187B LEU* 2.8 15.1 + - - +
212B LEU* 3.6 11.8 - - - +
215B VAL* 3.7 14.8 - - - -
216B MET* 3.9 3.2 - - - +
219B LEU* 3.9 7.0 - - - -
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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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142B LEU* 4.9 0.4 - - + -
159B ALA* 4.0 11.4 - - + +
162B LEU* 3.7 7.6 - - + +
163B MET* 3.9 38.8 - - + +
180B ILE* 2.8 20.8 + - + +
181B ALA* 3.6 3.1 - - - +
183B GLY* 1.3 70.5 - - - +
185B PHE* 1.3 64.9 + - - +
187B LEU* 3.3 0.5 + - - -
188B ALA* 2.9 23.7 + - - +
219B LEU* 3.6 18.1 - - + +
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Residues in contact with PHE 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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142B LEU* 4.3 12.8 - - + +
145B ALA* 3.8 38.4 - - + -
146B SER* 4.3 10.8 - - - -
149B GLY 4.6 10.3 - - - -
150B GLU* 6.4 0.2 - - + -
155B GLN* 3.2 27.1 + - + -
156B HIS* 5.8 2.7 - - - -
159B ALA* 4.2 13.8 - - + +
181B ALA 2.8 21.3 + - - +
182B ALA* 3.5 4.9 - - - +
184B ALA* 1.3 74.0 - - - +
186B SER* 1.3 51.4 + - - +
189B LEU* 2.8 52.6 + - + +
197B TRP* 3.3 20.2 - + + -
201B LEU* 3.8 28.9 - - + -
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Residues in contact with SER 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 ALA 2.9 18.2 + - - -
183B GLY* 2.8 13.1 + - - -
185B PHE* 1.3 71.9 - - - +
187B LEU* 1.3 56.3 + - - -
189B LEU* 3.1 8.3 - - - +
190B LYS* 2.9 28.6 + - - +
197B TRP* 3.6 35.0 + - - +
209B GLU* 6.0 0.3 - - - -
212B LEU* 4.1 8.7 - - - +
216B MET* 3.2 21.6 - - - +
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Residues in contact with LEU 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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162B LEU* 4.1 20.2 - - + -
183B GLY 2.8 14.0 + - - +
184B ALA 3.8 2.0 - - - +
186B SER* 1.3 69.6 - - - +
188B ALA* 1.3 54.4 + - - +
189B LEU 3.0 1.3 - - - -
190B LYS* 2.7 24.6 + - + +
191B ILE* 2.8 42.3 + - + +
216B MET* 3.5 37.6 - - + +
219B LEU* 4.0 27.1 - - + -
220B ALA* 4.3 20.4 - - + +
223B VAL* 4.8 1.6 - - + -
257B ALA* 5.7 4.3 - - - +
258B LEU* 5.2 9.4 - - + -
260B GLN* 5.4 4.9 - - - +
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Residues in contact with ALA 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 GLN* 2.8 29.9 - - - +
158B LEU* 3.7 19.7 - - + -
159B ALA* 3.9 13.9 - - + +
162B LEU* 3.5 20.6 - - + +
184B ALA 2.9 17.2 + - - +
187B LEU* 1.3 76.3 - - - +
189B LEU* 1.3 59.4 + - - +
191B ILE* 3.4 1.4 + - - +
192B LEU* 3.3 22.0 + - - +
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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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150B GLU* 6.5 0.9 - - + -
155B GLN* 2.9 23.9 - - + +
185B PHE* 2.8 27.4 + - + +
186B SER 3.1 13.7 - - - +
188B ALA* 1.3 78.2 - - - +
190B LYS* 1.3 54.2 + - - -
193B ASP* 2.6 54.9 + - - +
195B GLY 3.6 9.2 - - - +
196B GLU 3.5 28.3 - - - +
197B TRP* 4.4 4.9 - - + +
201B LEU* 3.8 22.9 - - + -
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Residues in contact with LYS 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 SER* 2.9 16.4 + - - +
187B LEU* 2.7 17.9 + - + +
189B LEU* 1.3 73.9 - - - +
191B ILE* 1.3 63.5 + - - +
194B ASN* 3.4 16.2 + - - +
195B GLY 4.2 12.8 - - - +
196B GLU* 5.8 5.4 - - - +
197B TRP 6.1 0.7 - - - +
216B MET* 3.7 21.0 - - + +
258B LEU* 4.5 25.9 - - + +
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Residues in contact with ILE 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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158B LEU* 3.9 21.1 - - + -
162B LEU* 4.6 4.0 - - + -
187B LEU* 2.8 51.4 + - + +
188B ALA* 3.8 4.3 - - - +
189B LEU 3.4 0.4 - - - -
190B LYS* 1.3 75.3 - - + +
192B LEU* 1.3 66.7 + - + +
194B ASN 5.0 0.5 + - - -
223B VAL* 6.0 1.8 - - + -
251B LEU* 5.3 2.2 - - + -
253B GLN* 3.4 23.8 - - + +
255B ASN* 3.5 34.5 - - + +
257B ALA* 5.7 6.5 - - + -
258B LEU* 5.2 12.3 - - + -
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Residues in contact with LEU 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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154B GLU* 3.9 25.8 - - + +
155B GLN* 3.3 43.3 - - + +
158B LEU* 3.3 30.5 - - + -
188B ALA 3.3 3.6 + - - +
191B ILE* 1.3 79.2 - - + +
193B ASP* 1.3 69.0 + - - +
194B ASN 3.3 1.9 + - - -
251B LEU* 3.7 24.5 - - + -
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Residues in contact with ASP 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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150B GLU* 5.9 3.3 - - - +
155B GLN* 5.2 1.1 - - - +
189B LEU* 2.6 42.4 + - + +
192B LEU* 1.3 81.7 - - - +
194B ASN* 1.3 59.0 + - - +
195B GLY* 2.9 26.1 - - - +
196B GLU 5.3 0.3 - - - +
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Residues in contact with ASN 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 LYS* 3.4 16.4 + - - -
192B LEU 3.3 3.0 - - - -
193B ASP* 1.3 78.5 - - - +
195B GLY* 1.3 56.0 + - - +
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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