Contacts of the helix formed by residues 229 - 240 (chain B) in PDB entry 2PGW
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 SER 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B GLN* 5.7 0.2 + - - -
225B THR* 4.7 0.2 + - - -
226B VAL* 3.4 16.3 + - - +
227B SER* 3.2 4.8 - - - +
228B TRP* 1.3 77.2 - - - +
230B ILE* 1.3 62.6 + - - +
231B PRO* 3.7 8.4 - - - +
232B ALA* 3.0 32.3 + - - +
233B MSE 3.3 17.2 + - - +
249B ALA* 5.7 0.9 - - - +
290C ALA 4.5 2.2 + - - -
291C ALA* 3.7 9.9 + - - -
292C GLY* 4.2 15.3 - - - -
254F TYR* 4.5 10.1 - - - -
257F TYR* 5.9 0.5 - - - -
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Residues in contact with ILE 230 (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 SER 5.0 2.7 - - - +
228B TRP 3.9 3.6 + - - +
229B SER* 1.3 71.8 - - - +
231B PRO* 1.4 74.1 - - + +
233B MSE 3.1 9.8 + - + +
234B ALA* 3.0 20.4 + - - +
249B ALA* 4.6 20.2 - - + +
255B ASP* 4.0 11.0 - - + +
258B GLU* 3.7 26.7 - - + -
259B ILE* 3.8 25.1 - - + -
262B GLN* 3.6 21.8 - - - +
264B ALA* 3.4 24.2 - - + -
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Residues in contact with PRO 231 (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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229B SER* 3.6 8.7 - - - +
230B ILE* 1.4 94.5 - - + +
232B ALA* 1.3 56.3 + - - +
234B ALA* 3.2 7.1 + - + +
235B HIS* 2.8 29.3 + - - +
262B GLN* 3.7 8.7 - - - +
263C ARG* 4.1 25.1 + - - +
257F TYR* 5.3 4.3 - - + -
258F GLU* 3.4 27.6 - - - +
261F ARG* 3.5 28.3 - - - +
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Residues in contact with ALA 232 (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 VAL* 4.3 7.1 - - + +
225B THR* 4.1 10.8 - - - +
226B VAL* 5.3 1.1 - - + -
229B SER* 3.0 29.6 + - - +
231B PRO* 1.3 77.4 - - - +
233B MSE 1.3 60.8 + - - +
235B HIS* 3.2 3.6 - - - +
236B VAL* 3.1 28.2 + - - +
263C ARG* 3.7 15.8 - - - +
291C ALA 3.9 11.7 - - - +
292C GLY* 4.1 12.6 - - - +
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Residues in contact with MSE 233 (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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223B GLN* 3.9 20.6 - - - +
224B PRO* 5.2 3.1 - - + -
225B THR* 3.6 16.5 + - - +
229B SER 3.3 8.2 + - - +
230B ILE* 3.1 10.1 + - + +
232B ALA* 1.3 77.8 - - - +
234B ALA* 1.3 59.2 + - - +
236B VAL* 3.3 5.3 + - - +
237B ARG* 2.9 27.0 + - - +
244B ILE* 4.2 16.2 - - + +
245B VAL 4.8 0.2 - - - +
246B ALA* 3.6 42.6 - - + -
249B ALA* 3.9 14.6 - - + -
259B ILE* 4.0 10.3 - - + -
264B ALA* 3.5 34.3 - - + +
265B ALA* 4.5 0.9 - - - -
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Residues in contact with ALA 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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230B ILE 3.0 11.1 + - - +
231B PRO* 3.6 10.3 - - + +
233B MSE 1.3 73.0 - - - +
235B HIS* 1.3 66.3 + - - +
237B ARG* 3.7 2.2 - - - +
238B GLU* 2.9 44.6 + - - +
262B GLN* 4.3 12.1 - - + +
263B ARG 4.5 1.8 - - - +
264B ALA* 3.7 29.6 + - + +
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Residues in contact with HIS 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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203B VAL* 3.6 16.1 - - + +
207B ILE* 4.8 0.4 - - + -
231B PRO 2.8 14.2 + - - +
232B ALA* 3.2 13.2 - - - +
234B ALA* 1.3 77.7 - - - +
236B VAL* 1.3 63.9 + - - +
238B GLU* 3.6 7.0 + - - +
239B LYS* 3.5 20.4 + - + +
237C ARG* 3.2 32.2 + - - +
263C ARG* 2.9 41.9 + - + +
265C ALA 3.5 21.1 - - - -
266C ASP* 2.6 29.8 + - - -
293C LEU* 4.5 0.7 - - + -
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Residues in contact with VAL 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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203B VAL* 3.8 31.4 - - + +
206B ALA* 3.9 19.1 - - + -
207B ILE* 4.6 6.3 - - + -
210B CYS* 5.2 0.7 - - - -
224B PRO* 4.2 15.9 - - + -
225B THR* 3.7 21.5 - - + -
232B ALA 3.1 13.6 + - - +
233B MSE 3.8 6.1 - - - +
235B HIS* 1.3 76.2 - - - +
237B ARG* 1.3 66.2 + - - +
239B LYS* 3.1 10.9 + - - -
240B VAL* 3.1 31.7 + - + +
244B ILE* 4.7 2.9 - - + -
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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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233B MSE 2.9 17.1 + - - +
234B ALA 3.3 3.5 + - - +
236B VAL* 1.3 77.8 - - - +
238B GLU* 1.3 88.4 + - - +
239B LYS 3.2 1.0 + - - -
240B VAL* 3.5 5.4 - - - +
244B ILE* 3.9 21.3 - - + +
263B ARG* 2.8 36.6 + - - +
264B ALA 3.8 5.1 - - - +
265B ALA* 3.8 20.2 - - - +
266B ASP* 3.5 23.6 - - - +
235G HIS* 2.9 34.3 + - - +
239G LYS* 3.0 56.5 - - - +
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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
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234B ALA* 2.9 34.2 + - - +
235B HIS* 3.9 6.5 - - - +
237B ARG* 1.3 100.7 + - - +
239B LYS* 1.3 65.3 + - + +
240B VAL 4.9 0.4 - - - -
262B GLN 5.0 3.6 - - - +
263B ARG* 6.1 0.2 - - - +
238C GLU* 5.0 8.3 - - - +
239G LYS* 4.9 7.9 - - - +
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Residues in contact with LYS 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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207B ILE* 3.8 32.6 - - + +
235B HIS 3.5 10.3 + - - +
236B VAL 3.1 7.4 + - - +
238B GLU* 1.3 85.2 + - + +
240B VAL* 1.3 62.9 + - - +
241B GLY 4.1 0.5 + - - -
237C ARG* 3.1 46.2 + - - +
238C GLU* 3.2 23.2 + - + +
239C LYS 4.1 2.2 + - - -
240C VAL 2.7 32.0 + - - -
241C GLY* 4.9 4.9 - - - -
242C ILE 6.4 0.2 - - - -
266C ASP* 6.2 0.2 - - - -
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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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207B ILE* 3.7 30.3 - - + +
210B CYS* 3.6 32.8 - - + -
236B VAL* 3.1 20.8 + - + +
237B ARG 4.0 2.9 - - - +
239B LYS* 1.3 81.0 - - - +
241B GLY* 1.3 60.2 + - - +
242B ILE 3.3 20.2 - - - +
244B ILE* 3.8 20.6 - - + -
239G LYS* 3.2 29.1 - - - +
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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