Contacts of the helix formed by residues 194 - 209 (chain B) in PDB entry 2BKU
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 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLU* 2.9 47.9 + - - +
152B LYS* 5.8 1.0 - - - +
193B THR* 1.3 79.3 + - - +
195B LYS* 1.3 66.4 + - - +
196B ALA* 3.2 10.7 + - - +
197B VAL* 3.7 9.2 + - - +
198B ARG* 3.0 20.3 + - - +
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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
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193B THR 3.6 2.2 + - - -
194B SER* 1.3 72.7 + - - +
196B ALA* 1.3 58.7 + - - +
198B ARG* 3.3 7.7 + - - +
199B LEU* 2.8 37.6 + - + +
237B ASP* 3.2 41.8 + - - +
238B ILE* 5.9 0.8 - - - +
239B GLU* 2.4 41.9 + - - +
240B VAL* 4.2 9.4 - - + +
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 4.1 11.2 - - - +
153B ARG* 3.8 22.4 - - - +
194B SER* 3.2 9.6 + - - +
195B LYS* 1.3 81.4 - - - +
197B VAL* 1.3 56.9 + - - +
199B LEU* 3.6 8.9 - - - +
200B ALA* 2.8 29.5 + - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 3.3 48.0 - - + +
152B LYS* 4.1 23.8 - - + -
153B ARG* 4.2 6.7 - - + +
156B LEU* 3.7 20.1 - - + +
187B GLY* 4.1 13.0 - - - +
193B THR* 4.3 7.4 - - + +
194B SER* 3.2 14.4 + - - +
196B ALA* 1.3 74.7 - - - +
198B ARG* 1.3 60.1 + - - +
200B ALA* 3.2 6.6 + - - +
201B ALA* 2.9 28.8 + - - +
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Residues in contact with ARG 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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187B GLY 3.5 7.9 - - - -
188B ALA* 2.8 34.2 + - + +
189B GLN* 5.1 2.0 - - - +
190B SER 3.8 9.5 + - - +
191B THR* 4.1 42.0 + - - +
193B THR* 3.7 12.7 + - - +
194B SER 3.0 15.6 + - - +
195B LYS* 3.6 7.0 - - - +
197B VAL* 1.3 78.5 - - - +
199B LEU* 1.3 60.6 + - - +
201B ALA* 3.4 3.1 + - - +
202B LEU* 3.2 31.1 + - + +
228B VAL 5.8 0.2 + - - -
231B GLU* 4.7 8.1 + - - +
232B ALA* 4.3 19.4 - - - +
235B ALA* 3.6 26.4 - - - +
237B ASP* 6.0 0.6 - - - +
240B VAL* 3.9 24.3 - - + +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 2.8 23.5 + - - +
196B ALA* 3.6 9.2 - - - +
198B ARG* 1.3 76.5 - - - +
200B ALA* 1.3 63.7 + - - +
201B ALA 3.1 0.5 + - - -
202B LEU* 3.2 6.5 + - - +
203B ASN* 3.0 42.5 + - - +
239B GLU* 3.6 55.0 - - + +
240B VAL* 3.9 13.6 - - + +
243B ALA* 4.1 7.2 - - + -
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Residues in contact with ALA 200 (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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153B ARG* 3.6 38.4 - - + +
156B LEU* 4.3 6.2 - - + +
157B LEU* 4.7 10.9 + - + +
196B ALA 2.8 21.1 + - - +
197B VAL* 3.2 6.5 + - - +
199B LEU* 1.3 73.5 - - - +
201B ALA* 1.3 56.0 + - - +
203B ASN* 3.8 7.4 + - - +
204B ALA* 3.0 28.5 + - - +
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Residues in contact with ALA 201 (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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156B LEU* 3.9 12.1 - - + +
184B ILE* 3.3 34.3 - - - +
187B GLY 3.6 18.4 - - - -
188B ALA* 3.6 6.1 - - + +
197B VAL 2.9 14.5 + - - +
198B ARG 3.6 3.8 - - - +
199B LEU 3.1 0.2 - - - -
200B ALA* 1.3 76.0 - - - +
202B LEU* 1.3 60.9 + - - +
204B ALA* 3.2 4.5 + - - -
205B LEU* 2.8 26.7 + - - +
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Residues in contact with LEU 202 (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 ALA* 3.8 20.9 - - + -
198B ARG* 3.2 18.4 + - + +
199B LEU 3.2 2.5 + - - +
201B ALA* 1.3 78.5 - - - +
203B ASN* 1.3 58.6 + - - +
205B LEU* 3.3 6.3 + - + +
206B ALA* 3.0 22.5 + - - +
228B VAL* 5.5 0.2 - - + -
229B VAL* 4.8 18.2 - - + -
