Contacts of the strand formed by residues 233 - 245 (chain B) in PDB entry 3RT0
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 HIS 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B LYS* 3.9 36.1 - - + -
215B LEU 3.3 16.8 - - - +
216B PRO* 3.9 13.3 - - + +
217B ILE 4.3 0.7 - - - +
231B LEU* 3.3 22.1 - - - +
232B THR* 1.3 122.5 + - + +
234B LEU* 1.3 64.6 + - - +
270B LYS* 3.9 20.7 + - - +
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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 TYR* 3.3 30.5 - - + +
184B LEU 5.9 0.2 - - - +
214B LYS* 3.6 2.8 - - - -
215B LEU* 2.7 39.0 + - - +
217B ILE* 3.3 33.2 - - + -
220B LEU* 3.9 22.2 - - + -
231B LEU* 4.1 2.7 - - + -
233B HIS* 1.3 78.6 - - - +
235B THR* 1.3 65.6 + - - +
335B CYS* 4.0 7.4 - - + -
336B SER* 3.9 27.6 - - - +
337B SER* 3.9 21.5 - - - +
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Residues in contact with THR 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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184B LEU 5.9 1.1 - - - +
186B CYS* 4.2 27.3 - - + +
211B HIS* 3.5 40.2 + - + +
213B LEU 3.3 8.1 + - - -
214B LYS* 4.8 5.7 - - - +
234B LEU* 1.3 74.8 - - - +
236B GLY* 1.3 60.3 + - - +
237B HIS* 4.3 4.3 + - + -
334B VAL 4.1 0.5 - - - +
335B CYS* 3.4 21.1 - - - +
336B SER 4.8 0.5 + - - -
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Residues in contact with GLY 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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212B PHE* 3.1 9.5 + - - +
213B LEU* 2.7 44.4 + - - +
215B LEU* 4.1 18.8 - - - -
234B LEU 3.6 0.8 + - - -
235B THR* 1.3 75.6 + - - +
237B HIS* 1.3 65.2 + - - -
333B LEU* 5.7 1.1 - - - -
334B VAL 3.6 6.3 - - - -
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Residues in contact with HIS 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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186B CYS* 2.7 46.2 + - - +
188B PRO* 3.6 30.2 - - + +
209B SER 3.8 3.6 - - - -
210B PRO* 3.7 7.5 - - + +
211B HIS* 2.9 40.8 + - - -
213B LEU* 5.7 0.4 - - - -
235B THR* 4.3 7.8 - - + +
236B GLY* 1.3 73.0 - - - -
238B PHE* 1.3 59.5 + - - +
239B PHE* 3.6 23.7 - + + -
332B ALA 3.6 1.4 - - - +
333B LEU* 3.2 8.9 - - - -
334B VAL* 3.0 50.7 + - + +
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Residues in contact with PHE 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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207B ALA* 3.9 17.5 - - + -
208B VAL* 3.2 4.5 - - - +
209B SER* 2.7 50.2 + - - +
212B PHE* 4.3 12.3 - + + -
213B LEU* 5.3 2.0 - - + -
236B GLY 4.1 0.4 + - - -
237B HIS* 1.3 71.8 - - - +
239B PHE* 1.3 67.6 + - - +
240B GLY 3.8 13.2 - - - -
242B TYR* 3.3 26.7 - - - -
258B LEU* 3.8 12.6 - - + -
259B HIS* 3.5 39.0 - + + -
262B LEU* 4.0 10.1 - - + -
331B VAL* 3.4 25.8 - - + -
332B ALA 3.8 1.6 - - - -
333B LEU* 3.9 19.1 - - + -
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Residues in contact with PHE 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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188B PRO* 4.9 10.3 - - + -
189B LEU 5.8 0.2 - - - -
190B TRP* 3.8 22.9 - + + -
207B ALA 3.4 3.4 - - - -
208B VAL* 3.7 32.1 - - + -
210B PRO* 6.0 0.7 - - + -
237B HIS* 3.6 33.0 - + + -
238B PHE* 1.3 82.7 - - - +
240B GLY* 1.3 58.8 + - - +
331B VAL* 3.3 3.6 - - - +
332B ALA* 2.8 46.3 + - + +
334B VAL* 3.8 17.5 - - + -
