Contacts of the helix formed by residues 228 - 242 (chain B) in PDB entry 5H2U
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 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B LEU* 1.3 73.1 - - - +
229B GLN* 1.3 85.5 + - + +
230B GLN* 2.8 48.3 + - + +
231B MET* 3.0 18.2 + - + +
232B LEU 3.0 8.7 + - - -
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Residues in contact with GLN 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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223B ARG* 2.0 37.7 + - - +
227B LEU 3.7 2.0 + - - -
228B HIS* 1.3 84.9 + - + +
230B GLN* 1.3 61.1 - - - +
232B LEU* 3.4 10.3 - - - +
233B GLN* 2.9 62.0 + - + +
255B SER* 3.1 18.7 + - - -
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Residues in contact with GLN 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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228B HIS* 2.8 33.3 + - + +
229B GLN* 1.3 80.0 - - - +
231B MET* 1.3 62.4 + - - +
233B GLN* 3.6 5.8 + - - +
234B SER* 3.2 21.0 + - - -
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Residues in contact with MET 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 3.6 29.8 - - + -
228B HIS* 3.0 12.6 + - + +
230B GLN* 1.3 76.0 - - - +
232B LEU* 1.3 59.7 + - - +
234B SER* 3.1 12.1 + - - -
235B GLU* 2.8 52.2 + - + +
335B ARG* 4.2 10.3 - - - +
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Residues in contact with LEU 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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223B ARG* 3.8 8.3 - - - +
226B LEU* 4.0 39.5 - - + -
227B LEU* 4.3 12.3 - - - +
228B HIS 3.0 12.5 + - - +
229B GLN* 3.4 35.7 - - - +
231B MET* 1.3 76.2 - - - +
233B GLN* 1.3 57.6 + - - +
235B GLU* 3.2 7.1 + - - +
236B ILE* 2.9 51.0 + - + +
255B SER* 4.7 2.2 - - - -
260B VAL* 4.6 9.0 - - + -
262B ILE* 5.8 0.2 - - + -
336B LEU* 4.1 26.0 - - + +
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Residues in contact with GLN 233 (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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185B GLU* 4.5 6.8 + - - +
229B GLN* 2.9 48.8 + - + +
230B GLN* 3.7 7.9 - - - +
232B LEU* 1.3 73.2 - - - +
234B SER* 1.3 62.8 + - - +
236B ILE* 3.4 19.6 + - - +
237B GLN* 3.2 39.5 + - + +
253B VAL* 5.4 0.6 - - - +
255B SER* 3.0 19.5 + - - -
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLN 3.2 11.2 + - - -
231B MET* 3.1 19.6 + - - -
233B GLN* 1.3 79.4 - - - +
235B GLU* 1.3 63.3 + - - +
237B GLN* 3.5 15.5 + - - +
238B ALA* 3.5 12.1 + - - +
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Residues in contact with GLU 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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227B LEU* 4.5 5.6 - - + -
231B MET* 2.8 37.0 + - + +
232B LEU 3.7 0.9 - - - +
234B SER* 1.3 72.8 + - - +
236B ILE* 1.3 61.2 + - - +
238B ALA* 3.4 10.2 + - - +
239B MET* 3.0 28.7 + - + +
308B TYR* 4.4 6.5 + - - +
335B ARG* 2.5 47.1 + - + +
336B LEU* 3.5 23.1 - - + +
504B GOL 3.3 22.3 + - - -
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Residues in contact with ILE 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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184B CXM 4.6 6.1 - - - +
232B LEU* 2.9 41.0 + - + +
233B GLN* 3.7 17.5 - - - +
234B SER 3.4 0.2 - - - -
235B GLU* 1.3 77.7 - - - +
237B GLN* 1.3 63.9 + - - +
239B MET* 3.2 9.4 + - - +
240B LYS* 2.9 30.8 + - + +
250B LEU* 5.0 2.0 - - + -
253B VAL* 4.2 35.9 - - + -
255B SER* 4.2 21.1 - - - -
260B VAL* 5.7 1.3 - - + -
262B ILE* 5.2 8.1 - - + -
336B LEU* 4.3 16.6 - - + -
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Residues in contact with GLN 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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233B GLN* 3.2 26.2 + - + +
234B SER* 3.7 10.1 - - - +
235B GLU 3.3 0.2 - - - -
236B ILE* 1.3 82.5 - - - +
238B ALA* 1.3 61.1 + - - +
240B LYS* 3.3 37.6 - - - +
241B LYS* 3.2 44.7 + - - +
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Residues in contact with ALA 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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234B SER 3.5 8.9 + - - +
235B GLU* 3.4 12.7 + - - +
236B ILE 3.3 0.4 - - - -
237B GLN* 1.3 77.4 - - - +
239B MET* 1.3 65.5 + - - +
241B LYS* 3.5 18.9 + - - +
242B LEU* 3.6 15.9 - - - +
308B TYR* 4.1 18.3 - - + -
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Residues in contact with MET 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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235B GLU* 3.0 15.0 + - + +
236B ILE* 3.2 8.7 + - - +
238B ALA* 1.3 79.0 - - - +
240B LYS* 1.3 59.7 + - - +
241B LYS 3.4 0.7 + - - -
242B LEU* 3.5 22.7 + - - +
250B LEU* 3.6 31.6 + - + +
262B ILE* 5.2 4.5 - - - -
308B TYR* 3.5 16.8 - - - +
331B PHE* 3.3 40.4 - - + +
332B GLY 3.3 24.7 - - - +
333B LEU* 3.6 7.0 - - - +
336B LEU* 3.8 30.5 - - + -
501B 1N1 6.2 0.7 - - - -
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Residues in contact with LYS 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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184B CXM 3.4 46.3 + - - +
236B ILE* 2.9 18.4 + - + +
237B GLN* 3.3 45.5 - - - +
239B MET* 1.3 75.1 - - - +
241B LYS* 1.3 68.9 + - + +
242B LEU 3.3 5.0 + - - +
243B ARG* 4.9 10.6 + - - -
249B ALA* 5.9 0.7 - - - +
250B LEU* 3.8 26.0 + - + +
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Residues in contact with LYS 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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237B GLN* 3.2 38.2 + - - +
238B ALA* 3.5 13.4 + - - +
239B MET 3.3 0.4 - - - -
240B LYS* 1.3 84.6 - - + +
242B LEU* 1.3 65.3 + - + +
243B ARG* 3.4 11.6 + - - +
302B TYR* 4.3 2.5 + - - -
306B GLN* 6.1 0.2 - - - +
280D ASP* 5.2 11.0 - - - -
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Residues in contact with LEU 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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238B ALA 3.6 9.9 - - - +
239B MET 3.7 10.5 - - - +
240B LYS 3.3 6.4 - - - +
241B LYS* 1.3 78.6 - - + +
243B ARG* 1.3 59.2 + - - +
247B ILE* 3.6 20.9 - - + +
249B ALA* 3.8 15.6 - - - +
250B LEU 5.0 0.3 + - - -
302B TYR* 3.5 8.1 - - + +
303B LEU* 4.0 5.2 - - + -
306B GLN* 3.8 38.8 - - + +
308B TYR* 3.6 40.8 - - + -
331B PHE* 3.5 31.5 - - + -
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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