232B ALA* 4.2 18.2 - - + -
240B VAL* 3.6 29.6 - - + +
243B ALA* 3.5 36.6 - - + +
244B ALA* 4.0 10.3 - - - +
247B CYS* 3.1 17.9 - - - -
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Residues in contact with ASN 203 (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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157B LEU* 6.0 5.8 - - + -
199B LEU* 3.0 36.7 + - - +
200B ALA* 4.1 7.1 - - - +
202B LEU* 1.3 75.0 - - - +
204B ALA* 1.3 62.5 + - - +
206B ALA* 3.3 9.3 + - - +
207B ASP* 3.0 31.3 + - - +
243B ALA* 4.1 16.3 - - - +
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Residues in contact with ALA 204 (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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156B LEU* 3.3 27.1 - - + +
157B LEU* 4.7 4.0 - - - +
160B GLY* 3.9 11.2 - - - -
184B ILE* 3.8 17.7 - - + -
200B ALA 3.0 20.7 + - - +
201B ALA* 3.2 6.0 + - - +
203B ASN* 1.3 72.5 - - - +
205B LEU* 1.3 62.4 + - - +
207B ASP* 3.5 4.4 + - - +
208B SER* 2.7 33.2 + - - -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 3.9 14.6 - - + -
184B ILE* 3.5 14.2 - - + +
185B VAL* 4.4 10.8 - - + -
201B ALA 2.8 13.6 + - - +
202B LEU* 3.4 13.9 - - + +
204B ALA* 1.3 74.9 - - - +
206B ALA* 1.3 65.9 + - - +
208B SER* 3.1 6.3 + - - -
209B LEU* 3.1 29.8 + - + +
212B ILE* 3.9 26.9 - - + -
225B LEU* 4.1 18.6 - - + -
229B VAL* 3.8 29.2 - - + -
247B CYS* 4.3 9.2 - - + -
251B ILE* 5.3 0.4 - - + -
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Residues in contact with ALA 206 (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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202B LEU 3.0 13.1 + - - +
203B ASN* 3.3 13.4 + - - +
205B LEU* 1.3 77.3 - - - +
207B ASP* 1.3 66.3 + - - +
208B SER 3.0 1.6 + - - -
209B LEU* 3.1 18.3 + - - +
246B GLY 5.7 1.6 - - - +
247B CYS* 4.0 15.8 - - - +
250B LYS* 3.1 32.1 + - + -
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Residues in contact with ASP 207 (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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106A ARG* 5.5 4.7 - - - +
110A ARG* 4.3 11.2 + - - -
157B LEU* 5.3 2.3 - - - +
160B GLY* 4.0 11.2 - - - +
161B TYR* 4.0 23.6 - - - -
164B GLU* 3.3 29.9 - - + +
203B ASN* 3.0 21.1 + - - +
204B ALA* 3.9 5.1 - - - +
205B LEU 3.4 0.2 - - - -
206B ALA* 1.3 80.6 - - - +
208B SER* 1.3 56.3 + - - +
211B PHE* 3.2 23.4 - - - -
250B LYS* 4.9 4.1 + - - +
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Residues in contact with SER 208 (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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159B LEU 4.2 0.2 + - - -
160B GLY* 3.8 9.7 - - - -
163B CYS* 3.4 29.1 - - - +
180B ILE* 5.8 0.7 - - - -
184B ILE* 4.3 8.1 - - - +
204B ALA 2.7 20.6 + - - -
205B LEU* 3.1 9.4 + - - -
206B ALA 3.0 1.2 - - - -
207B ASP* 1.3 79.2 - - - +
209B LEU* 1.3 63.8 + - - +
210B ILE 3.2 2.9 - - - -
211B PHE* 2.9 20.2 + - - -
212B ILE* 3.1 23.5 + - - +
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Residues in contact with LEU 209 (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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205B LEU* 3.1 27.4 + - + +
206B ALA* 3.1 13.6 + - - +
207B ASP 3.5 0.8 - - - -
208B SER* 1.3 77.8 - - - +
210B ILE* 1.3 54.7 + - - +
212B ILE* 3.4 29.5 - - + +
216B MET* 4.8 4.3 - - + -
225B LEU* 5.1 1.1 - - + -
247B CYS* 4.2 4.9 - - + +
250B LYS* 3.4 45.1 - - + +
251B ILE* 3.8 35.0 - - + +
254B LYS* 4.6 4.0 - - + -
255B TYR* 2.5 40.6 + - + -
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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