Contacts of the helix formed by residues 193 - 211 (chain B) in PDB entry 2O98
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 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B TYR* 2.7 18.7 + - - +
188B TYR* 4.2 1.0 + - - -
191B LEU* 3.4 19.1 + - - +
192B ASN* 1.3 75.5 + - - +
194B PRO* 1.3 68.2 - - - +
195B ASP 3.1 0.5 + - - -
196B ARG* 3.2 23.9 + - - -
197B ALA* 3.1 19.3 + - - +
1004B SO4 3.0 30.4 + - - -
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Residues in contact with PRO 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.8 33.0 - - + -
192B ASN* 3.7 15.0 - - - +
193B SER* 1.3 85.1 - - - +
195B ASP* 1.3 65.0 + - - +
197B ALA* 3.2 0.7 + - - +
198B CYS* 2.9 38.5 + - - -
237B TRP* 5.8 2.2 - - + +
1004B SO4 3.9 8.3 - - - +
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PRO* 1.3 78.2 - - - +
196B ARG* 1.3 57.2 + - - -
198B CYS* 4.2 5.1 - - - +
199B ASN* 3.1 38.8 + - - +
1004B SO4 2.8 32.5 + - - +
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.8 45.4 - - + -
191B LEU* 5.7 2.0 - - - +
193B SER* 3.2 19.4 + - - +
195B ASP* 1.3 71.8 - - - +
197B ALA* 1.3 63.9 + - - +
199B ASN* 4.1 5.2 - - - +
200B LEU* 3.1 26.7 + - - +
1004B SO4 2.9 39.4 + - - +
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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
----------------------------------------------------------
184B SER* 3.4 31.7 - - - +
187B TYR* 4.1 3.1 - - - +
188B TYR* 3.8 17.7 - - + +
193B SER 3.1 12.0 + - - +
194B PRO 3.4 8.7 - - - +
196B ARG* 1.3 80.1 - - - +
198B CYS* 1.3 56.7 + - - +
201B ALA* 3.0 29.6 + - - +
237B TRP* 3.6 17.5 - - + -
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Residues in contact with CYS 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 PRO* 2.9 25.4 + - - +
195B ASP* 4.2 6.5 - - - +
197B ALA* 1.3 73.9 - - - +
199B ASN* 1.3 58.4 + - - +
201B ALA* 4.5 0.7 - - - -
202B LYS* 2.8 39.2 + - - +
234B LEU* 3.6 19.2 - - + +
237B TRP* 3.8 36.8 - - - -
238B THR* 5.0 6.7 - - - +
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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
----------------------------------------------------------
195B ASP* 3.1 25.9 + - - +
196B ARG* 4.1 5.5 - - - +
198B CYS* 1.3 77.5 - - - +
200B LEU* 1.3 63.1 + - - +
202B LYS* 4.3 4.3 - - - +
203B GLN* 3.1 38.9 + - - +
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Residues in contact with LEU 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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162B GLN* 4.0 24.5 - - - +
180B ALA* 3.6 37.9 - - + +
183B PHE* 3.7 31.2 - - + -
184B SER* 4.3 4.5 - - - +
187B TYR* 3.8 21.3 - - + -
196B ARG 3.1 16.6 + - - +
197B ALA 3.8 3.1 - - - +
199B ASN* 1.3 81.2 - - - +
201B ALA* 1.3 62.1 + - - +
203B GLN* 3.6 6.4 - - - +
204B ALA* 3.1 20.2 + - + +
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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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184B SER* 4.1 12.1 - - - +
197B ALA 3.0 17.6 + - - +
198B CYS 3.8 2.7 - - - +
200B LEU* 1.3 75.6 - - - +
202B LYS* 1.3 65.8 + - - +
204B ALA* 3.2 2.9 + - - +
205B PHE* 2.9 23.7 + - - +
230B LEU* 4.0 28.3 - - + +
233B ASN* 5.9 0.4 - - + -
234B LEU* 3.9 21.3 - - + -
