Contacts of the helix formed by residues 190 - 200 (chain B) in PDB entry 2O6S
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 ILE 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B LYS 5.2 3.1 - - - +
161B SER* 6.1 2.0 - - - -
183B TRP* 4.8 4.3 - - + -
184B ASP 3.5 22.6 + - - +
185B CYS* 3.5 34.8 - - - +
186B THR 3.1 9.4 + - - +
189B GLY* 1.3 75.4 - - - +
191B ARG* 1.3 66.7 + - - +
192B TYR 3.4 0.7 - - - -
193B LEU* 3.3 21.0 + - + +
194B SER* 3.0 19.2 + - - -
225B VAL* 3.8 31.0 - - + +
228B ILE* 3.8 10.1 - - + -
230B CYS* 3.5 22.4 - - - -
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Residues in contact with ARG 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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188B PRO* 2.9 28.1 + - - +
189B GLY 3.2 0.4 - - - -
190B ILE* 1.3 78.2 - - - +
192B TYR* 1.3 59.7 + - - +
194B SER* 3.9 2.6 - - - -
195B GLU* 2.8 70.3 + - + +
229B ILE* 6.1 0.4 - - - +
230B CYS* 3.3 42.6 + - + +
231B PRO 2.9 30.3 + - - -
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Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 4.0 13.9 - - + -
163B PRO 3.9 10.1 - - - -
164B ASP* 3.6 23.1 + - + +
165B GLY* 3.3 36.1 - - - -
166B VAL 3.8 5.6 - - - -
167B PHE* 3.0 48.1 + + - +
168B ASP* 3.8 10.4 + - - -
189B GLY 4.3 3.1 + - - +
190B ILE 3.4 0.8 - - - -
191B ARG* 1.3 78.3 - - - +
193B LEU* 1.3 61.8 + - - +
195B GLU* 3.7 4.4 - - + +
196B TRP* 2.8 47.8 + + + +
199B LYS* 6.2 2.5 - - - -
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B SER* 5.7 0.4 - - - -
162B VAL* 4.3 19.3 - - + +
167B PHE* 4.1 26.5 - - + -
178B LEU* 4.3 11.0 - - + -
183B TRP* 3.6 45.3 - - + -
189B GLY 5.3 0.6 + - - -
190B ILE* 3.3 18.1 + - + +
192B TYR* 1.3 81.1 - - + +
194B SER* 1.3 65.5 + - - +
196B TRP* 3.7 3.5 - - + +
197B ILE* 3.0 45.2 + - + +
225B VAL* 4.1 16.8 - - + -
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 3.0 21.6 + - - -
191B ARG* 3.9 4.0 - - - -
193B LEU* 1.3 75.3 - - - +
195B GLU* 1.3 67.4 + - - +
197B ILE* 3.3 3.4 + - - +
198B ASN* 3.0 39.0 + - - -
225B VAL* 3.4 27.8 + - - +
226B ARG* 3.7 2.5 - - - +
228B ILE* 2.7 28.1 + - - -
229B ILE* 4.8 0.3 - - - +
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Residues in contact with GLU 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 ARG* 2.8 61.8 + - + +
192B TYR* 4.0 4.5 - - + +
194B SER* 1.3 78.4 - - - +
196B TRP* 1.3 62.6 + - - +
198B ASN* 3.2 8.7 + - - +
199B LYS* 2.9 45.7 + - + +
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Residues in contact with TRP 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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167B PHE* 3.5 38.8 + + + +
168B ASP* 5.9 0.4 - - - -
170B LEU* 6.0 1.1 - - + -
173B LEU* 4.4 12.6 - - + -
176B ILE* 3.8 41.1 - - + -
178B LEU* 4.6 3.4 - - + -
192B TYR* 2.8 47.4 + + + +
193B LEU* 3.7 7.4 - - + +
194B SER 3.2 0.2 - - - -
195B GLU* 1.3 77.2 - - - +
197B ILE* 1.3 73.4 + - + +
199B LYS* 3.1 10.8 + - - +
200B HIS* 2.9 76.2 + + + -
203B VAL* 4.1 10.1 - - + -
204B VAL* 4.3 11.2 - - + -
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Residues in contact with ILE 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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178B LEU* 4.1 17.0 - - + -
193B LEU* 3.0 27.4 + - + +
194B SER 3.8 3.4 - - - +
196B TRP* 1.3 92.3 - - + +
198B ASN* 1.3 64.2 + - - +
200B HIS 3.1 11.6 + - - +
201B SER* 3.2 14.0 + - - -
204B VAL* 4.1 14.6 - - + -
213B PRO* 3.7 26.9 - - + +
216B ALA* 4.0 22.2 - - + -
225B VAL* 4.0 23.1 - - + -
226B ARG* 3.7 15.6 - - + +
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Residues in contact with ASN 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 SER* 3.0 32.0 + - - +
195B GLU* 3.6 9.2 - - - +
196B TRP 3.2 0.2 - - - -
197B ILE* 1.3 77.2 - - - +
199B LYS* 1.3 61.6 + - + +
200B HIS 3.4 0.4 + - - -
201B SER* 4.4 9.8 + - - -
226B ARG* 3.0 46.1 + - - +
229B ILE* 4.2 11.9 - - - +
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Residues in contact with LYS 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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192B TYR* 5.2 2.6 + - - -
195B GLU* 2.9 52.6 + - + +
196B TRP* 3.1 10.4 + - - +
197B ILE 3.1 0.2 - - - -
198B ASN* 1.3 79.6 - - + +
200B HIS* 1.3 78.3 + - + +
201B SER 3.7 1.3 - - - -
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Residues in contact with HIS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TRP* 2.9 76.8 + + + +
197B ILE 3.1 5.0 + - - +
199B LYS* 1.3 96.4 + - + +
201B SER* 1.3 63.0 + - - +
202B GLY 3.2 3.1 - - - -
203B VAL* 3.0 35.2 + - + +
204B VAL* 3.8 8.5 + - - +
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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