Contacts of the helix formed by residues 197 - 213 (chain B) in PDB entry 1B3U
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 LEU 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B LEU 3.6 3.2 + - - -
196B GLU* 1.3 70.0 - - - +
198B ASP* 1.3 67.4 + - - +
200B VAL* 3.0 23.5 + - + +
201B LYS* 3.0 39.9 + - - +
233B LEU* 3.8 23.8 - - + +
234B LEU* 4.0 19.5 - - + -
235B PRO* 4.6 13.5 - - + -
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Residues in contact with ASP 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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196B GLU* 3.1 5.5 - - + +
197B LEU* 1.3 84.5 - - - +
199B ASN* 1.3 62.2 + - - +
201B LYS* 3.5 14.8 + - - +
202B SER* 2.8 30.9 + - - -
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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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392A GLU* 5.1 1.9 + - - +
166B ARG* 3.8 36.3 + - - +
195B LEU* 4.2 15.9 - - + +
196B GLU* 2.7 52.7 + - - +
198B ASP* 1.3 74.3 - - - +
200B VAL* 1.3 58.7 + - - +
202B SER* 3.5 8.0 + - - -
203B GLU* 2.9 33.9 + - + +
204B ILE* 3.3 6.4 + - - +
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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
----------------------------------------------------------
192B ALA* 3.9 23.8 - - + +
195B LEU* 4.0 11.0 - - + +
196B GLU 2.9 16.4 + - - +
197B LEU* 3.2 19.5 - - + +
199B ASN* 1.3 78.0 - - - +
201B LYS* 1.3 63.1 + - - +
204B ILE* 3.1 45.3 + - + +
205B ILE* 3.2 8.2 + - + +
230B ILE* 4.9 11.4 - - + -
233B LEU* 5.0 15.3 - - + -
234B LEU* 4.2 20.0 - - + -
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Residues in contact with LYS 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.0 44.1 + - + +
198B ASP* 3.8 14.9 + - - +
200B VAL* 1.3 77.9 - - - +
202B SER* 1.3 58.7 + - - +
205B ILE* 3.5 27.6 - - - +
206B PRO* 4.2 1.0 - - - +
234B LEU* 4.0 17.7 - - + -
235B PRO* 4.5 1.8 - - - +
238B ASP* 3.1 31.6 + - - +
242B LEU* 4.1 19.6 - - + +
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP 2.8 22.4 + - - -
199B ASN* 3.5 11.4 + - - -
201B LYS* 1.3 79.0 - - - +
203B GLU* 1.3 68.5 + - - +
206B PRO* 3.3 16.5 - - - +
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Residues in contact with GLU 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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166B ARG* 3.0 53.6 + - - +
170B ARG* 3.0 35.3 + - - +
195B LEU* 5.5 0.4 - - + -
199B ASN* 2.9 22.3 + - - +
202B SER* 1.3 87.9 + - - +
204B ILE* 1.3 65.0 + - + +
205B ILE 3.5 1.1 - - - -
206B PRO* 3.1 15.2 - - - +
207B MET* 3.2 24.9 - - + +
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Residues in contact with ILE 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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188B LEU* 4.1 25.1 - - + -
191B PHE* 4.2 12.1 - - + -
192B ALA* 4.1 27.6 - - + -
195B LEU* 3.6 32.8 - - + -
199B ASN 3.3 0.2 + - - -
200B VAL* 3.1 24.4 + - + +
203B GLU* 1.3 73.7 - - - +
205B ILE* 1.3 57.0 + - - +
207B MET* 2.9 14.8 + - + +
208B PHE* 2.7 32.2 + - - +
230B ILE* 3.8 27.8 - - + -
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Residues in contact with ILE 205 (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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200B VAL* 3.2 9.1 + - + +
201B LYS* 3.5 23.8 - - - +
204B ILE* 1.3 77.1 - - + +
206B PRO* 1.3 62.0 - - + +
208B PHE* 3.0 14.0 + - + +
209B SER* 2.6 40.5 + - - -
230B ILE* 4.1 25.8 - - + -
234B LEU* 4.5 5.6 - - + -
242B LEU* 4.0 51.4 - - + +
243B VAL* 4.6 0.9 - - + -
