Contacts of the helix formed by residues 187 - 203 (chain B) in PDB entry 1BK6
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 VAL 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B SER* 1.3 74.8 - - - +
188B GLU* 1.3 68.4 + - + +
190B LYS* 3.3 12.7 + - + +
191B GLU* 3.0 23.2 + - + +
226B SER* 6.2 3.1 - - - -
228B LYS* 4.2 30.3 - - + +
231B LEU* 3.9 24.2 - - + +
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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
----------------------------------------------------------
145B GLU* 5.6 0.7 - - - +
146B MET* 5.4 2.8 - - - +
149B LEU* 3.5 33.7 - - + +
186B SER* 3.3 9.9 + - - +
187B VAL* 1.3 76.8 - - + +
189B VAL* 1.3 63.2 + - - +
191B GLU* 3.0 23.8 + - - +
192B GLN* 3.2 5.7 + - - +
228B LYS* 5.8 7.2 - - - +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 3.7 28.5 - - + +
148B GLN* 4.5 5.4 - - + +
149B LEU* 3.8 31.0 - - + +
181B LEU* 3.9 34.5 - - + +
185B GLY* 3.9 15.7 - - - -
186B SER* 3.3 21.5 + - - +
187B VAL 3.2 0.4 - - - -
188B GLU* 1.3 76.6 - - - +
190B LYS* 1.3 65.9 + - - +
192B GLN* 3.1 6.1 + - + +
193B ALA* 3.0 19.1 + - - +
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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
----------------------------------------------------------
181B LEU 3.7 12.6 - - - +
182B LEU* 3.0 29.2 + - + +
183B TYR 4.1 8.7 + - - -
185B GLY 3.1 20.6 - - - +
186B SER 3.0 21.7 + - - +
187B VAL* 3.7 11.4 - - + +
188B GLU 3.3 0.2 - - - -
189B VAL* 1.3 75.4 - - - +
191B GLU* 1.3 64.5 + - - +
193B ALA* 3.1 8.1 + - - +
194B ILE* 2.9 27.5 + - - +
223B LEU* 3.7 26.5 - - + +
231B LEU* 4.1 11.0 - - + -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 3.0 16.1 + - + +
188B GLU* 3.0 18.2 - - - +
190B LYS* 1.3 76.5 - - - +
192B GLN* 1.3 61.5 + - + +
194B ILE* 3.3 13.7 - - - +
195B TRP* 3.4 24.1 + - - +
228B LYS* 5.7 4.0 - - - +
230B SER* 3.3 26.7 - - - +
231B LEU* 3.3 29.6 - - + +
234B THR* 2.9 28.1 + - - +
131E LYS* 4.7 9.5 + - - -
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Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.4 36.5 - - + +
152B ALA* 4.1 15.0 - - + -
153B TRP* 3.3 27.2 - - + +
156B THR* 3.4 25.8 + - - +
188B GLU 3.2 2.7 + - - +
189B VAL* 3.1 9.4 + - - +
191B GLU* 1.3 79.1 - - - +
193B ALA* 1.3 59.7 + - - +
195B TRP* 3.2 11.1 + - - +
196B ALA 2.9 24.8 + - - -
131E LYS* 2.7 46.3 + - - +
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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
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152B ALA* 5.0 1.5 - - - +
178B PHE* 3.5 38.0 - - - +
181B LEU* 4.1 16.4 - - + -
182B LEU* 3.8 9.0 - - + -
189B VAL 3.0 12.6 + - - +
190B LYS* 3.1 8.0 + - - +
192B GLN* 1.3 77.4 - - - +
194B ILE* 1.3 61.7 + - - +
196B ALA* 3.3 2.9 + - - +
197B LEU* 2.9 29.3 + - - +
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Residues in contact with ILE 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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182B LEU* 3.9 8.8 - - + +
190B LYS 2.9 14.1 + - - +
191B GLU 3.3 14.6 - - - +
193B ALA* 1.3 76.7 - - - +
195B TRP* 1.3 60.8 + - - +
197B LEU* 3.5 9.3 + - + +
198B GLY 2.9 14.6 + - - -
220B ILE* 3.8 33.9 - - + -
223B LEU* 3.9 17.3 - - + -
231B LEU* 4.2 12.8 - - + -
234B THR* 3.6 20.4 - - + -
235B ALA* 3.8 16.8 - - - +
238B THR* 2.8 43.6 + - + +
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Residues in contact with TRP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B THR* 4.7 9.5 + - + -
157B ASN* 5.6 0.2 + - - -
191B GLU* 3.4 25.5 + - - +
192B GLN* 3.2 14.3 + - - +
194B ILE* 1.3 80.0 - - - +
196B ALA* 1.3 67.7 + - - +
198B GLY* 2.9 11.8 + - - -
199B ASN* 3.2 19.0 + - - +
234B THR* 3.8 23.3 - - + -
237B TRP* 4.0 9.4 - + - -
129E LYS* 2.9 41.2 + - + +
130E ARG 3.6 25.4 - - - -
131E LYS* 3.6 45.0 - - + +
132E VAL* 5.1 1.1 - - + -
