Contacts of the strand formed by residues 182 - 192 (chain F) in PDB entry 4BEI
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 GLY 182 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177F VAL* 3.7 21.9 - - - +
181F GLY* 1.3 74.5 - - - -
183F PHE* 1.3 58.2 + - - -
237F ASN* 3.5 6.5 + - - +
238F PHE* 2.7 42.7 + - - +
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Residues in contact with PHE 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E GLN* 3.5 26.5 - - + -
174F ILE* 4.5 9.2 - - - +
177F VAL* 4.4 1.3 - - - +
182F GLY* 1.3 72.1 - - - -
184F VAL* 1.3 63.7 + - - +
185F PRO* 3.9 30.8 - - + +
235F GLY* 3.6 22.9 - - - -
236F ILE 3.5 12.1 - - - -
237F ASN* 3.8 15.3 - - + +
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Residues in contact with VAL 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ASN* 3.7 21.5 - - - +
174F ILE* 4.0 18.4 - - + +
177F VAL* 3.8 23.6 - - + -
183F PHE* 1.3 78.5 - - - +
185F PRO* 1.3 70.6 - - + +
186F PHE* 3.5 33.4 - - + -
235F GLY* 3.4 1.5 - - - -
236F ILE 2.9 28.6 + - - -
238F PHE* 3.8 19.5 - - + -
268F VAL* 4.4 7.9 - - + -
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Residues in contact with PRO 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ASN* 4.1 0.6 - - - +
171F GLN* 3.2 42.8 + - - +
172F PHE* 3.6 26.2 - - + +
174F ILE* 4.5 7.4 - - + -
183F PHE* 3.9 24.5 - - + +
184F VAL* 1.3 92.7 - - + +
186F PHE* 1.3 64.4 + - - +
233F VAL* 4.0 12.1 - - + -
235F GLY* 3.7 8.1 - - - -
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Residues in contact with PHE 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ILE* 4.7 2.7 - - + -
169F LYS 3.3 8.5 - - - +
170F ASN* 3.5 35.0 - - + -
171F GLN* 4.7 0.2 - - - -
184F VAL* 3.5 37.2 - - + -
185F PRO* 1.3 76.3 - - - +
187F THR* 1.3 66.3 + - - +
188F VAL* 3.8 3.3 + - + +
204F MET* 4.5 16.8 - - + -
216F VAL* 5.6 1.1 - - + -
233F VAL* 3.4 4.0 - - - -
234F ARG* 2.8 47.7 + - - +
235F GLY 5.1 0.2 - - - -
236F ILE* 3.7 19.1 - - + -
249F ILE* 3.7 27.4 - - + -
266F MET* 4.0 27.1 - - + -
268F VAL* 4.1 7.2 - - + -
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Residues in contact with THR 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ASP 3.5 2.3 + - - +
168F ILE* 3.3 7.1 - - - +
169F LYS* 3.0 52.0 + - - +
171F GLN* 3.6 37.0 - - + +
186F PHE* 1.3 74.0 - - - +
188F VAL* 1.3 62.6 + - - +
189F ASP* 4.4 11.7 + - - -
232F LYS 3.7 4.5 - - - -
233F VAL* 4.4 10.1 - - + +
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Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ASP 3.6 2.7 - - - -
168F ILE* 4.1 15.3 - - + -
186F PHE 4.1 9.4 - - - +
187F THR* 1.3 78.9 - - - +
189F ASP* 1.3 65.4 + - - +
190F LEU* 3.7 22.9 - - + -
202F PHE* 4.0 20.6 - - + -
204F MET* 4.2 22.2 - - + -
230F TYR* 4.7 10.1 - - + -
231F SER* 3.4 4.0 - - - -
232F LYS* 2.8 46.9 + - + +
234F ARG* 4.4 10.3 - - + -
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Residues in contact with ASP 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F THR* 3.8 1.9 - - - +
166F ILE* 3.6 0.9 - - - -
167F ASP* 2.7 61.9 + - + +
169F LYS* 5.6 2.6 + - - -
187F THR* 4.4 13.2 + - - -
188F VAL* 1.3 76.6 - - - +
190F LEU* 1.3 62.3 + - - +
191F ASN* 3.9 2.5 + - + +
229F THR* 4.2 9.3 - - + +
230F TYR 3.5 1.6 - - - -
231F SER* 2.6 30.5 + - - -
232F LYS 5.3 0.2 - - - +
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Residues in contact with LEU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LEU* 4.4 5.4 - - + -
165F THR 3.4 5.4 - - - +
166F ILE* 4.2 29.6 - - + -
168F ILE* 4.7 2.7 - - + -
188F VAL* 3.7 21.3 - - + -
189F ASP* 1.3 77.7 - - - +
191F ASN* 1.3 59.8 + - - +
192F ASN 3.9 1.6 + - - -
200F VAL* 4.5 10.5 - - + -
202F PHE* 4.4 22.4 - - + -
222F TRP* 5.9 1.1 - - + -
224F ILE* 4.2 18.6 - - + +
228F ASP 4.1 0.3 - - - +
229F THR* 3.5 4.9 - - - +
230F TYR* 2.9 59.0 + - + +
253F VAL* 4.4 11.4 - - + -
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Residues in contact with ASN 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F GLY 3.5 0.7 - - - +
164F LEU* 3.5 3.1 - - - -
165F THR* 2.8 56.3 + - + +
189F ASP* 3.9 3.7 - - + +
190F LEU* 1.3 71.2 - - - +
192F ASN* 1.3 71.2 + - - +
193F GLY* 3.2 11.1 + - - +
227F GLY* 4.2 6.1 - - - +
228F ASP 3.5 9.8 - - - +
229F THR* 4.0 17.1 + - + -
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Residues in contact with ASN 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LEU* 3.5 12.1 - - + +
190F LEU 3.9 1.0 + - - -
191F ASN* 1.3 72.8 + - - +
193F GLY* 1.3 59.4 + - - +
194F ARG* 3.0 30.6 + - - +
196F GLY 3.2 19.7 + - - -
198F ALA* 3.4 14.4 - - - +
224F ILE* 2.8 44.5 + - + -
225F ALA 3.2 11.3 + - - +
226F SER* 4.4 1.6 - - - -
227F GLY* 3.0 28.8 + - - -
228F ASP 3.1 8.1 + - - +
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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