237B TRP* 4.4 7.2 - - + -
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Residues in contact with LYS 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 CYS 2.8 21.9 + - - +
199B ASN* 4.3 4.0 - - - +
201B ALA* 1.3 73.7 - - - +
203B GLN* 1.3 53.8 + - + +
205B PHE* 3.3 5.8 + - + +
206B ASP* 2.8 58.9 + - - +
234B LEU* 3.9 23.2 - - + +
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASN* 3.1 30.6 + - - +
200B LEU* 3.6 6.0 - - - +
202B LYS* 1.3 77.4 - - - +
204B ALA* 1.3 57.0 + - - +
206B ASP* 3.2 5.6 + - - +
207B GLU* 2.9 50.6 + - + +
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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
----------------------------------------------------------
171B PRO 4.6 1.0 - - - +
176B ARG* 6.3 1.8 - - + +
177B LEU* 3.9 12.2 - - + +
180B ALA* 3.2 35.4 - - + -
200B LEU* 3.1 12.2 + - + +
201B ALA 3.8 3.6 - - - +
203B GLN* 1.3 75.7 - - - +
205B PHE* 1.3 68.0 + - - +
207B GLU* 3.7 12.8 + - - +
208B ALA* 3.3 19.8 + - - +
230B LEU* 4.6 6.1 - - + -
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ALA 2.9 15.7 + - - +
202B LYS* 3.4 9.9 - - + +
204B ALA* 1.3 78.2 - - - +
206B ASP* 1.3 73.6 + - - +
208B ALA* 3.0 21.5 + - - +
209B ILE* 3.1 43.2 + - + +
227B MET* 3.4 43.1 - - + -
228B GLN* 5.1 0.7 - - - -
230B LEU* 4.3 11.5 - - + +
231B ARG* 4.0 34.8 - - + -
234B LEU* 4.8 6.3 - - + -
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LYS* 2.8 54.0 + - - +
203B GLN* 3.2 6.0 + - - +
205B PHE* 1.3 86.2 - - - +
207B GLU* 1.3 61.8 + - + +
209B ILE* 3.4 8.8 + - - +
210B ALA* 2.8 28.6 + - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 5.5 0.9 + - - +
171B PRO* 3.7 25.8 - - + +
176B ARG* 3.4 23.0 + - - -
203B GLN* 2.9 41.5 + - + +
204B ALA* 3.9 8.3 - - - +
206B ASP* 1.3 76.8 - - + +
208B ALA* 1.3 62.4 + - - +
210B ALA* 3.3 8.3 + - - +
211B GLU* 3.2 18.9 + - - +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 3.9 17.6 - - - +
172B THR* 3.6 17.2 - - + +
177B LEU* 4.0 6.3 - - + -
204B ALA 3.3 11.8 + - - +
205B PHE 3.0 11.3 + - - +
207B GLU* 1.3 78.5 - - - +
209B ILE* 1.3 60.9 + - - +
211B GLU 3.1 20.8 + - - -
212B LEU* 3.4 4.2 + - - +
227B MET* 3.8 29.6 - - + -
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Residues in contact with ILE 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 PHE* 3.1 46.4 + - + +
206B ASP* 3.7 8.7 - - - +
208B ALA* 1.3 72.1 - - - +
210B ALA* 1.3 62.0 + - - +
211B GLU 3.0 5.2 + - - -
212B LEU* 3.0 37.6 + - + +
227B MET* 3.6 22.9 - - + -
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP 2.8 21.5 + - - +
207B GLU* 3.3 9.2 + - - +
209B ILE* 1.3 73.0 - - - +
211B GLU* 1.3 65.8 + - + +
212B LEU 3.7 0.8 + - - -
213B ASP* 3.9 5.9 - - - +
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Residues in contact with GLU 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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170B ALA* 5.2 0.3 - - - +
171B PRO* 3.3 36.5 - - + +
172B THR* 3.9 5.2 - - - +
207B GLU 3.2 9.8 + - - +
208B ALA 3.1 7.8 + - - +
209B ILE 3.0 1.6 - - - -
210B ALA* 1.3 86.7 - - + +
212B LEU* 1.3 50.1 + - - +
213B ASP* 3.0 19.1 - - - +
214B THR* 2.7 53.9 + - - +
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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