Contacts of the strand formed by residues 233 - 243 (chain B) in PDB entry 4HH3
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 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B VAL 3.3 9.0 - - - +
226B LEU* 3.7 30.4 - - + +
231B GLN 4.0 1.6 + - - -
232B LYS* 1.3 72.8 - - - +
234B LEU* 1.3 64.5 + - - +
255B PRO* 3.9 1.4 - - - +
256B ALA* 2.9 26.6 + - + -
257B ASP* 3.1 44.9 + - - +
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Residues in contact with LEU 234 (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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182B LEU* 3.9 27.6 - - + +
183B LEU* 4.1 14.1 - - + -
199B PHE* 4.5 6.7 - - + -
224B GLU* 3.6 5.7 - - - +
225B VAL* 2.8 39.3 + - + +
227B ALA* 3.8 23.3 - - + -
232B LYS* 3.7 21.8 - - + +
233B ARG* 1.3 84.3 - - - +
235B LEU* 1.3 66.0 + - - +
236B VAL 4.2 0.4 - - - -
253B ILE* 3.7 20.6 - - + -
254B ASP 3.3 13.7 - - - +
255B PRO* 4.0 8.5 - - + -
256B ALA* 3.8 3.4 - - - +
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Residues in contact with LEU 235 (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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222B PRO* 3.6 31.4 - - + +
223B VAL 3.6 1.1 - - - -
224B GLU* 4.1 24.9 - - + +
234B LEU* 1.3 79.1 - - - +
236B VAL* 1.3 62.9 + - - +
237B VAL* 4.2 2.0 - - + +
252B GLN 3.6 1.6 - - - +
253B ILE* 3.4 5.2 - - - +
254B ASP* 2.7 45.3 + - + +
255B PRO 4.3 6.1 - - - +
256B ALA* 3.7 26.2 - - + +
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Residues in contact with VAL 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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199B PHE* 4.5 12.8 - - + -
207B PHE* 5.4 2.5 - - + -
211B MET* 4.0 17.5 - - + -
222B PRO* 3.3 3.6 - - - +
223B VAL* 3.0 38.7 + - + +
225B VAL* 3.8 28.0 - - + -
235B LEU* 1.3 77.4 - - - +
237B VAL* 1.3 65.4 + - - +
238B PRO* 3.6 6.2 - - - +
251B CYS* 3.7 34.5 - - + -
252B GLN 3.5 2.5 - - - +
253B ILE* 4.4 17.9 - - + -
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Residues in contact with VAL 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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220B ALA* 3.5 45.8 - - + +
222B PRO* 4.0 16.4 - - + -
235B LEU* 5.3 2.0 - - + +
236B VAL* 1.3 77.8 - - - +
238B PRO* 1.3 65.9 - - - +
239B ARG* 3.8 24.1 + - + +
250B LEU 3.6 1.2 - - - +
251B CYS* 3.5 1.2 - - - -
252B GLN* 2.9 47.2 + - + +
254B ASP* 5.7 4.7 - - - +
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Residues in contact with PRO 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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211B MET* 3.6 44.9 - - + +
214B LEU* 3.8 26.0 - - + -
215B ALA* 3.8 13.0 - - + +
220B ALA* 5.6 5.0 - - - -
221B ALA 5.5 1.1 - - - +
236B VAL 3.6 9.2 - - - +
237B VAL* 1.3 90.1 - - + +
239B ARG* 1.3 68.3 + - - +
249B LEU* 3.7 19.3 - - + -
250B LEU 3.5 7.0 - - - +
251B CYS* 4.6 1.8 - - - -
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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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153A VAL* 5.6 2.5 - - + -
157A VAL* 3.4 37.0 - - - +
215B ALA* 4.1 4.0 - - - -
220B ALA* 5.0 8.4 - - - +
237B VAL* 3.8 21.2 + - - +
238B PRO* 1.3 79.2 - - - +
240B VAL* 1.3 65.6 + - - +
241B PHE* 4.4 5.1 - - + -
248B LEU 4.0 0.3 - - - +
249B LEU* 3.5 2.9 - - - +
250B LEU* 2.8 47.7 + - + +
252B GLN* 2.6 34.3 + - - +
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Residues in contact with VAL 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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167B MET* 3.4 40.2 - - + -
212B THR* 4.5 14.4 - - + +
215B ALA* 3.7 23.7 + - + +
239B ARG* 1.3 80.1 - - - +
241B PHE* 1.3 71.1 + - - +
247B ARG* 6.0 0.2 - - + -
248B LEU 3.4 2.7 - - - +
249B LEU* 3.9 15.3 - - + -
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Residues in contact with PHE 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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149A THR* 3.7 31.0 - - + -
150A ARG* 4.5 11.4 - - - -
153A VAL* 4.0 33.0 - - + -
154A VAL* 6.4 0.4 - - + -
164B LEU* 3.8 14.8 - - + -
239B ARG* 4.4 7.0 - - + -
240B VAL* 1.3 84.2 - - - +
242B ARG* 1.3 66.0 + - - +
243B ALA* 4.1 2.2 - - + -
247B ARG* 3.7 1.9 - - - +
248B LEU* 2.9 71.5 + - + +
250B LEU* 4.0 24.5 - - + -
270C GLN* 6.1 2.9 - - + +
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Residues in contact with ARG 242 (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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149A THR* 3.7 13.0 + - - +
241B PHE* 1.3 77.9 - - - +
243B ALA* 1.3 61.4 + - - +
244B ALA 4.0 1.2 + - - -
245B GLY* 4.7 11.8 + - - +
246B GLU 3.4 4.5 - - - +
247B ARG* 4.3 20.9 - - + +
268C ASP* 4.6 3.8 - - - +
269C PRO 5.4 2.8 - - - +
270C GLN* 5.3 4.7 - - - +
274C GLY 6.1 0.2 - - - -
275C ALA* 3.6 24.6 - - - +
303C SER* 3.9 29.3 + - - +
322C SER* 2.9 33.5 + - - -
323C ARG* 2.9 24.0 + - - +
324C THR* 4.0 4.4 + - - -
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Residues in contact with ALA 243 (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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146A GLU* 3.6 27.1 - - + +
149A THR* 3.7 26.7 - - + -
241B PHE* 4.1 3.4 - - + -
242B ARG* 1.3 75.6 - - - +
244B ALA* 1.3 71.7 + - - +
245B GLY 3.3 0.2 - - - -
246B GLU* 2.7 30.1 + - - +
248B LEU* 4.1 15.3 - - + -
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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