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Residues in contact with PRO 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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170B ARG* 6.5 0.7 - - - -
201B LYS 4.2 1.3 - - - +
202B SER 3.3 24.9 - - - +
203B GLU* 3.1 20.2 - - - +
205B ILE* 1.3 99.8 - - + +
207B MET* 1.3 54.2 + - + +
209B SER* 4.4 5.6 - - - -
210B ASN* 2.9 40.1 + - - +
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Residues in contact with MET 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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166B ARG* 4.2 14.4 - - + +
169B PHE* 3.9 26.5 - - + -
170B ARG* 3.9 39.5 - - + +
173B CYS* 4.0 18.4 - - + +
188B LEU* 4.2 14.8 - - + -
191B PHE* 5.1 4.9 - - + -
195B LEU* 5.9 0.4 - - + -
203B GLU* 3.2 29.8 - - + +
204B ILE* 2.9 20.9 + - + +
206B PRO* 1.3 78.7 - - + +
208B PHE* 1.3 63.7 + - - +
210B ASN* 3.7 4.7 - - - +
211B LEU* 3.1 31.0 + - - +
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Residues in contact with PHE 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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188B LEU* 3.9 12.1 - - + +
204B ILE 2.7 15.6 + - - +
205B ILE* 3.3 20.2 - - + +
207B MET* 1.3 70.8 - - - +
209B SER* 1.3 68.2 + - - +
211B LEU* 3.4 4.3 + - + +
212B ALA* 3.0 20.3 + - - +
223B ALA* 3.5 33.9 - - + -
226B ALA* 4.4 7.9 - - + -
227B CYS* 3.6 31.9 - - + -
230B ILE* 3.5 28.3 - - + -
242B LEU 4.9 1.8 - - - -
243B VAL* 4.7 19.3 - - + -
246B THR* 3.8 33.7 - - + -
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 2.6 24.4 + - - -
206B PRO* 4.0 7.4 - - - -
208B PHE* 1.3 76.6 - - - +
210B ASN* 1.3 64.4 + - - +
212B ALA* 3.5 8.6 + - - +
213B SER* 3.2 22.3 + - - -
246B THR* 4.3 19.1 + - - +
249B GLN* 5.1 1.6 - - - +
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Residues in contact with ASN 210 (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 SER* 5.3 6.2 + - - +
206B PRO* 2.9 25.2 + - - +
207B MET* 3.7 6.2 - - - +
209B SER* 1.3 77.5 + - - +
211B LEU* 1.3 65.9 + - + +
213B SER* 3.1 19.7 + - - -
214B ASP* 3.4 9.7 + - - +
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Residues in contact with LEU 211 (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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173B CYS* 3.8 41.5 - - + +
181B ARG* 4.0 21.8 - - + +
185B ALA* 4.0 22.0 - - + -
188B LEU* 3.9 24.9 - - + -
207B MET 3.1 21.5 + - - +
208B PHE* 3.8 3.1 - - - +
210B ASN* 1.3 76.3 - - + +
212B ALA* 1.3 59.1 + - - +
213B SER 3.0 4.9 + - - -
214B ASP* 3.1 22.9 + - - +
219B VAL* 4.0 18.7 - - + +
220B ARG* 3.7 10.4 - - - -
223B ALA* 4.6 9.0 - - + -
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Residues in contact with ALA 212 (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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208B PHE* 3.0 17.8 + - + +
209B SER 3.7 4.7 - - - +
210B ASN 3.2 0.2 - - - -
211B LEU* 1.3 75.9 - - - +
213B SER* 1.3 57.9 + - - +
214B ASP 3.6 0.7 - - - -
220B ARG* 3.1 20.0 - - - +
223B ALA* 3.8 21.5 - - + +
246B THR* 3.5 30.5 - - + -
249B GLN* 3.9 10.6 - - - +
253B ASP* 4.8 2.8 - - - +
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Residues in contact with SER 213 (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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209B SER 3.2 12.0 + - - -
210B ASN* 3.1 16.0 + - - -
211B LEU 3.0 0.8 - - - -
212B ALA* 1.3 80.4 - - - +
214B ASP* 1.3 63.9 + - - +
215B GLU* 3.7 2.6 + - - +
220B ARG* 3.7 4.3 - - - +
249B GLN* 4.5 13.7 - - - -
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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