Contacts of the helix formed by residues 236 - 246 (chain B) in PDB entry 3JXI
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 CYS 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 5.2 2.9 - - - -
188B LEU* 3.4 32.8 - - - -
191B GLY* 4.7 5.6 - - - -
231B ALA* 3.1 16.8 + - - +
234B ARG* 3.9 19.3 - - - -
235B ARG* 1.3 73.1 - - - +
237B LYS* 1.3 65.2 - - - +
238B HIS 3.2 2.2 - - - -
239B TYR* 3.1 29.0 + - + -
240B VAL* 3.0 21.9 + - - +
286B ILE* 5.6 0.2 - - - -
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Residues in contact with LYS 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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235B ARG 3.6 6.0 + - - +
236B CYS* 1.3 73.2 - - - +
238B HIS* 1.3 64.5 + - - +
240B VAL* 3.3 9.1 + - + +
241B GLU* 3.0 52.3 + - + +
285B HIS* 3.8 46.3 + - + +
286B ILE* 3.9 21.5 - - + +
289B TYR* 4.9 6.3 - - + +
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Residues in contact with HIS 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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192B ARG* 3.5 30.8 + - - +
197B PRO* 5.6 4.0 - - + -
236B CYS 3.2 1.0 - - - -
237B LYS* 1.3 77.0 - - - +
239B TYR* 1.3 77.9 + + + +
241B GLU* 3.3 16.2 + - + +
242B LEU* 3.1 44.2 + - + +
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.0 22.9 - - + -
188B LEU* 4.0 12.8 - - + -
191B GLY 3.4 21.1 - - - -
192B ARG* 3.3 22.4 - - - +
193B ASN 3.0 31.3 + - - -
194B ASP* 4.4 2.3 + - - -
196B ILE* 3.9 29.8 - - + -
197B PRO* 4.6 5.5 - - + +
231B ALA* 4.5 2.2 - - + -
236B CYS* 3.1 29.9 + - + +
238B HIS* 1.3 92.7 - + + +
240B VAL* 1.3 58.7 + - - +
242B LEU* 3.4 11.0 + - + +
243B LEU* 2.9 40.0 + - + +
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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
----------------------------------------------------------
228B LEU* 4.0 18.6 - - + +
231B ALA* 3.8 17.1 - - + +
232B ILE* 3.8 25.6 - - + -
236B CYS 3.0 21.0 + - - +
237B LYS* 3.4 13.0 - - + +
239B TYR* 1.3 75.9 - - - +
241B GLU* 1.3 56.3 + - - +
243B LEU* 3.4 1.4 + - - +
244B VAL* 2.9 33.8 + - - +
286B ILE* 4.2 18.8 - - + -
289B TYR* 4.2 11.7 - - + -
290B LEU* 4.1 20.2 - - + -
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Residues in contact with GLU 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 LYS* 3.0 51.0 + - + +
238B HIS* 3.5 16.3 - - + +
240B VAL* 1.3 72.0 - - - +
242B LEU* 1.3 57.1 + - - +
244B VAL 3.2 0.9 + - - -
245B GLU* 2.8 48.9 + - - +
289B TYR* 3.3 48.6 + - + +
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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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196B ILE* 4.1 8.5 - - + -
197B PRO* 4.2 21.1 - - + -
200B LEU* 3.9 20.9 - - + -
238B HIS* 3.1 27.7 + - + +
239B TYR* 3.5 29.4 - - + +
241B GLU* 1.3 77.8 - - - +
243B LEU* 1.3 63.6 + - + +
245B GLU* 3.5 17.4 + - - +
246B LYS* 3.1 52.9 + - - +
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Residues in contact with LEU 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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181B LEU* 4.1 21.1 - - + -
185B LEU* 4.3 7.4 - - + -
196B ILE* 5.3 3.8 - - + -
200B LEU* 4.1 30.7 - - + -
213B ILE* 4.0 12.6 - - + +
227B ALA* 3.7 35.9 - - + +
228B LEU* 3.9 7.2 - - + +
231B ALA* 3.8 14.8 - - + -
239B TYR* 2.9 19.3 + - + +
240B VAL 3.7 3.8 - - - +
242B LEU* 1.3 80.0 - - + +
244B VAL* 1.3 59.9 + - - +
246B LYS 3.3 3.8 + - - -
247B GLY 3.3 6.2 + - - -
248B ALA* 2.9 32.1 + - + +
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Residues in contact with VAL 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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228B LEU* 4.1 10.3 - - + -
240B VAL 2.9 19.1 + - - +
241B GLU 3.7 2.9 - - - +
243B LEU* 1.3 75.6 - - - +
245B GLU* 1.3 61.4 + - - +
247B GLY* 3.1 13.5 + - - -
248B ALA* 3.9 8.4 + - + +
250B VAL* 4.1 14.4 - - + -
289B TYR* 3.8 17.7 - - + +
290B LEU* 4.0 21.1 - - + -
293B ASN* 3.9 15.9 - - - +
295B HIS* 3.2 11.6 + - + +
296B LYS* 3.6 30.1 - - + +
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Residues in contact with GLU 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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241B GLU* 2.8 36.4 + - - +
242B LEU* 3.6 23.4 - - - +
243B LEU 3.4 0.2 - - - -
244B VAL* 1.3 72.2 - - - +
246B LYS* 1.3 65.9 + - + +
247B GLY 3.4 0.4 - - - -
289B TYR* 3.9 14.6 + - - +
295B HIS* 3.3 36.5 + - + -
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Residues in contact with LYS 246 (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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197B PRO* 6.1 0.4 - - - -
200B LEU* 3.9 18.2 - - + -
201B ASP* 6.3 0.4 - - - +
204B GLU* 4.1 16.8 + - - -
209B MET* 3.3 45.8 - - + +
210B ARG* 5.2 2.3 - - - -
213B ILE* 3.4 20.0 - - + +
242B LEU* 3.1 34.5 + - + +
243B LEU 3.7 2.0 - - - -
244B VAL 3.2 0.2 - - - -
245B GLU* 1.3 83.3 - - + +
247B GLY* 1.3 57.0 + - - +
295B HIS* 5.0 0.7 - - - -
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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