Contacts of the strand formed by residues 235 - 241 (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 GLU 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B ILE* 3.1 12.3 - - - +
232B TYR* 3.3 17.3 + - - +
234B GLN* 1.3 80.3 - - - +
236B GLU* 1.3 62.3 + - - +
237B ASP* 3.2 9.9 + - + +
251B THR* 4.2 20.6 - - + +
253B LEU* 6.4 2.2 - - + -
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Residues in contact with GLU 236 (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 19.5 + - + +
229B ARG* 3.2 45.9 + - + +
230B ASP 3.8 5.4 - - - +
231B ILE* 4.3 4.3 - - + -
234B GLN 3.6 3.4 + - - -
235B GLU* 1.3 72.6 + - - +
237B ASP* 1.3 56.9 + - - +
238B LEU 4.0 12.6 - - - +
239B ARG* 2.8 45.1 + - - +
250B VAL* 3.0 24.0 - - + +
251B THR* 3.2 8.4 - - - +
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Residues in contact with ASP 237 (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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73A MET* 3.8 19.3 - - - +
230B ASP* 3.0 30.9 + - - +
232B TYR* 3.8 13.6 + - + +
235B GLU* 3.2 5.3 + - + +
236B GLU* 1.3 71.4 - - - +
238B LEU* 1.3 66.5 + - - +
249B ALA* 3.3 1.7 - - - -
250B VAL* 2.3 39.8 + - - -
251B THR* 3.0 30.9 + - + +
253B LEU* 4.4 8.1 - - + -
254B GLY* 3.0 29.3 - - - +
257B ASP* 4.9 1.6 - - - +
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Residues in contact with LEU 238 (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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228B HIS* 5.5 1.8 - - + -
229B ARG* 4.0 2.8 - - - -
230B ASP* 3.3 42.1 + - + +
236B GLU* 4.0 4.2 - - - +
237B ASP* 1.3 90.5 + - - +
239B ARG* 1.3 67.1 + - - +
247B TYR* 3.9 24.2 - - + -
248B ARG 3.1 20.0 - - - +
249B ALA* 4.2 0.4 - - - +
250B VAL* 3.3 6.1 - - - +
254B GLY 3.6 18.4 - - - +
257B ASP* 3.9 24.7 - - + +
258B ALA* 3.6 20.4 - - + +
261B TRP* 5.3 6.3 - - + -
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Residues in contact with ARG 239 (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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225B ARG* 5.8 1.8 - - - +
227B LEU* 3.5 23.2 - - + +
228B HIS 3.5 15.7 - - - +
229B ARG* 3.1 31.2 - - + +
230B ASP 5.2 0.2 - - - +
236B GLU* 2.8 33.1 + - - +
238B LEU* 1.3 76.4 - - - +
240B PHE* 1.3 70.5 + - - +
241B ASP* 4.6 6.5 - - - +
247B TYR* 2.8 21.7 - - - -
248B ARG* 2.7 31.9 + - + +
250B VAL* 3.5 24.8 - - + +
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Residues in contact with PHE 240 (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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226B PHE* 4.4 15.3 - + - -
227B LEU* 3.2 9.1 - - - +
228B HIS* 3.0 29.6 + - + -
239B ARG* 1.3 82.4 - - - +
241B ASP* 1.3 81.9 - - - +
242B SER* 3.8 7.2 - - - -
245B GLY* 4.1 16.8 - - - -
246B GLU 3.9 12.6 - - - -
247B TYR* 3.3 40.6 - + + -
248B ARG* 4.6 1.1 - - - +
268B LEU* 3.6 20.0 - - + -
271B ARG* 3.3 44.2 - - + -
272B ARG* 4.1 6.5 - - + -
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Residues in contact with ASP 241 (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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225B ARG* 2.4 43.9 + - - +
226B PHE 3.7 4.9 - - - +
227B LEU* 3.7 10.6 - - + +
239B ARG* 4.6 6.9 - - - +
240B PHE* 1.3 82.8 - - - +
242B SER* 1.3 75.9 + - - +
243B ASP* 2.7 29.5 + - - +
244B VAL* 2.8 21.6 + - + +
245B GLY 2.7 31.2 + - - -
246B GLU 4.3 3.0 + - - -
248B ARG* 6.3 0.4 - - - +
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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