Contacts of the helix formed by residues 186 - 201 (chain B) in PDB entry 4BT9
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 ASP 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B THR 3.8 2.6 + - - +
185B ILE* 1.3 72.0 - - - +
187B LYS* 1.3 67.1 + - - +
188B VAL* 2.6 43.8 + - - +
189B SER* 3.1 24.3 + - - +
190B VAL* 3.3 16.0 + - - +
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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
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174B LEU* 4.5 10.9 - - + +
177B LEU* 3.6 48.2 + - + +
178B ASP* 3.3 28.1 + - - +
185B ILE 3.8 2.4 + - - +
186B ASP* 1.3 73.4 + - - +
188B VAL* 1.3 62.3 + - - +
190B VAL* 3.3 5.9 + - - +
191B LEU* 3.0 30.5 + - + +
217B LEU* 3.7 29.0 - - + +
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Residues in contact with VAL 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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186B ASP* 2.6 24.4 + - - +
187B LYS* 1.3 72.0 - - - +
189B SER* 1.3 62.0 + - - +
191B LEU* 3.2 6.9 + - - +
192B ASP* 3.0 22.3 + - + +
214B LEU* 3.8 12.6 - - + +
217B LEU* 3.8 32.5 - - + -
218B ASP* 4.3 16.2 - - + +
221B HIS* 3.8 31.4 - - + +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.7 20.1 - - - -
185B ILE* 6.4 0.4 - - - -
186B ASP* 3.1 22.7 + - - +
188B VAL* 1.3 78.4 - - - +
190B VAL* 1.3 62.6 + - - +
192B ASP* 3.2 14.5 + - - +
193B TYR* 3.2 30.9 - - - -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 3.6 19.3 - - + -
170B MET* 3.7 38.9 - - + +
173B ALA* 4.8 1.6 - - + -
174B LEU* 4.3 16.2 - - + +
177B LEU* 4.4 4.3 - - + -
185B ILE* 3.6 28.7 - - + -
186B ASP 3.3 14.3 + - - +
187B LYS* 3.5 11.0 - - - +
189B SER* 1.3 79.2 - - - +
191B LEU* 1.3 59.8 + - + +
192B ASP 3.3 0.2 + - - -
193B TYR* 3.4 2.1 + - - +
194B LEU* 2.8 29.9 + - + +
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Residues in contact with LEU 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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174B LEU* 4.1 25.4 - - + -
187B LYS* 3.0 23.3 + - + +
188B VAL 3.2 4.2 + - - +
190B VAL* 1.3 73.7 - - + +
192B ASP* 1.3 61.4 + - - +
194B LEU* 4.3 6.1 - - + -
195B SER* 2.8 35.7 + - - -
210B LEU* 3.8 37.5 - - + +
213B LYS* 4.2 8.1 - - + -
214B LEU* 3.7 34.5 - - + +
217B LEU* 3.8 25.1 - - + -
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Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.0 12.9 + - + +
189B SER* 3.3 14.5 - - - +
190B VAL 3.2 0.2 - - - -
191B LEU* 1.3 79.3 - - - +
193B TYR* 1.3 67.8 + - + +
195B SER* 3.2 12.5 + - - -
196B TYR* 3.5 9.5 + - - +
214B LEU* 4.0 8.2 - - + +
221B HIS* 4.0 7.9 + - - +
223B ARG* 2.5 42.4 + - - -
227B ASN* 5.9 1.2 + - - -
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Residues in contact with TYR 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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151B PHE* 4.1 12.1 - + - -
155B LYS* 3.9 25.8 - - + -
158B TYR* 3.7 49.6 - + + -
166B THR* 4.5 4.7 - - + +
170B MET* 3.7 29.8 - - + -
189B SER* 3.2 36.3 + - - -
190B VAL 3.9 1.8 - - - +
192B ASP* 1.3 83.3 - - + +
194B LEU* 1.3 63.1 + - - +
196B TYR* 3.2 6.7 + - - +
197B ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 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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167B GLU* 3.8 32.8 - - - +
