Contacts of the helix formed by residues 235 - 248 (chain B) in PDB entry 1WG8
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 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B GLN* 3.2 35.4 + - + +
202B ARG* 3.6 18.8 - - - -
203B ILE* 3.5 30.0 - - + +
208B GLU* 3.8 9.5 + - - +
209B LEU* 4.2 6.0 - - + +
234B PHE* 1.3 79.2 - - + +
236B SER* 1.3 67.4 + - - +
237B LEU* 3.4 11.6 + - + +
238B GLU* 3.0 70.6 + - + +
239B ASP* 3.0 21.3 + - - +
276B LYS* 4.3 2.2 - - - -
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLU* 4.2 15.9 + - - -
234B PHE 4.1 0.8 + - - -
235B HIS* 1.3 71.4 - - - +
237B LEU* 1.3 64.7 + - - +
239B ASP* 3.9 1.0 - - - +
240B ARG* 3.0 46.0 + - - +
276B LYS* 4.1 16.3 + - - +
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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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148B GLU 3.2 27.4 - - - +
149B LEU* 3.6 24.9 - - + +
151B GLU* 4.1 16.5 + - + +
199B GLN* 5.5 1.6 - - - +
203B ILE* 4.3 5.6 - - + -
209B LEU* 3.9 26.0 - - + -
235B HIS* 3.2 15.7 + - + +
236B SER* 1.3 81.2 - - - +
238B GLU* 1.3 62.1 + - - +
240B ARG* 3.4 29.6 + - - +
241B VAL* 3.2 23.5 + - - +
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.6 29.4 - - + +
98B GLY 5.1 0.2 + - - -
202B ARG* 4.5 2.5 + - - -
208B GLU* 4.1 9.6 - - + +
209B LEU* 4.8 4.0 - - + +
212B LEU* 3.8 20.0 - - + +
233B ALA* 3.6 8.1 - - + -
234B PHE* 2.6 29.7 + - - +
235B HIS* 3.0 56.0 + - + +
237B LEU* 1.3 71.4 - - - +
239B ASP* 1.3 66.3 + - - +
241B VAL* 3.1 7.4 + - - +
242B VAL* 2.9 25.8 + - - +
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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
----------------------------------------------------------
233B ALA* 3.6 18.5 - - + +
235B HIS 3.0 15.8 + - - +
236B SER* 3.9 3.4 - - - +
238B GLU* 1.3 77.2 - - - +
240B ARG* 1.3 61.4 + - - +
242B VAL* 3.2 2.5 + - - +
243B LYS* 2.8 30.0 + - - +
276B LYS* 3.7 43.2 + - - +
278B ARG* 2.7 43.6 + - - -
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLU* 3.2 23.4 + - - -
236B SER* 3.0 31.5 + - - +
237B LEU* 3.7 25.9 - - - +
239B ASP* 1.3 78.8 - - - +
241B VAL* 1.3 58.3 + - + +
243B LYS* 3.6 28.8 - - - +
244B ARG* 2.8 35.2 + - - +
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Residues in contact with VAL 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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209B LEU* 4.3 17.7 - - + -
212B LEU* 3.7 22.2 - - + -
213B LYS* 3.7 42.4 - - + -
216B LEU* 4.2 7.6 - - + -
237B LEU 3.2 14.1 + - - +
238B GLU* 3.1 9.9 + - - +
240B ARG* 1.3 76.8 - - - +
242B VAL* 1.3 58.1 + - - +
244B ARG* 3.8 5.2 - - - +
245B PHE* 2.9 29.4 + - + +
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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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97B LEU* 4.5 3.6 - - + -
212B LEU* 4.1 19.1 - - + -
216B LEU* 4.1 11.0 - - + -
231B VAL* 3.7 39.9 - - + +
233B ALA* 4.6 4.5 - - + -
238B GLU 2.9 18.7 + - - +
239B ASP* 3.6 8.3 - - - +
241B VAL* 1.3 74.8 - - - +
243B LYS* 1.3 64.7 - - - +
245B PHE* 3.0 2.1 + - - +
246B LEU* 2.8 46.9 + - + +
278B ARG* 4.1 18.8 - - + -
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Residues in contact with LYS 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 ASP* 2.8 21.3 + - - +
240B ARG* 3.6 28.0 - - - +
242B VAL* 1.3 74.7 - - - +
244B ARG* 1.3 64.0 + - - +
246B LEU* 3.4 4.3 + - - +
247B ARG* 3.1 45.1 + - + +
278B ARG* 3.6 42.3 - - - +
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Residues in contact with ARG 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 ARG 2.8 21.0 + - - +
241B VAL* 3.8 4.7 - - - +
243B LYS* 1.3 74.5 - - - +
245B PHE* 1.3 63.3 + - - +
247B ARG* 3.3 26.8 + - - +
248B GLU* 3.2 55.1 + - - +
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Residues in contact with PHE 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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213B LYS* 5.1 3.1 - - - -
216B LEU* 3.2 52.0 - - + -
217B GLU* 3.7 24.5 - - + -
220B ALA* 3.9 13.9 - - + -
229B LEU* 4.3 13.9 - - + -
241B VAL* 2.9 19.3 + - + +
242B VAL 3.5 3.1 - - - +
244B ARG* 1.3 78.0 - - - +
246B LEU* 1.3 77.6 + - + +
247B ARG 3.2 0.2 + - - -
248B GLU* 3.5 5.6 + - + -
249B SER* 2.9 51.3 + - - -
251B LEU* 4.5 1.3 - - + -
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Residues in contact with LEU 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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216B LEU* 4.9 1.6 - - + -
229B LEU* 4.6 12.6 - - + +
231B VAL* 5.6 2.0 - - + -
242B VAL* 2.8 39.1 + - + +
243B LYS* 3.9 4.3 - - - +
245B PHE* 1.3 89.0 - - + +
247B ARG* 1.3 67.1 + - + +
249B SER* 2.9 19.7 + - - +
251B LEU* 4.1 4.0 - - - +
253B VAL* 3.7 26.4 - - + +
255B THR* 5.0 1.1 - - - +
278B ARG* 3.7 33.7 - - + +
279B ALA* 4.1 22.4 - - - +
280B ALA* 4.0 14.6 - - + -
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LYS* 3.1 32.7 + - + +
244B ARG* 3.4 42.5 - - - +
245B PHE 3.2 0.2 - - - -
246B LEU* 1.3 80.7 - - - +
248B GLU* 1.3 67.5 + - + +
249B SER 3.2 2.8 + - - -
250B GLY* 4.0 4.9 + - - -
251B LEU 5.0 1.7 - - - +
253B VAL* 4.5 10.0 - - + +
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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
----------------------------------------------------------
244B ARG* 3.2 47.2 + - - +
245B PHE* 3.7 5.3 - - + +
247B ARG* 1.3 86.1 + - + +
249B SER* 1.3 59.1 + - - +
250B GLY 3.5 1.1 - - - -
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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