Contacts of the helix formed by residues 233 - 247 (chain B) in PDB entry 5WN1
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 THR 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B LEU* 3.8 28.9 - - + -
182B LEU* 3.8 9.5 - - + +
227B LYS 3.5 3.1 - - - -
228B LYS* 4.0 10.5 - - - -
229B ASN 3.4 17.7 - - - +
231B GLY 3.9 0.2 - - - -
232B PHE* 1.3 83.0 - - - +
234B PRO* 1.3 76.0 - - - +
235B GLN* 3.8 10.1 + - - -
236B GLU* 3.2 32.6 + - - +
237B ARG* 3.2 19.0 + - - +
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Residues in contact with PRO 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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227B LYS* 3.6 14.1 - - + +
228B LYS* 5.8 1.3 - - + -
232B PHE 4.4 0.4 - - - +
233B THR* 1.3 85.6 - - - +
235B GLN* 1.3 74.0 + - - +
237B ARG* 3.4 8.7 + - + +
238B GLN* 2.9 54.1 + - - +
402B NA 4.7 5.6 - - - -
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Residues in contact with GLN 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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182B LEU* 3.0 37.7 - - + +
186B GLN* 3.5 39.0 - - + +
189B ASP* 4.7 2.4 - - - +
233B THR* 4.1 5.2 + - - +
234B PRO* 1.3 93.8 - - - +
236B GLU* 1.3 58.1 + - - +
238B GLN* 4.0 9.0 + - - +
239B GLY* 3.0 26.0 + - - -
402B NA 3.5 14.6 - - - -
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Residues in contact with GLU 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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175B ALA* 3.5 17.7 + - - +
182B LEU* 4.0 10.5 - - + -
185B ARG* 2.9 39.1 + - + +
186B GLN* 6.3 0.2 - - + -
189B ASP* 4.7 8.4 - - - +
212B ASN 3.4 2.9 - - - +
213B VAL* 3.5 24.1 - - + +
230B ALA* 3.4 6.9 - - - -
231B GLY* 2.4 36.4 + - - -
232B PHE 3.7 0.3 + - - -
233B THR* 3.2 29.3 + - - +
234B PRO 3.2 0.2 - - - -
235B GLN* 1.3 74.0 - - - +
237B ARG* 1.3 66.8 + - - +
239B GLY* 3.5 1.0 + - - -
240B PHE* 3.1 17.7 + - - +
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Residues in contact with ARG 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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213B VAL* 4.1 7.4 - - + -
214B ALA 3.4 12.6 - - - +
215B HIS* 2.9 30.7 + - + +
216B GLU* 2.9 32.3 + - - +
217B GLU* 4.1 11.1 + - - +
227B LYS* 4.4 12.1 - - - +
232B PHE* 3.2 55.0 + - + +
233B THR 3.2 11.5 + - - +
234B PRO* 4.0 6.6 - - + +
236B GLU* 1.3 75.7 - - - +
238B GLN* 1.3 60.2 + - + +
240B PHE* 3.2 5.6 + - - +
241B GLY* 3.0 23.6 + - - -
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Residues in contact with GLN 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* 2.9 40.3 + - - +
235B GLN* 4.0 7.3 - - - +
237B ARG* 1.3 74.4 - - + +
239B GLY* 1.3 59.6 + - - +
241B GLY* 3.1 3.4 + - - +
242B GLU* 2.8 43.4 + - + +
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Residues in contact with GLY 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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189B ASP* 4.3 19.1 - - - +
193B ARG* 4.8 8.5 + - - -
235B GLN 3.0 16.5 + - - -
236B GLU 3.9 1.8 - - - -
238B GLN* 1.3 76.7 - - - +
240B PHE* 1.3 61.2 + - - +
242B GLU* 3.3 13.1 + - - +
243B LEU* 2.9 24.1 + - - +
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Residues in contact with PHE 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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189B ASP* 5.2 0.2 + - - -
