Contacts of the helix formed by residues 232 - 243 (chain B) in PDB entry 3R29
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 VAL 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B GLU* 3.5 29.2 - - - +
231B PRO* 1.3 78.2 - - - +
233B GLU* 1.3 72.4 + - + +
234B ARG 3.0 5.8 - - - -
235B ILE* 2.9 20.5 + - + +
236B LEU 3.1 8.1 + - - -
365B THR* 3.3 29.6 - - + +
369B CYS* 4.0 15.7 - - - -
399B SER* 4.3 19.3 - - - +
400B LEU* 5.4 0.4 - - - -
403B TYR* 4.3 19.1 - - + +
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Residues in contact with GLU 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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228B GLU* 4.7 6.9 - - - +
231B PRO* 4.3 4.8 - - - +
232B VAL* 1.3 92.0 + - + +
234B ARG* 1.3 86.0 + - - +
236B LEU* 3.2 18.7 - - + +
237B GLU* 2.8 35.3 + - - +
365B THR* 5.3 2.2 - - - -
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Residues in contact with ARG 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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231B PRO* 4.5 27.7 - - + +
232B VAL 3.0 0.4 - - - -
233B GLU* 1.3 100.8 + - - +
235B ILE* 1.3 52.7 + - - +
237B GLU* 2.7 36.8 + - - +
238B ALA* 2.6 34.2 + - - +
285B ARG 5.3 3.1 - - - +
287B PRO* 4.9 16.2 - - + -
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Residues in contact with ILE 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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230B MET* 4.1 19.1 - - + -
231B PRO 3.0 27.1 - - - +
232B VAL* 2.9 14.5 + - + +
234B ARG* 1.3 67.4 - - - +
236B LEU* 1.3 64.5 + - - +
238B ALA* 3.4 10.3 - - + +
239B GLU* 3.1 22.7 + - - +
282B TRP* 5.7 1.1 - - + -
286B ILE* 4.1 22.0 - - + -
287B PRO* 4.7 5.1 - - + +
365B THR* 4.6 1.8 - - - +
368B GLY* 3.6 34.1 - - - +
369B CYS* 4.0 12.8 - - - +
372B ALA* 4.9 3.6 - - + -
396B VAL* 4.5 18.6 - - + -
399B SER* 6.1 1.6 - - - -
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Residues in contact with LEU 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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232B VAL 3.1 6.0 + - - +
233B GLU* 3.2 21.8 - - + +
234B ARG 3.0 0.4 - - - -
235B ILE* 1.3 76.7 - - - +
237B GLU* 1.3 65.0 + - + +
239B GLU* 2.8 17.2 + - - +
240B LEU* 2.9 38.7 + - + +
364B LYS* 3.6 34.8 - - + -
365B THR* 3.5 26.8 - - - +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLU* 2.8 23.3 + - - +
234B ARG* 2.7 49.4 + - - +
236B LEU* 1.3 68.9 - - + +
238B ALA* 1.3 49.1 + - - +
240B LEU* 2.9 20.2 + - + +
241B ALA* 2.7 35.6 + - - +
285B ARG* 5.7 1.1 - - - -
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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 ARG 2.6 14.1 + - - +
235B ILE* 3.4 17.0 - - - +
237B GLU* 1.3 73.6 - - - +
239B GLU* 1.3 62.3 + - - +
240B LEU 3.2 0.5 + - - -
241B ALA* 3.4 14.5 + - - +
242B VAL* 3.5 18.5 + - - +
282B TRP* 3.9 13.2 - - + +
285B ARG* 4.1 33.5 - - + +
286B ILE* 4.4 10.5 - - + -
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Residues in contact with GLU 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 ILE 3.1 16.1 + - - +
236B LEU* 2.8 12.6 + - + +
238B ALA* 1.3 73.4 - - - +
240B LEU* 1.3 62.4 + - + +
242B VAL* 3.4 10.4 - - - +
243B GLU* 3.3 28.8 + - - +
282B TRP* 2.3 39.9 + - - +
312B SER* 5.0 1.0 + - - -
364B LYS* 3.9 20.9 - - + +
367B LEU* 3.8 18.9 - - + +
368B GLY* 3.5 25.4 - - - +
371B ARG* 3.0 15.8 + - - -
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Residues in contact with LEU 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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236B LEU* 2.9 44.4 + - + +
237B GLU* 2.9 24.1 + - + +
239B GLU* 1.3 76.0 - - + +
241B ALA* 1.3 68.0 + - - +
243B GLU* 3.3 29.8 + - - +
245B LYS* 5.7 5.5 - - - +
364B LYS* 5.2 7.9 - - + +
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Residues in contact with ALA 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 GLU 2.7 14.3 + - - +
238B ALA 3.5 9.6 - - - +
240B LEU* 1.3 75.8 - - - +
242B VAL* 1.3 62.4 + - + +
243B GLU 3.3 5.0 + - - +
285B ARG* 3.3 41.7 - - - +
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Residues in contact with VAL 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 3.5 6.7 + - - +
239B GLU* 3.4 18.8 - - - +
241B ALA* 1.3 81.5 - - + +
243B GLU* 1.3 66.0 + - - +
244B PRO* 3.5 4.9 - - - +
278B THR* 3.5 52.2 + - + +
281B GLU* 4.8 7.0 - - + -
282B TRP* 3.6 42.0 - - + +
285B ARG* 5.4 2.0 - - - +
371B ARG* 5.5 2.9 - - - +
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Residues in contact with GLU 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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239B GLU* 3.3 22.6 + - - +
240B LEU* 3.5 31.2 - - - +
241B ALA 3.2 7.3 - - - +
242B VAL* 1.3 81.1 - - - +
244B PRO* 1.3 81.2 - - + +
245B LYS* 3.2 9.2 + - + +
316B ARG* 6.0 1.8 - - - +
364B LYS* 3.5 33.1 + - - +
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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