Contacts of the helix formed by residues 234 - 248 (chain B) in PDB entry 4XJO
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 PRO 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B VAL* 4.2 19.5 - - + -
232B HIS 3.4 5.8 - - - +
233B ASP* 1.3 93.6 - - - +
235B ARG* 1.3 56.7 + - + +
237B LEU* 2.9 22.3 + - + +
238B HIS 3.5 0.3 + - - -
271B HIS* 3.6 47.8 - - + +
272B ALA* 3.2 19.3 - - + +
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Residues in contact with ARG 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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195B TYR* 3.6 48.6 - - + +
233B ASP* 2.9 37.0 + - - +
234B PRO* 1.3 77.4 - - + +
236B TYR* 1.3 61.1 + - - +
238B HIS* 3.1 14.4 + - + +
239B ASP* 3.0 24.6 + - - +
272B ALA* 5.8 0.2 - - - +
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Residues in contact with TYR 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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153B TRP* 4.2 18.1 - - + -
191B VAL* 3.6 14.8 - - + -
192B PRO* 3.4 38.2 - - + +
194B ASP 2.7 26.9 + - - -
195B TYR* 3.7 15.3 - + - -
196B ASP* 2.8 33.2 + - - +
199B TYR* 3.6 21.8 - + - -
200B SER* 3.4 16.8 + - - -
232B HIS* 4.2 2.0 - - + -
233B ASP* 3.1 27.8 + - + +
234B PRO 3.1 0.6 - - - -
235B ARG* 1.3 79.0 - - - +
237B LEU* 1.3 57.3 + - - +
239B ASP* 3.3 6.4 + - - +
240B LEU* 3.0 30.9 + - - +
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Residues in contact with LEU 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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153B TRP* 4.0 13.5 - - + -
219B VAL* 4.2 4.5 - - + -
221B PRO* 3.5 38.8 - - + -
222B VAL* 3.8 23.6 - - + +
232B HIS* 3.9 15.0 - - + +
234B PRO* 2.9 15.9 + - + +
236B TYR* 1.3 74.4 - - - +
238B HIS* 1.3 65.8 + - - +
240B LEU* 3.3 6.5 + - + +
241B ARG* 3.0 23.9 + - - +
253B PHE* 3.9 28.3 - - + -
268B ALA 4.5 3.6 - - - +
269B ALA* 4.7 2.5 - - - -
272B ALA* 3.9 14.6 - - + -
274B VAL* 4.2 5.7 - - + +
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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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234B PRO 3.5 2.9 + - - +
235B ARG* 3.1 19.5 + - + +
237B LEU* 1.3 78.6 - - - +
239B ASP* 1.3 69.3 + - - +
241B ARG* 3.4 4.7 + - - +
242B ASP* 3.2 25.3 + - + +
272B ALA* 4.1 16.2 - - + +
273B GLY 5.5 1.3 - - - -
274B VAL* 3.8 24.0 - - + -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TYR* 2.5 35.8 + - - -
200B SER* 2.6 34.3 + - - +
235B ARG 3.0 12.6 + - - +
236B TYR 3.5 7.9 - - - +
237B LEU 3.2 0.2 - - - -
238B HIS* 1.3 81.5 + - - +
240B LEU* 1.3 60.0 + - + +
242B ASP* 3.2 10.2 + - - +
243B ILE* 2.8 39.3 + - + +
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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
----------------------------------------------------------
153B TRP* 3.7 24.0 - - + -
203B PHE* 3.5 47.1 - - + -
217B VAL* 4.4 7.4 - - + -
219B VAL* 3.7 35.4 - - + -
236B TYR 3.0 17.8 + - - +
237B LEU* 3.3 12.5 + - + +
239B ASP* 1.3 77.9 - - + +
241B ARG* 1.3 57.2 + - - +
243B ILE* 3.4 5.9 + - + +
244B CYS* 2.9 36.4 + - - +
251B LEU* 4.1 14.6 - - + -
253B PHE* 4.8 0.2 - - + -