211B LEU* 3.6 28.0 - - + -
213B VAL* 3.6 30.1 - - + -
215B HIS* 3.2 48.7 - + + +
236B GLU 3.1 14.4 + - - +
237B ARG 3.4 8.7 - - - +
238B GLN 3.2 0.2 - - - -
239B GLY* 1.3 75.4 - - - +
241B GLY* 1.3 62.7 + - - +
243B LEU* 3.2 13.9 + - + +
244B LEU* 3.2 37.2 + - + +
251B ASP* 4.4 3.4 - - - -
284B TYR* 3.5 29.6 - + - -
286B LEU* 4.1 19.7 - - + -
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Residues in contact with GLY 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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215B HIS* 4.0 17.1 - - - -
237B ARG 3.0 13.7 + - - -
238B GLN* 3.1 3.3 + - - -
240B PHE* 1.3 74.8 - - - +
242B GLU* 1.3 62.7 + - - +
244B LEU* 3.2 17.3 + - - +
245B GLN* 3.2 18.2 + - - +
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Residues in contact with GLU 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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193B ARG* 3.0 36.9 + - - +
238B GLN* 2.8 31.3 + - + +
239B GLY* 3.7 7.6 + - - +
241B GLY* 1.3 72.2 - - - +
243B LEU* 1.3 58.6 + - - +
245B GLN* 3.8 9.7 - - - +
246B ALA* 2.9 35.3 + - + +
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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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192B PHE* 5.1 7.2 - - + -
193B ARG* 3.6 38.9 - - + +
196B LEU* 4.0 12.3 - - + -
207B LEU* 4.2 15.3 - - + -
211B LEU* 5.2 2.7 - - + -
239B GLY 2.9 13.4 + - - +
240B PHE* 3.2 18.8 + - + +
242B GLU* 1.3 77.2 - - - +
244B LEU* 1.3 63.0 + - - +
245B GLN 3.1 1.0 + - - -
247B VAL* 3.2 47.5 + - + +
249B LEU* 4.2 4.6 + - + +
286B LEU* 4.1 24.2 - - + -
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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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215B HIS* 3.9 26.2 - - + +
240B PHE* 3.2 28.4 + - + +
241B GLY* 3.2 8.7 + - - +
243B LEU* 1.3 78.2 - - + +
245B GLN* 1.3 57.2 + - + +
248B PRO* 3.1 7.8 - - - +
249B LEU* 2.7 48.8 + - + +
250B ALA* 5.8 0.2 - - - -
251B ASP* 4.6 13.7 - - + +
286B LEU* 4.0 31.6 - - + -
289B HIS* 4.9 0.9 + - - -
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Residues in contact with GLN 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 GLY 3.2 15.3 + - - +
242B GLU* 4.0 8.3 - - - +
243B LEU 3.1 0.6 - - - -
244B LEU* 1.3 78.7 - - + +
246B ALA* 1.3 65.5 + - + +
247B VAL 3.5 0.4 - - - -
248B PRO* 3.7 12.2 - - - +
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Residues in contact with ALA 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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193B ARG* 4.1 22.9 - - + -
197B LYS* 3.2 37.3 + - - +
242B GLU* 2.9 17.3 + - + +
245B GLN* 1.3 77.2 - - + +
247B VAL* 1.3 65.4 + - - +
248B PRO* 4.6 0.8 - - - +
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Residues in contact with VAL 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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193B ARG* 4.4 5.2 - - + +
196B LEU* 4.0 17.7 - - + +
197B LYS* 4.3 17.8 + - + +
200B ALA* 3.6 32.5 - - + +
205B LEU* 4.5 1.1 - - + -
243B LEU* 3.2 38.3 + - + +
246B ALA* 1.3 79.2 - - - +
248B PRO* 1.4 77.3 - - + +
249B LEU* 3.5 21.3 - - + -
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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