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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
----------------------------------------------------------
156B THR* 3.0 37.3 - - + +
159B ALA* 5.0 2.0 - - + +
178B PHE* 3.4 33.2 - - + -
192B GLN 2.9 7.5 + - - +
193B ALA 3.6 6.7 - - - +
195B TRP* 1.3 75.4 - - - +
197B LEU* 1.3 63.2 + - - +
199B ASN* 2.9 17.9 + - - +
200B VAL* 3.1 16.0 + - - +
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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
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175B VAL* 4.3 22.4 - - + -
178B PHE* 3.8 32.5 - - + -
179B ILE* 4.2 11.9 - - + -
182B LEU* 3.9 28.9 - - + -
193B ALA 2.9 23.2 + - - +
194B ILE* 3.7 10.8 - - + +
196B ALA* 1.3 75.8 - - - +
198B GLY* 1.3 57.2 + - - +
200B VAL* 3.3 5.4 + - + +
201B ALA* 2.9 33.6 + - - +
211B VAL* 4.3 20.5 - - + +
216B ALA* 4.9 6.1 - - + -
220B ILE* 5.2 1.3 - - + -
238B THR* 4.3 9.0 - - + -
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE 2.9 7.3 + - - -
195B TRP 2.9 9.9 + - - -
197B LEU* 1.3 77.7 - - - +
199B ASN* 1.3 56.9 + - - +
201B ALA* 3.8 1.4 - - - +
202B GLY* 2.9 22.9 + - - -
237B TRP* 3.9 14.5 - - - -
238B THR* 3.4 28.5 + - - -
241B ASN* 3.3 12.3 + - - -
127E LYS 4.3 0.2 - - - +
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Residues in contact with ASN 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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156B THR 3.3 22.6 + - - -
159B ALA* 3.2 26.2 - - + +
160B SER* 3.9 3.5 - - - -
195B TRP* 3.2 21.8 + - - -
196B ALA* 2.9 8.4 + - - +
198B GLY* 1.3 74.1 - - - +
200B VAL* 1.3 65.6 + - - +
202B GLY* 3.2 1.6 + - - -
203B ASP* 3.2 16.8 + - - +
237B TRP* 3.7 3.0 - - - -
128E LYS* 3.3 23.9 + - + +
129E LYS 2.8 44.8 + - - -
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Residues in contact with VAL 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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159B ALA* 4.6 9.2 - - + -
166B THR* 4.2 13.9 - - + -
169B VAL* 5.5 3.6 - - + -
170B VAL* 3.9 29.4 - - + -
175B VAL* 4.3 15.9 - - + -
178B PHE* 5.1 9.2 - - + -
196B ALA 3.1 13.4 + - - +
197B LEU* 3.3 8.9 + - + +
199B ASN* 1.3 71.5 - - - +
201B ALA* 1.3 63.9 + - - +
202B GLY 2.9 3.8 - - - -
203B ASP* 2.9 14.6 + - - +
207B TYR* 3.3 30.0 - - + +
210B TYR* 5.2 1.8 - - + -
211B VAL* 3.9 20.0 - - + -
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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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197B LEU 2.9 18.4 + - - +
198B GLY* 4.0 4.0 - - - +
200B VAL* 1.3 76.5 - - - +
202B GLY* 1.3 60.6 + - - +
203B ASP 3.6 0.3 + - - -
204B SER 4.0 3.5 - - - +
208B ARG* 3.7 32.4 - - - +
211B VAL* 4.3 7.6 - - + +
238B THR* 5.0 1.6 - - + +
241B ASN* 4.2 17.4 - - + +
242B LEU* 3.7 31.9 - - + +
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Residues in contact with GLY 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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198B GLY 2.9 16.4 + - - -
199B ASN 3.2 4.2 + - - -
200B VAL 2.9 2.0 - - - -
201B ALA* 1.3 80.0 - - - +
203B ASP* 1.3 63.6 + - - +
204B SER 3.6 0.2 - - - -
241B ASN* 4.0 11.9 - - - +
127E LYS* 3.9 23.4 + - - +
128E LYS* 4.4 6.0 - - - +
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Residues in contact with ASP 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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163B SER* 3.1 40.6 + - - -
166B THR* 3.7 5.7 + - + -
199B ASN 3.2 4.2 + - - +
200B VAL 2.9 15.0 + - - +
202B GLY* 1.3 79.8 - - - +
204B SER* 1.3 70.2 + - - +
207B TYR* 3.7 21.7 - - + -
128E LYS* 2.6 36.4 + - - +
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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
------------------------------------------------------------
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