Contacts of the helix formed by residues 183 - 195 (chain B) in PDB entry 3BUN
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 LYS 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B ILE* 3.5 2.9 - - - +
182B THR* 1.3 88.3 + - + +
184B ALA* 1.3 67.8 + - - +
185B ASP* 3.3 3.1 - - + +
186B ALA* 3.2 17.5 + - + +
187B ALA* 2.8 23.4 + - - +
242B ASP* 4.5 0.8 + - - +
245B THR* 3.8 28.5 + - - +
246B ARG* 4.3 6.1 - - + +
249B GLN* 2.9 44.0 + - + +
250B PRO* 6.0 1.1 - - - -
251B TRP* 5.6 6.5 - - + +
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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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181B ILE 5.4 0.7 - - - -
182B THR 3.6 4.8 + - - -
183B LYS* 1.3 72.3 - - - +
185B ASP* 1.3 66.4 + - - +
187B ALA* 3.1 11.2 + - - +
188B GLU* 3.0 20.7 + - - +
191B ARG* 3.8 8.0 + - - +
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Residues in contact with ASP 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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183B LYS* 3.3 2.7 - - + +
184B ALA* 1.3 74.3 - - - +
186B ALA* 1.3 66.5 + - - +
188B GLU* 3.2 8.8 + - - +
189B PHE* 3.1 21.8 + - - +
250B PRO* 5.9 1.4 - - - +
251B TRP* 3.5 41.9 + - + +
252B SER* 4.7 4.7 + - - -
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Residues in contact with ALA 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* 4.0 4.3 - - + -
183B LYS* 3.2 16.7 + - + +
185B ASP* 1.3 78.8 - - - +
187B ALA* 1.3 63.5 + - - +
189B PHE* 3.2 3.7 + - - +
190B TRP 3.0 18.4 + - - -
241B PHE* 3.4 19.8 - - + -
245B THR* 3.6 34.1 - - - +
251B TRP* 3.8 21.0 - - + -
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Residues in contact with ALA 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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181B ILE* 3.5 32.4 - - + +
183B LYS 2.8 13.2 + - - +
184B ALA* 3.1 15.0 - - - +
186B ALA* 1.3 76.7 - - - +
188B GLU* 1.3 60.6 + - - +
190B TRP* 3.3 4.5 + - - +
191B ARG* 2.9 50.5 + - - +
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Residues in contact with GLU 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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184B ALA 3.0 10.2 + - - +
185B ASP* 3.2 10.5 + - - +
187B ALA* 1.3 72.0 - - - +
189B PHE* 1.3 67.1 + - - +
191B ARG* 3.0 38.3 + - - +
192B LYS* 2.9 40.9 + - - +
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Residues in contact with PHE 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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185B ASP 3.1 7.2 + - - +
186B ALA 3.2 7.4 + - - +
188B GLU* 1.3 79.3 - - - +
190B TRP* 1.3 66.3 + + - +
192B LYS* 4.0 4.6 - - - +
193B ALA* 3.1 26.7 + - + +
194B PHE* 4.3 16.6 - + - -
205B PHE* 4.3 5.2 - + - -
208B ALA* 3.5 29.4 - - + -
209B LEU* 3.7 29.8 - - + -
212B VAL* 3.8 22.0 - - + -
241B PHE* 3.6 29.8 - + - -
251B TRP* 3.5 31.9 - + + +
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Residues in contact with TRP 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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181B ILE* 3.3 25.4 - - + -
186B ALA 3.0 8.7 + - - +
187B ALA 3.7 0.2 - - - +
188B GLU 3.2 0.4 - - - -
189B PHE* 1.3 83.2 - + - +
191B ARG* 1.3 55.9 + - - +
194B PHE* 2.7 67.3 + + + +
195B GLY 3.3 15.8 + - - -
196B GLU* 5.5 0.4 - - - -
197B LYS 3.2 23.6 + - - -
198B THR 4.5 2.5 - - - -
200B VAL* 4.0 18.4 - - + -
205B PHE* 4.0 8.3 - + - -
236B ILE* 3.6 23.8 - - + -
237B SER 4.0 0.2 - - - -
238B VAL* 3.8 36.2 - - + +
241B PHE* 3.4 42.2 - + + -
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Residues in contact with ARG 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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184B ALA* 3.8 7.9 + - - +
187B ALA* 2.9 50.0 + - - +
188B GLU* 3.0 43.9 + - - +
190B TRP* 1.3 75.3 - - + +
192B LYS* 1.3 58.5 + - - +
195B GLY* 2.9 39.7 + - - +
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Residues in contact with LYS 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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188B GLU* 2.9 29.9 + - - +
189B PHE* 4.1 4.5 - - - +
191B ARG* 1.3 77.6 - - - +
193B ALA* 1.3 61.5 + - + +
195B GLY 4.7 0.4 + - - -
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Residues in contact with ALA 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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189B PHE* 3.1 23.7 + - + +
192B LYS* 1.3 81.1 - - + +
194B PHE* 1.3 78.2 + - + +
195B GLY 3.8 0.2 - - - -
208B ALA* 4.1 25.8 - - + -
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Residues in contact with PHE 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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189B PHE* 4.3 7.2 - + - -
190B TRP* 2.7 66.2 + + + +
193B ALA* 1.3 89.5 - - + +
195B GLY* 1.3 62.0 + - - +
196B GLU 3.1 0.5 + - - -
197B LYS* 2.9 35.8 + - + +
200B VAL* 3.8 23.6 - - + -
204B SER* 3.8 22.9 - - - -
205B PHE* 3.9 26.2 - + - -
208B ALA* 3.5 25.6 - - + -
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Residues in contact with GLY 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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190B TRP* 3.3 11.9 + - - -
191B ARG* 2.9 41.7 + - - +
193B ALA 3.8 1.0 - - - -
194B PHE* 1.3 74.1 - - - +
196B GLU* 1.3 66.1 + - - +
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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