Contacts of the helix formed by residues 238 - 249 (chain B) in PDB entry 1XJB
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 ASP 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B TYR* 2.7 35.4 + - + +
234B VAL 3.6 2.0 + - - -
235B LEU 2.8 17.4 + - - +
236B LEU 3.3 1.2 - - - -
237B GLU* 1.4 75.9 - - - +
239B PRO* 1.3 71.1 - - - +
240B VAL* 2.9 15.8 + - - +
241B LEU* 2.8 36.8 + - + +
242B CYS* 2.9 31.9 + - - -
299B LEU* 3.5 21.5 - - - +
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Residues in contact with PRO 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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196B TYR* 4.7 0.9 - - - +
237B GLU 3.3 5.5 - - - +
238B ASP* 1.3 96.3 - - - +
240B VAL* 1.3 72.7 + - + +
242B CYS* 3.4 5.0 + - + +
243B ALA* 2.9 29.2 + - - +
299B LEU* 5.5 0.7 - - + -
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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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238B ASP* 2.9 8.2 + - - +
239B PRO* 1.3 86.4 - - + +
241B LEU* 1.3 65.0 + - - +
243B ALA* 3.2 6.3 + - - +
244B LEU* 2.9 43.8 + - + +
295B ALA* 4.3 20.6 - - + +
299B LEU* 3.7 30.3 - - + -
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Residues in contact with LEU 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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195B PRO* 4.4 10.1 - - + -
235B LEU* 3.9 42.8 - - + +
236B LEU* 5.0 0.7 - - + -
238B ASP* 2.8 25.6 + - + +
240B VAL* 1.3 72.6 - - - +
242B CYS* 1.3 52.8 + - - +
244B LEU* 3.4 4.8 + - + +
245B ALA* 2.7 36.6 + - - +
252B PRO* 4.1 27.6 - - + +
255B ILE* 3.9 28.0 - - + +
256B ALA* 4.4 7.2 - - + +
296B ILE* 4.3 17.3 - - + -
299B LEU* 3.8 17.7 - - + -
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Residues in contact with CYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU 3.4 23.3 - - - -
237B GLU* 3.9 11.7 - - - -
238B ASP 2.9 24.0 + - - +
239B PRO* 3.7 6.1 - - + +
241B LEU* 1.3 76.2 - - - +
243B ALA* 1.3 57.5 + - - +
245B ALA* 3.2 8.1 + - - +
246B LYS* 3.0 30.4 + - - +
252B PRO* 3.8 9.9 - - + -
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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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239B PRO 2.9 18.0 + - - +
240B VAL* 3.2 9.2 + - + +
242B CYS* 1.3 73.6 - - - +
244B LEU* 1.3 67.3 + - + +
246B LYS* 3.0 9.7 + - - +
247B LYS* 2.9 22.9 + - - +
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Residues in contact with LEU 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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240B VAL* 2.9 38.5 + - + +
241B LEU* 3.8 4.5 - - - +
243B ALA* 1.3 73.9 - - + +
245B ALA* 1.3 62.2 + - - +
247B LYS* 3.4 12.7 + - + +
248B HIS* 3.1 31.6 + - + +
255B ILE* 3.9 21.0 - - + +
288B LEU* 5.5 1.1 - - + -
292B GLU* 3.6 43.7 - - + +
295B ALA* 4.8 4.7 - - + -
296B ILE* 3.8 29.8 - - + -
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Residues in contact with ALA 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 LEU 2.7 22.9 + - - +
242B CYS* 3.4 6.1 - - - +
243B ALA 3.1 0.2 - - - -
244B LEU* 1.3 71.7 - - - +
246B LYS* 1.3 57.3 + - - +
248B HIS 3.4 0.2 + - - -
249B LYS* 2.9 8.7 + - - -
250B ARG 2.8 31.6 + - - +
251B THR* 3.3 37.7 - - - +
252B PRO* 3.4 7.6 - - + -
255B ILE* 3.8 10.5 - - + +
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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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242B CYS 3.0 14.4 + - - +
243B ALA* 3.0 10.7 + - - +
245B ALA* 1.3 73.7 - - - +
247B LYS* 1.3 65.6 + - - +
249B LYS* 2.9 24.3 + - - +
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Residues in contact with LYS 247 (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 ALA 2.9 12.2 + - - +
244B LEU* 3.6 17.3 - - + +
246B LYS* 1.3 76.5 - - - +
248B HIS* 1.3 64.4 + - + +
249B LYS* 3.3 6.4 + - - +
289B THR* 6.0 0.6 - - - +
291B GLU* 4.6 14.5 + - - -
292B GLU* 3.2 38.4 + - - +
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Residues in contact with HIS 248 (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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208A SER* 5.4 12.0 + - - -
244B LEU* 3.1 31.1 + - - +
245B ALA 4.2 1.1 - - - +
247B LYS* 1.3 84.2 - - + +
249B LYS* 1.3 73.7 + - - +
250B ARG* 3.6 26.3 + - + +
255B ILE* 4.5 3.1 - - + -
286B PHE* 4.3 13.9 - + + +
287B GLN 3.5 24.9 + - - -
288B LEU* 3.7 13.2 - - + +
289B THR* 5.8 0.4 - - + -
292B GLU* 2.5 37.5 + - - -
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Residues in contact with LYS 249 (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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245B ALA 2.9 7.8 + - - -
246B LYS* 2.9 18.4 + - - +
247B LYS 3.1 5.3 - - - +
248B HIS* 1.3 84.6 - - - +
250B ARG* 1.3 66.9 + - - +
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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