Contacts of the strand formed by residues 211 - 220 (chain F) in PDB entry 4BQ7
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 THR 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168E ASP* 3.1 17.1 - - - +
169F PRO* 3.1 34.5 - - - +
181F CYS 3.6 0.8 + - - -
182F LYS* 2.5 50.8 + - + +
184F GLU* 4.6 7.0 - - + -
201F ASN* 3.9 6.8 - - - +
202F VAL 3.3 11.2 - - - -
203F PRO* 3.9 20.0 - - + -
204F VAL* 4.4 1.1 - - - +
208F SER 4.5 0.4 - - - +
209F SER 3.5 3.7 + - - +
210F ALA* 1.3 78.2 - - - +
212F ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 212 (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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167E GLY* 5.4 4.3 - - - -
168E ASP* 4.0 13.0 - - - +
169F PRO* 4.3 7.2 - - - -
201F ASN* 3.2 4.8 - - - -
202F VAL* 2.8 39.1 + - - +
204F VAL* 5.4 2.7 - - + -
211F THR* 1.3 75.9 - - - +
213F THR* 1.3 60.9 + - - +
288F TYR* 3.3 42.6 - - + -
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Residues in contact with THR 213 (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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165E LEU* 3.4 17.4 - - + +
166E PHE* 6.1 0.3 - - - -
169F PRO* 3.8 6.3 - - - +
199F VAL* 4.1 8.3 - - + -
200F THR 3.4 8.5 - - - +
201F ASN* 2.7 17.8 + - - +
212F ALA* 1.3 72.2 - - - +
214F ASN* 1.3 59.2 + - - +
215F LYS 3.4 25.6 - - - +
216F ILE* 3.8 19.3 - - + -
288F TYR* 3.4 11.3 - - - +
289F LEU* 2.8 47.8 + - + +
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Residues in contact with ASN 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991B ASP* 4.9 0.5 - - - +
200F THR* 3.0 33.5 + - - +
202F VAL* 4.0 31.6 - - + +
212F ALA 3.8 1.0 + - - -
213F THR* 1.3 74.3 - - - +
215F LYS* 1.4 63.3 + - - +
235F VAL* 3.2 7.3 - - - +
236F THR* 3.1 39.8 + - - +
288F TYR* 4.9 3.4 - - + -
289F LEU* 3.9 5.6 - - - -
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Residues in contact with LYS 215 (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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990B LYS* 3.7 27.3 - - - +
991B ASP* 3.1 19.8 + - - -
1009B GLN* 3.2 42.7 - - + +
1010B PRO 4.7 1.6 + - - -
199F VAL* 3.3 6.1 - - - -
200F THR* 3.1 34.1 + - - -
213F THR* 3.4 8.5 - - - +
214F ASN* 1.4 84.2 + - - +
216F ILE* 1.3 64.4 + - - +
217F THR* 4.0 1.8 - - - +
233F GLN* 3.6 25.5 - - - +
234F ALA 3.4 10.8 - - - +
235F VAL* 3.8 18.6 - - + -
289F LEU* 4.0 0.7 - - - -
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Residues in contact with ILE 216 (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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165E LEU* 6.2 0.4 - - + -
197F VAL* 4.8 0.7 - - + -
198F GLN 3.7 3.6 - - - +
199F VAL* 3.9 7.9 - - + -
213F THR* 3.8 13.9 - - + -
215F LYS* 1.3 78.6 - - - +
217F THR* 1.3 63.6 + - - +
218F ILE* 3.8 27.8 - - + -
232F TYR* 3.8 2.2 - - + +
233F GLN* 3.3 5.4 - - - +
234F ALA* 2.9 34.6 + - + +
282F VAL* 4.1 18.8 - - + -
289F LEU* 3.7 25.1 - - + +
290F THR 3.7 23.8 - - - +
291F LEU* 3.8 29.8 - - + -
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Residues in contact with THR 217 (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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1009B GLN* 2.9 20.4 + - - -
1010B PRO* 3.8 13.9 - - + -
1046B LEU* 3.8 23.6 - - + -
196F SER 3.8 0.7 - - - +
197F VAL* 3.4 5.5 - - - +
198F GLN* 2.8 39.8 + - - +
215F LYS* 4.0 0.2 - - - +
216F ILE* 1.3 71.3 - - - +
218F ILE* 1.3 66.0 + - - +
219F ILE* 4.4 7.9 - - + -
231F VAL* 4.0 13.9 - - + -
232F TYR 3.4 7.6 - - - +
233F GLN* 2.8 27.7 + - - +
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Residues in contact with ILE 218 (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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195F LEU* 3.8 18.2 - - + -
196F SER 3.3 5.8 - - - +
197F VAL* 4.2 14.6 - - + -
216F ILE* 3.8 20.4 - - + -
217F THR* 1.3 76.6 - - - +
219F ILE* 1.3 63.7 + - - +
220F PHE* 3.5 31.0 - - + -
230F LYS 3.8 1.2 - - - +
231F VAL* 3.3 4.9 - - - +
232F TYR* 2.8 68.1 + - + +
271F MET* 3.8 13.5 - - + -
280F VAL* 3.9 22.9 - - + -
282F VAL* 4.3 1.1 - - + -
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Residues in contact with ILE 219 (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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1010B PRO* 5.9 1.6 - - + -
1043B GLY 4.2 5.4 - - - +
1044B ASN* 3.4 52.9 - - + +
1045B ARG 4.2 0.4 - - - +
1046B LEU* 4.5 20.0 - - + -
195F LEU* 3.4 7.2 - - - +
196F SER* 2.7 46.7 + - - +
217F THR* 4.4 11.4 - - + -
218F ILE* 1.3 74.6 - - - +
220F PHE* 1.3 62.7 + - - +
221F LYS* 3.4 9.2 + - + +
229F GLN* 4.0 21.5 - - + +
230F LYS 3.6 3.6 - - - +
231F VAL* 4.2 15.3 - - + -
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Residues in contact with PHE 220 (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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194F TYR 4.3 0.4 - - - -
195F LEU* 3.5 23.3 - - + -
218F ILE* 3.5 27.8 - - + -
219F ILE* 1.3 69.9 - - - +
221F LYS* 1.3 66.2 + - - +
227F THR* 5.4 0.2 - - + -
228F ASP 4.2 1.2 - - - +
229F GLN* 3.4 2.9 - - - +
230F LYS 2.9 38.2 + - - +
232F TYR* 4.8 0.2 - - + -
243F PHE* 3.9 21.5 - + - -
258F LEU* 3.7 26.9 - - + -
271F MET* 3.7 40.2 - - + -
273F ALA* 3.8 21.8 - - + -
275F TYR* 3.7 18.8 - - - +
276F ILE* 4.7 0.9 - - + -
278F THR* 5.3 1.6 - - + -
280F VAL* 4.4 9.0 - - + -
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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