Contacts of the strand formed by residues 188 - 192 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C C7B 3.7 59.7 + + + +
162D ASN* 4.3 19.7 - - - -
163D GLU 2.6 21.5 + - - +
164D VAL* 3.4 2.8 - - + -
165D ILE* 2.6 34.1 + - - +
186D LYS 5.7 0.7 - - - -
187D PHE* 1.3 81.5 - - - +
189D VAL* 1.3 56.7 + - - +
190D ILE* 5.5 0.7 - - + -
212D ILE 3.6 3.6 - - - -
213D GLU* 3.6 38.9 - - + +
215D THR* 5.6 0.4 - - - +
178E SER* 5.4 1.5 + - - -
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ILE* 3.4 12.3 - - + +
167D THR* 3.8 11.2 - - - +
178D LEU* 3.8 29.8 - - + -
187D PHE* 3.6 26.2 - - + -
188D HIS* 1.3 77.4 - - - +
190D ILE* 1.3 65.5 + - - +
191D VAL* 3.7 23.5 + - + -
207D LEU* 4.3 5.8 - - + -
212D ILE* 3.7 19.1 + - + -
213D GLU 3.7 1.7 + - - +
214D THR* 3.3 9.9 - - - +
215D THR 2.9 23.6 + - - -
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Residues in contact with ILE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C C7B 3.6 44.6 - - + -
164D VAL* 3.7 22.0 - - + -
165D ILE 2.5 20.9 + - - +
166D MET* 3.4 8.5 - - + +
167D THR 3.1 23.1 + - - +
188D HIS 5.3 0.9 - - - +
189D VAL* 1.3 73.2 - - - +
191D VAL* 1.3 61.3 + - - +
192D ALA 3.5 1.6 + - - +
215D THR* 3.3 19.1 - - + +
217D MET* 4.2 34.3 - - + -
225D VAL* 3.8 15.3 - - + -
229D VAL* 4.3 7.6 - - + -
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Residues in contact with VAL 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D THR* 3.6 7.6 - - - +
169D GLY 4.5 1.3 - - - +
189D VAL* 3.7 20.8 + - + -
190D ILE* 1.3 70.5 - - - +
192D ALA* 1.3 64.1 + - - +
193D GLU 3.8 1.9 + - - -
200D GLY* 3.5 33.0 - - - +
203D MET* 4.2 22.4 - - + -
204D ALA* 4.4 5.6 - - + +
207D LEU* 4.0 15.5 - - + -
214D THR* 3.7 26.0 - - + -
215D THR 2.9 16.3 + - - +
216D VAL* 3.6 17.3 - - - +
217D MET 3.8 0.5 + - - -
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET* 4.8 9.4 - - + -
167D THR 2.9 12.0 + - - +
168D ILE* 3.6 19.4 - - + +
169D GLY 3.6 20.8 + - - -
190D ILE 3.5 3.3 + - - +
191D VAL* 1.3 76.5 - - - +
193D GLU* 1.3 65.8 + - - +
200D GLY* 4.5 1.4 - - - -
217D MET* 4.2 30.1 - - + -
218D THR 4.3 7.2 - - - +
219D ASP* 5.2 0.4 - - - +
222D ILE* 5.2 3.8 - - + -
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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