Contacts of the helix formed by residues 185 - 200 (chain B) in PDB entry 3UNE
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 THR 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ALA* 3.7 3.6 - - - -
40B ASN* 4.5 2.9 - - - +
41B ASP* 3.1 18.2 + - - -
183B GLU 3.5 5.7 + - - +
184B MET* 1.3 74.2 - - - +
186B LEU* 1.3 63.9 + - - +
187B LYS* 3.8 12.6 + - + +
188B SER* 2.9 28.3 + - - +
189B ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.7 5.1 - - + +
41B ASP* 2.8 26.7 + - - +
42B GLY* 3.8 6.1 - - - +
43B VAL* 3.7 30.1 - - - +
44B LEU* 3.9 24.7 - - + -
185B THR* 1.3 76.4 + - - +
187B LYS* 1.3 60.2 + - - +
189B ALA* 3.7 2.1 - - - +
190B LEU* 3.2 34.9 + - + +
215B THR* 4.7 13.7 - - + -
217B THR* 3.6 25.1 - - + +
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 3.2 12.8 + - + +
186B LEU* 1.3 80.5 - - - +
188B SER* 1.3 58.7 + - - +
189B ALA 3.7 0.2 + - - -
190B LEU* 3.9 8.1 + - - +
191B ALA* 3.7 17.0 + - - +
236B LEU* 5.3 2.1 - - - +
239B LYS* 5.5 12.4 - - - +
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B MET* 3.2 20.3 - - - +
185B THR* 2.9 38.7 + - - +
187B LYS* 1.3 77.1 - - - +
189B ALA* 1.3 59.0 + - - +
190B LEU 3.4 0.2 - - - -
191B ALA* 3.6 8.6 + - - +
192B LEU* 3.2 28.1 + - - +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.2 31.1 - - + +
38B LEU 5.2 2.5 - - - +
39B ALA* 4.3 8.7 - - + -
44B LEU* 3.7 17.3 - - + -
179B TYR* 6.4 0.2 - - + -
184B MET* 5.1 7.2 - - + -
185B THR 2.9 17.9 + - - +
186B LEU* 3.7 8.5 - - - +
187B LYS 3.3 0.2 - - - -
188B SER* 1.3 77.3 + - - +
190B LEU* 1.3 59.7 + - - +
192B LEU* 3.2 3.1 + - - -
193B ALA* 3.0 24.9 + - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.1 13.2 - - + -
186B LEU* 3.2 30.7 + - + +
187B LYS* 4.2 7.0 - - - +
188B SER 3.4 0.2 - - - -
189B ALA* 1.3 76.1 - - - +
191B ALA* 1.3 60.8 + - - +
193B ALA* 3.6 6.5 + - + +
194B VAL* 3.3 28.6 + - - +
213B ILE* 3.8 31.3 - - + +
215B THR* 4.1 22.0 - - + -
228B LEU* 4.1 13.5 - - + -
236B LEU* 3.8 29.0 - - + +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS 3.7 11.2 + - - +
188B SER* 3.6 11.4 + - - +
189B ALA 3.3 0.4 - - - -
190B LEU* 1.3 77.2 - - - +
192B LEU* 1.3 60.7 + - - +
194B VAL* 3.8 4.4 + - - +
195B LYS* 3.3 21.3 + - - +
236B LEU* 4.1 11.6 - - + +
239B LYS* 5.5 11.4 - - + +
240B HIS* 4.7 7.0 - - - +
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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
----------------------------------------------------------
37B ILE* 4.4 6.5 - - + -
174B MET 5.1 0.2 - - - +
175B LEU* 3.8 32.5 - - + +
178B ASP* 3.8 38.6 - - + +
179B TYR* 4.1 12.1 - - + +
184B MET* 3.8 32.5 - - + -
188B SER 3.2 11.1 + - - +
189B ALA* 3.2 10.3 + - - +
191B ALA* 1.3 76.7 - - - +
193B ALA* 1.3 63.6 + - - +
195B LYS* 3.3 9.3 + - + +
196B VAL* 3.2 35.3 + - + +
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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
----------------------------------------------------------
35B LEU* 3.9 25.3 - - + +
37B ILE* 4.5 4.2 - - + +
44B LEU* 4.3 17.5 - - + -
46B ALA* 4.3 8.5 - - + -
175B LEU* 5.8 0.4 - - - -