170B MET* 3.9 16.5 - - + +
171B GLU* 4.0 26.0 - - + +
174B LEU* 4.2 23.6 - - + -
190B VAL* 2.8 23.7 + - + +
191B LEU* 4.1 5.8 - - + +
193B TYR* 1.3 74.1 - - - +
195B SER* 1.3 57.4 + - - +
197B ALA* 3.2 3.5 + - + +
198B VAL* 2.9 49.8 + - + +
210B LEU* 3.8 22.9 - - + -
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Residues in contact with SER 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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191B LEU 2.8 24.7 + - - -
192B ASP* 3.2 9.9 + - - -
194B LEU* 1.3 77.9 - - - +
196B TYR* 1.3 60.7 + - - +
198B VAL* 4.1 1.9 - - - +
199B TYR* 3.3 22.7 + - - +
207B ALA* 4.1 16.4 - - - +
210B LEU* 4.2 26.7 - - - +
211B THR* 4.5 10.0 + - - -
214B LEU* 5.3 3.2 - - - +
227B ASN* 4.9 9.9 + - - -
231B PHE* 5.1 5.9 - - - -
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Residues in contact with TYR 196 (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 TYR* 3.6 33.7 - + + +
163B TYR* 3.4 30.2 + + - -
192B ASP 3.5 8.0 + - - +
193B TYR* 3.2 9.4 + - - +
195B SER* 1.3 79.8 + - - +
197B ALA* 1.3 65.7 + - - +
199B TYR* 3.3 6.0 + + + +
200B GLN* 3.1 66.8 + - + +
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Residues in contact with ALA 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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158B TYR* 5.4 0.2 - - + -
163B TYR* 3.8 32.3 - - + +
166B THR* 3.7 25.8 - - + -
167B GLU* 4.3 6.3 - - - +
193B TYR 3.0 15.7 + - - +
194B LEU* 3.7 6.1 - - - +
196B TYR* 1.3 79.0 - - + +
198B VAL* 1.3 61.4 + - - +
200B GLN* 3.3 4.9 + - - +
201B GLN* 3.2 27.3 + - - +
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 3.8 20.6 - - + +
194B LEU* 2.9 38.0 + - + +
195B SER 4.1 2.9 - - - +
197B ALA* 1.3 75.5 - - - +
199B TYR* 1.3 62.3 + - - +
201B GLN* 3.1 13.2 + - - +
202B GLY 3.3 0.5 + - - -
203B ASP* 3.2 36.9 + - + +
206B LYS* 3.6 41.5 - - + +
207B ALA* 3.7 6.7 - - - +
210B LEU* 4.0 7.6 - - + -
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Residues in contact with TYR 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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195B SER 3.3 15.0 + - - +
196B TYR* 3.3 6.9 + + + +
198B VAL* 1.3 79.9 - - - +
200B GLN* 1.3 74.7 + - - +
202B GLY* 2.9 20.8 + - - -
203B ASP 4.1 6.1 - - - +
204B LEU* 3.6 37.5 - - + -
207B ALA* 3.9 11.0 - - + -
230B TYR* 4.7 9.1 + + - -
231B PHE* 3.7 26.7 - + + -
234B ILE* 3.4 19.6 - - + +
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Residues in contact with GLN 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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163B TYR* 3.6 28.7 - - + -
196B TYR* 3.1 63.7 + - + +
197B ALA 3.6 2.0 - - - +
198B VAL 3.3 0.4 - - - -
199B TYR* 1.3 91.7 - - - +
201B GLN* 1.3 61.2 + - - +
202B GLY* 3.2 1.0 + - - -
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Residues in contact with GLN 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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163B TYR* 3.7 18.5 + - + +
164B TYR* 3.4 46.7 + - - +
167B GLU* 3.8 19.5 + - - +
197B ALA 3.2 15.9 - - - +
198B VAL 3.1 8.8 + - - +
200B GLN* 1.3 78.8 - - - +
202B GLY* 1.3 59.2 + - - +
203B ASP* 3.7 2.0 - - + +
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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