Contacts of the strand formed by residues 188 - 192 (chain C) in PDB entry 6O81
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 HIS 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C ASN* 4.5 19.5 - - - -
163C GLU 2.5 22.5 + - - +
164C VAL* 3.3 5.6 - - + +
165C ILE* 2.8 35.6 + - - +
186C LYS 5.7 0.4 - - - -
187C PHE* 1.3 80.4 - - - +
189C VAL* 1.3 60.2 + - - +
190C ILE* 5.9 0.7 - - + -
212C ILE 3.6 3.1 - - - -
213C GLU* 3.5 38.6 - - + +
215C THR* 5.7 0.2 - - + -
401C C7B 3.2 58.5 + + + +
178F SER* 5.3 2.0 + - - -
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ILE* 3.3 11.0 - - + +
167C THR* 4.2 7.9 - - - +
178C LEU* 3.8 22.4 - - + -
187C PHE* 3.6 24.2 - - + -
188C HIS* 1.3 79.1 - - - +
190C ILE* 1.3 63.2 + - - +
191C VAL* 3.8 16.2 - - + -
207C LEU* 3.8 23.3 - - + -
212C ILE* 3.8 19.1 + - + +
213C GLU 3.9 1.6 + - - +
214C THR* 3.0 14.8 + - - +
215C THR* 2.9 25.2 + - - -
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C VAL* 4.9 7.2 - - + -
165C ILE 2.4 28.8 + - - +
166C MET* 3.4 17.4 - - + +
167C THR 3.0 27.7 + - - +
188C HIS 5.7 0.2 - - - -
189C VAL* 1.3 68.1 - - - +
191C VAL* 1.3 63.2 + - - +
192C ALA 3.9 0.2 + - - -
215C THR* 3.4 19.1 - - - +
217C MET* 3.6 31.0 - - + -
225C VAL* 3.9 14.4 - - + -
229C VAL* 4.2 16.4 - - + -
401C C7B 3.7 41.3 - - + -
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Residues in contact with VAL 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C THR* 3.7 7.6 - - - +
169C GLY 5.0 1.6 - - - +
189C VAL* 3.8 14.4 - - + -
190C ILE* 1.3 73.9 - - - +
192C ALA* 1.3 64.4 + - - +
193C GLU 3.9 0.6 + - - +
200C GLY* 3.3 38.1 - - - +
203C MET* 4.8 13.0 - - - -
204C ALA* 4.4 16.8 - - + +
207C LEU* 4.6 7.9 - - + -
214C THR* 3.3 21.5 - - - +
215C THR 2.9 11.6 + - - +
216C VAL* 3.4 6.0 - - + +
217C MET* 2.9 28.1 + - - +
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Residues in contact with ALA 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C MET* 4.3 22.9 - - + -
167C THR 3.2 14.1 + - - +
168C ILE* 3.4 28.2 - - + +
169C GLY 3.8 8.1 + - - -
190C ILE* 3.9 1.6 + - + -
191C VAL* 1.3 77.6 - - - +
193C GLU* 1.3 62.7 + - - +
200C GLY* 4.8 0.9 - - - -
217C MET* 3.3 9.0 - - + -
218C THR 3.4 19.7 - - - +
219C ASP* 4.4 2.9 - - - -
222C ILE* 4.8 0.9 - - + -
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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
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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