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Residues in contact with ARG 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 LEU 3.0 6.4 + - - +
238B HIS 3.6 8.5 - - - +
239B ASP 3.3 0.2 - - - -
240B LEU* 1.3 75.7 - - - +
242B ASP* 1.3 58.7 + - - +
244B CYS* 3.8 18.2 - - - +
245B ARG* 3.0 58.2 + - - +
251B LEU* 3.7 15.3 - - + +
274B VAL* 3.5 32.3 - - + -
275B SER 2.9 30.8 + - - +
276B PRO* 3.7 3.4 - - - +
277B ASP* 2.9 45.0 + - - +
503B SO4 3.8 14.6 + - - -
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Residues in contact with ASP 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 HIS* 3.2 17.7 + - + +
239B ASP* 3.2 13.4 + - - +
241B ARG* 1.3 76.0 - - - +
243B ILE* 1.3 64.7 + - - +
245B ARG* 3.3 21.4 + - - +
246B ARG* 2.8 66.4 + - - +
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Residues in contact with ILE 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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200B SER* 3.7 24.9 - - - +
203B PHE* 4.2 14.4 - - + -
204B GLU* 3.7 36.3 - - + +
207B LEU* 4.0 32.3 - - + -
239B ASP* 2.8 37.0 + - + +
240B LEU* 3.8 7.2 - - + +
242B ASP* 1.3 72.8 - - - +
244B CYS* 1.3 58.8 + - - +
246B ARG* 3.3 10.7 + - - +
247B TYR* 3.0 38.6 + - + +
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Residues in contact with CYS 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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203B PHE* 6.1 0.2 - - - -
207B LEU* 4.7 3.4 - - - -
217B VAL* 3.7 36.8 - - - -
240B LEU* 2.9 22.2 + - - +
241B ARG* 3.8 14.4 - - - +
243B ILE* 1.3 77.3 - - - +
245B ARG* 1.3 57.9 + - - +
248B GLU* 3.0 25.5 + - - -
249B VAL* 3.0 38.0 + - - +
250B LEU 4.0 1.8 - - - -
251B LEU* 4.0 15.9 - - + -
503B SO4 3.7 2.2 + - - -
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 3.0 49.6 + - - +
242B ASP* 3.5 34.6 + - - +
243B ILE 3.3 0.2 - - - -
244B CYS* 1.3 78.9 - - - +
246B ARG* 1.3 68.7 + - + +
247B TYR 3.4 0.2 + - - -
248B GLU* 3.5 13.0 + - - +
503B SO4 4.4 8.7 + - - -
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Residues in contact with ARG 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLU* 2.8 44.4 + - - -
242B ASP* 2.8 52.7 + - - +
243B ILE* 3.3 11.9 + - - +
245B ARG* 1.3 84.3 - - + +
247B TYR* 1.3 73.7 + - + +
248B GLU* 3.8 4.2 + - - +
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Residues in contact with TYR 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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147B LYS* 4.4 1.6 + - - -
204B GLU* 3.4 36.6 + - + +
207B LEU* 3.5 22.9 - - + -
208B ALA* 3.5 35.6 - - + +
211B ALA* 4.1 16.2 - - + +
243B ILE* 3.0 28.0 + - + +
246B ARG* 1.3 93.9 + - + +
248B GLU* 1.3 71.6 + - - +
249B VAL* 3.5 7.7 + - + +
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Residues in contact with GLU 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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139B TRP* 3.3 15.0 - - + -
142B ARG* 3.7 22.9 + - - -
147B LYS* 2.8 25.2 + - - +
244B CYS 3.0 6.2 + - - -
245B ARG 3.5 8.2 + - - +
246B ARG 3.4 4.8 - - - +
247B TYR* 1.3 80.0 - - - +
249B VAL* 1.3 59.1 + - - +
503B SO4 3.4 24.4 + - - +
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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