429B LEU* 3.6 11.4 - - + +
497B ILE* 4.0 13.7 - - + -
499B ILE* 3.6 37.5 - - + -
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Residues in contact with GLY 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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206B PHE* 3.2 6.9 - - - +
207B ALA 2.8 35.2 + - - +
238B PHE* 3.8 2.4 - - - -
239B PHE* 1.3 74.6 - - - +
241B VAL* 1.3 64.5 + - - +
242B TYR* 3.8 20.9 - - - -
330B VAL 3.3 9.4 - - - -
331B VAL* 4.2 1.8 - - - -
429B LEU* 4.4 0.9 - - - -
497B ILE* 3.7 2.2 - - - +
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Residues in contact with VAL 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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204B ASP* 5.6 0.2 - - - +
205B ALA 3.7 8.5 - - - +
206B PHE* 4.5 4.0 - - + -
240B GLY* 1.3 78.9 - - - +
242B TYR* 1.3 71.0 + - - +
243B ASP 4.1 1.6 + - - +
328B THR* 4.3 1.7 + - - -
329B ALA* 3.6 1.0 - - - -
330B VAL* 2.9 43.3 + - + +
347B SER* 4.8 1.5 + - - +
429B LEU* 3.9 22.0 - - + +
430B ALA* 4.2 1.8 - - - -
431B SER* 4.0 28.5 - - - +
495B SER* 4.0 17.0 - - - +
497B ILE* 3.7 27.4 - - + +
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Residues in contact with TYR 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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204B ASP* 3.4 4.3 - - - -
205B ALA 2.8 49.0 + - - +
207B ALA* 4.0 7.8 - - + +
238B PHE* 3.3 32.7 - - - -
240B GLY* 3.8 18.8 - - - -
241B VAL* 1.3 82.7 - - - +
243B ASP* 1.3 59.8 + - - +
244B GLY 3.5 2.6 + - - -
251B ALA* 3.7 15.4 - - + +
254B CYS* 3.6 22.2 + - + -
255B ARG* 3.7 31.0 - - - -
258B LEU* 3.8 12.9 - - + +
327B SER* 3.6 13.2 - - - +
328B THR 3.4 3.8 - - - -
329B ALA* 3.5 28.5 - - + -
331B VAL* 3.9 10.9 - - + +
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Residues in contact with ASP 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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199B ARG* 5.8 0.7 + - - -
204B ASP* 3.2 17.4 - - - +
241B VAL* 4.1 0.8 - - - +
242B TYR* 1.3 68.5 - - - +
244B GLY* 1.3 70.8 + - - +
245B HIS* 4.0 3.3 + - - -
327B SER* 3.4 3.6 + - - -
328B THR* 3.0 47.6 + - + +
346B ASP* 5.0 0.9 - - - +
347B SER* 3.5 10.4 + - - +
431B SER* 3.6 14.5 - - - -
432B ASP* 3.0 19.8 + - - +
512B MG 2.5 30.6 - - - -
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Residues in contact with GLY 244 (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 ARG* 4.7 3.8 + - - -
203B GLU* 2.9 35.8 + - - +
242B TYR 3.5 1.4 + - - -
243B ASP* 1.3 86.7 + - - +
245B HIS* 1.3 61.0 + - - +
247B GLY 4.1 9.9 - - - -
251B ALA* 4.1 5.2 - - - -
326B GLY 3.4 11.0 - - - -
327B SER* 3.6 7.4 + - - -
81D SER* 4.3 1.2 + - - -
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Residues in contact with HIS 245 (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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243B ASP 4.0 4.6 + - - -
244B GLY* 1.3 77.3 - - - +
246B GLY* 1.3 58.7 + - - +
247B GLY 3.1 10.3 + - - +
324B THR 5.0 1.3 - - - -
325B VAL* 3.6 0.3 - - - -
326B GLY* 2.9 33.4 + - - +
327B SER* 3.7 17.5 - - - -
394B LEU* 4.0 21.3 - - + +
396B MET* 3.8 37.8 - - + +
399B SER* 3.9 2.0 - - - -
402B ASP* 2.5 40.7 + - - -
81D SER* 3.5 19.1 - - - +
82D GLY* 4.2 11.2 - - - -
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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