Contacts of the strand formed by residues 223 - 232 (chain B) in PDB entry 1HQR
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 ARG 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B PHE* 3.2 41.9 + - + +
222B GLU* 1.3 86.7 - - + +
224B VAL* 1.3 107.5 + - - +
242B SER* 5.2 6.9 - - - -
275B VAL* 4.5 26.0 - - - +
280B ARG* 4.0 8.9 - - - +
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B HIS 2.9 25.1 - - - +
217B PHE* 3.8 21.3 - - + +
218B PHE* 5.0 2.9 - - - -
221B THR* 4.1 3.1 - - - +
223B ARG* 1.3 112.3 + - - +
225B ARG* 1.3 78.0 + - - +
275B VAL* 4.3 8.5 - - + +
279B CYS* 3.7 26.2 - - + -
280B ARG* 3.8 39.7 - - + +
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Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLU 3.7 0.9 - - - +
215B CYS* 3.6 3.5 - - - -
216B HIS* 2.9 52.6 + - + +
218B PHE* 4.7 15.6 - - + -
223B ARG* 4.8 0.4 - - - +
224B VAL* 1.3 85.8 - - - +
226B PHE* 1.3 70.3 + - - +
227B LEU* 4.7 17.9 - - - +
239B ARG* 5.8 1.8 - - - +
241B ASP* 2.4 34.4 + - - +
242B SER* 4.1 6.3 - - - +
243B ASP* 3.4 21.0 + - - +
275B VAL* 5.0 1.8 - - - -
279B CYS* 4.8 0.2 - - - -
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B TYR* 3.7 32.8 - + + -
214B GLU 3.4 17.0 - - - -
225B ARG* 1.3 75.8 - - - +
227B LEU* 1.3 67.5 + - - +
228B HIS* 4.5 12.1 - - + -
240B PHE* 4.4 12.3 - + - -
241B ASP* 3.7 5.7 - - - +
242B SER* 2.8 34.1 + - - +
271B ARG* 4.0 26.7 - - - +
274B ALA* 3.8 17.7 - - + -
275B VAL* 4.0 15.7 - - + +
278B TYR* 3.3 37.2 - + - -
279B CYS* 3.9 9.0 - - - -
412C ILE* 3.9 10.8 - - + -
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LYS 3.4 2.3 - - - +
214B GLU* 2.9 65.7 + - + +
216B HIS* 4.9 7.6 - - + +
225B ARG* 4.7 18.2 - - - +
226B PHE* 1.3 81.7 - - - +
228B HIS* 1.3 58.4 + - - +
229B ARG* 3.4 30.5 - - + +
239B ARG* 3.5 30.1 - - + +
240B PHE 3.2 23.1 - - - +
241B ASP* 3.7 18.2 - - + +
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Residues in contact with HIS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ASP* 3.0 23.5 + - - -
212B LYS 3.4 7.0 - - - -
213B TYR* 3.4 45.4 + + + -
226B PHE* 4.5 8.6 - - + -
227B LEU* 1.3 73.4 - - - +
229B ARG* 1.3 88.6 + - - +
230B ASP* 4.0 13.5 + - + -
238B LEU* 5.5 1.6 - - + -
239B ARG* 3.5 7.1 - - - +
240B PHE* 3.0 35.2 + - + -
247B TYR* 2.7 42.0 + + - +
271B ARG* 4.3 1.1 - - - -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 4.9 6.9 + - - +
143A HIS* 4.4 17.1 - - - -
210B GLN 3.6 1.7 - - - +
211B ASP* 3.6 1.0 - - - -
212B LYS* 3.0 36.5 + - + +
214B GLU* 3.7 21.8 + - - +
227B LEU* 3.4 26.8 - - + +
228B HIS* 1.3 86.9 - - - +
230B ASP* 1.3 61.8 + - - +
231B ILE* 3.5 12.9 - - + +
236B GLU* 3.2 35.3 + - + +
238B LEU 4.0 3.1 - - - -
239B ARG* 3.1 29.5 - - + +
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Residues in contact with ASP 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ASN* 5.2 7.4 + - - +
73A MET* 4.8 9.7 - - - +
209B GLN* 3.4 22.7 + - - +
211B ASP* 2.6 28.8 - - - +
228B HIS* 4.0 11.5 + - + +
229B ARG* 1.3 71.9 - - - +
231B ILE* 1.3 59.5 + - - +
236B GLU* 3.8 1.4 - - - -
237B ASP* 3.0 35.4 + - - +
238B LEU* 3.3 38.5 + - + +
257B ASP* 5.6 1.7 - - - +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 3.7 35.0 - - + +
209B GLN* 3.4 9.0 - - - +
210B GLN* 2.8 63.7 + - + +
212B LYS* 3.9 20.2 - - + -
229B ARG* 3.5 15.0 - - + +
230B ASP* 1.3 77.7 - - - +
232B TYR* 1.3 60.2 + - - +
233B ASN 3.5 1.8 + - - +
234B GLN* 3.4 31.0 - - - +
235B GLU 3.1 19.7 - - - +
236B GLU* 4.7 2.0 - - - -
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Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.9 11.7 - - + -
73A MET* 3.9 32.8 - - + -
74A THR* 3.3 29.7 + - - -
77A SER* 3.0 32.7 + - - -
80A THR* 3.3 21.2 + - + -
207B PHE* 3.7 14.2 - - + -
208B LEU 3.2 16.6 - - - -
209B GLN* 4.2 5.1 + - - +
231B ILE* 1.3 69.9 - - - +
233B ASN* 1.3 77.7 + - - +
234B GLN 2.6 19.2 + - - -
235B GLU* 3.3 17.6 + - + +
237B ASP* 3.8 6.0 + - + +
253B LEU* 3.8 22.0 - - + -
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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