Contacts of the strand formed by residues 179 - 187 (chain W) in PDB entry 5O9G
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 179 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J G 5.7 0.5 + - - -
176W PHE* 5.9 0.7 - - - -
178W GLY* 1.3 72.4 - - - -
180W ASP* 1.3 70.0 + - - +
181W ILE* 4.6 4.3 - - - +
182W VAL* 5.5 1.6 - - + -
215W ILE* 3.7 32.1 - - + -
216W LYS 4.1 2.7 - - - -
217W TRP* 4.2 9.2 - - + -
218W THR* 4.4 3.7 - - - +
233W ILE* 4.1 12.3 - - + -
236W VAL* 3.7 20.4 - - + -
237W ARG 2.9 10.9 + - - +
238W GLY* 3.4 31.8 - - - +
239W LEU* 4.0 11.0 - - + -
241W ARG* 4.2 17.6 + - + -
242W LEU* 4.9 19.7 - - + +
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Residues in contact with ASP 180 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178W GLY 3.7 1.4 + - - -
179W ILE* 1.3 73.7 - - - +
181W ILE* 1.3 70.1 + - - +
216W LYS* 2.5 50.4 + - + +
218W THR* 3.5 26.9 + - - +
241W ARG* 2.4 46.5 + - - +
318W GLU* 5.5 3.5 - - - +
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Residues in contact with ILE 181 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179W ILE* 5.0 1.8 - - - -
180W ASP* 1.3 94.4 - - - +
182W VAL* 1.3 67.1 + - - +
183W ILE* 4.2 13.2 - - + -
215W ILE* 3.9 4.5 - - - +
216W LYS* 2.9 44.3 + - + +
222W HIS* 4.2 23.1 - - + +
241W ARG* 4.5 6.1 - - - +
281W PHE* 4.8 14.1 - - + -
284W PHE* 5.2 4.5 - - + -
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Residues in contact with VAL 182 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179W ILE* 5.5 2.9 - - + -
181W ILE* 1.3 79.8 - - - +
183W ILE* 1.3 65.0 + - - +
184W ASN 4.3 8.3 - - - +
213W PHE* 4.9 2.5 - - + -
214W LEU 3.7 11.4 - - - +
215W ILE* 4.0 13.9 - - + -
241W ARG* 4.7 5.4 - - + +
242W LEU* 3.8 36.6 - - + +
245W TYR* 3.7 47.6 - - + -
281W PHE* 3.5 20.6 - - - -
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Residues in contact with ILE 183 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181W ILE* 4.2 14.6 - - + -
182W VAL* 1.3 78.0 - - - +
184W ASN* 1.3 64.3 + - + +
214W LEU* 2.9 33.4 + - + +
216W LYS* 3.7 29.6 - - + +
222W HIS* 4.5 8.1 - - + -
225W ASN* 3.5 26.0 - - - +
245W TYR* 4.1 10.4 + - - -
277W ARG* 5.6 0.7 - - - +
278W LEU* 5.4 4.7 - - + +
281W PHE* 3.2 49.7 - - + +
285W HIS* 5.4 4.9 - - - +
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Residues in contact with ASN 184 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182W VAL* 4.3 3.5 - - - +
183W ILE* 1.3 82.3 - - + +
185W HIS* 1.3 84.6 + - - +
186W ARG* 5.6 1.0 - - - +
213W PHE* 3.6 2.3 - - - +
214W LEU* 2.7 44.4 + - + +
227W TRP* 3.3 28.1 - - + -
278W LEU* 4.3 22.9 - - + +
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Residues in contact with HIS 185 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184W ASN* 1.3 95.0 + - - +
186W ARG* 1.3 67.4 + - - +
212W GLU 3.9 5.8 - - - -
213W PHE* 3.6 25.6 - - + -
227W TRP* 4.0 2.7 - - - -
245W TYR* 2.9 38.6 + + + -
249W PHE* 3.3 45.3 - + - -
252W GLU* 5.0 4.5 - - - -
274W ARG* 3.5 22.7 + - + -
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Residues in contact with ARG 186 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184W ASN* 5.6 0.7 - - - +
185W HIS* 1.3 79.3 - - - +
187W LEU* 1.3 65.6 + - + +
211W TYR* 3.3 17.2 - - - +
212W GLU* 2.7 58.4 + - + +
213W PHE* 4.9 0.2 - - - -
227W TRP* 3.6 57.0 - - + +
249W PHE* 6.5 0.4 - - - -
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Residues in contact with LEU 187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186W ARG* 1.3 83.9 - - + +
188W LYS* 1.3 61.8 + - - +
189W THR 4.6 11.4 - - - +
190W SER* 4.2 22.0 - - - +
210W ASN 3.8 7.2 - - - +
211W TYR* 3.6 20.4 - - + -
212W GLU* 3.2 20.0 - - - +
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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