189B ALA 3.0 16.2 + - - +
190B LEU* 3.9 8.3 - - + +
191B ALA 3.4 0.4 - - - -
192B LEU* 1.3 77.0 - - - +
194B VAL* 1.3 61.3 + - + +
196B VAL* 3.6 3.8 + - - +
197B LEU* 3.2 30.7 + - - +
213B ILE* 6.0 3.4 - - + -
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU 3.3 16.9 + - - +
191B ALA* 4.1 5.4 - - - +
192B LEU 3.3 0.4 - - - -
193B ALA* 1.3 74.4 - - + +
195B LYS* 1.3 64.5 + - - +
197B LEU* 3.9 7.2 - - + +
198B ASN* 3.0 25.2 + - + +
206B LEU* 3.8 23.1 - - + +
213B ILE* 4.6 17.5 - - + -
233B VAL* 6.1 0.2 - - + -
236B LEU* 4.0 38.1 - - + +
237B ILE* 4.2 9.2 - - + +
240B HIS* 4.1 17.0 - - + +
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Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B MET* 4.3 7.0 - - + +
178B ASP* 2.9 30.9 + - - +
191B ALA 3.3 13.4 + - - +
192B LEU* 3.3 14.3 + - + +
194B VAL* 1.3 80.6 - - - +
196B VAL* 1.3 63.4 + - + +
198B ASN* 3.8 2.6 + - - +
199B LYS* 3.6 19.8 + - - +
240B HIS* 3.4 33.1 + - + +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.8 21.8 - - + -
171B ALA* 3.8 33.4 - - + +
174B MET* 3.9 24.9 - - + +
175B LEU* 3.8 24.2 - - + +
178B ASP* 6.4 0.4 - - - -
192B LEU* 3.2 25.2 + - + +
193B ALA* 4.1 3.8 - - - +
195B LYS* 1.3 77.9 - - + +
197B LEU* 1.3 56.7 + - - +
199B LYS* 3.3 2.3 + - - +
200B THR* 2.7 38.2 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 4.3 30.7 - - + +
35B LEU* 3.9 21.1 - - + -
46B ALA* 3.8 29.2 - - + +
47B ALA 4.9 0.9 - - - +
48B GLU* 4.9 9.2 - - + +
193B ALA 3.2 21.6 + - - +
194B VAL* 3.5 6.9 + - + +
196B VAL* 1.3 79.2 - - - +
198B ASN* 1.3 61.8 + - - +
199B LYS 3.6 0.2 + - - -
200B THR* 3.9 7.3 - - - +
201B MET* 3.3 30.2 - - - +
206B LEU* 4.5 11.4 - - + -
211B VAL* 4.2 21.5 - - + -
213B ILE* 5.4 5.8 - - + -
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Residues in contact with ASN 198 (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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194B VAL 3.0 18.5 + - - +
195B LYS 4.1 4.7 - - - +
196B VAL 3.3 0.2 - - - -
197B LEU* 1.3 78.2 - - - +
199B LYS* 1.3 69.6 + - - +
201B MET* 4.3 7.9 - - - +
204B SER* 4.3 15.9 - - - -
205B LYS* 3.8 16.6 + - - +
206B LEU* 3.5 34.7 - - + +
240B HIS* 3.8 26.2 + - + +
241B GLU* 5.7 5.3 + - - -
244B GLU* 4.8 6.1 + - - -
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Residues in contact with LYS 199 (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 MET* 3.8 29.2 - - + -
195B LYS 3.6 12.2 + - - +
196B VAL 3.3 1.4 + - - -
198B ASN* 1.3 89.1 - - + +
200B THR* 1.3 59.8 + - - +
201B MET 3.2 9.5 + - - +
244B GLU* 6.1 1.6 - - - -
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 3.9 24.1 + - - +
35B LEU* 5.5 0.2 - - - +
167B ASN* 4.1 24.3 + - + +
170B ALA* 4.2 11.0 - - + -
171B ALA* 4.0 30.7 - - - +
174B MET* 3.9 23.3 - - + -
196B VAL* 2.7 30.1 + - - +
197B LEU* 3.9 6.0 - - - +
199B LYS* 1.3 73.1 - - - +
201B MET* 1.3 60.1 + - - +
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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
------------------------------------------------------------
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