Contacts of the helix formed by residues 229 - 240 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A ALA 4.6 2.2 + - - -
291A ALA* 3.8 9.3 + - - -
292A GLY* 4.3 15.5 - - - -
254B TYR* 4.6 9.9 - - - -
257B TYR* 6.0 0.3 - - - -
223F GLN* 5.7 0.5 + - - -
225F THR* 4.7 0.3 + - - -
226F VAL* 3.4 13.7 + - - +
227F SER 3.2 4.6 - - - -
228F TRP* 1.3 77.1 - - - +
230F ILE* 1.3 64.2 + - - +
231F PRO* 3.7 8.8 - - - +
232F ALA* 2.9 33.3 + - - +
233F MSE 3.3 17.2 + - - +
249F ALA* 5.7 0.6 - - - +
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Residues in contact with ILE 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B GLU* 6.2 0.4 - - - -
227F SER 4.7 2.0 - - - +
228F TRP 3.9 4.1 + - - +
229F SER* 1.3 72.5 - - - +
231F PRO* 1.4 73.2 - - + +
233F MSE 3.1 8.9 + - + +
234F ALA* 3.1 18.2 + - - +
249F ALA* 3.7 31.9 - - + +
255F ASP* 5.0 4.7 - - + +
258F GLU* 4.4 10.3 - - + +
259F ILE* 3.5 32.3 - - + -
262F GLN* 3.5 26.9 - - - +
264F ALA* 3.5 22.2 - - + +
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Residues in contact with PRO 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ARG* 3.9 26.6 + - - +
257B TYR* 5.3 3.6 - - + -
258B GLU* 3.5 26.9 - - - +
261B ARG* 3.9 19.1 - - - +
229F SER* 3.5 8.7 - - - +
230F ILE* 1.4 95.9 - - + +
232F ALA* 1.3 55.9 + - - +
234F ALA* 3.3 6.5 + - + +
235F HIS* 2.9 29.8 + - - +
262F GLN* 3.7 15.9 - - - +
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Residues in contact with ALA 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ARG* 3.7 21.7 - - - +
291A ALA 4.1 4.7 - - - +
292A GLY* 4.2 12.6 - - - +
203F VAL* 4.4 6.2 - - + +
225F THR* 4.1 11.7 - - - +
226F VAL* 5.3 1.8 - - + +
229F SER* 2.9 30.6 + - - +
231F PRO* 1.3 76.6 - - - +
233F MSE 1.3 63.7 + - - +
235F HIS* 3.2 4.0 - - - +
236F VAL* 3.1 27.1 + - - +
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Residues in contact with MSE 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F GLN* 3.6 22.4 - - - +
224F PRO* 5.1 2.7 - - + -
225F THR* 3.6 17.2 + - - +
229F SER 3.3 7.1 + - - +
230F ILE* 3.1 10.8 + - + +
232F ALA* 1.3 76.3 - - - +
234F ALA* 1.3 60.7 + - - +
236F VAL* 3.2 5.1 + - - +
237F ARG* 2.9 27.0 + - - +
244F ILE* 4.2 18.1 - - + +
245F VAL 4.8 0.2 - - - +
246F ALA* 3.5 41.7 - - + -
249F ALA* 3.8 16.4 - - + -
259F ILE* 4.0 10.5 - - + -
264F ALA* 3.5 32.5 - - + +
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Residues in contact with ALA 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F ILE 3.1 8.2 + - - +
231F PRO* 3.7 10.3 - - + +
233F MSE 1.3 76.0 - - - +
235F HIS* 1.3 62.7 - - - +
237F ARG* 3.2 3.6 + - - +
238F GLU* 2.9 44.1 + - - +
262F GLN* 4.3 11.9 - - + +
263F ARG 4.5 2.2 - - - +
264F ALA* 3.7 31.6 + - + +
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Residues in contact with HIS 235 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A ARG* 3.2 35.6 + - - +
263A ARG* 3.0 42.6 + - + +
265A ALA 3.4 25.4 - - - -
266A ASP* 2.7 23.8 + - - -
293A LEU* 4.6 0.2 - - + -
203F VAL* 3.7 17.2 - - + +
207F ILE* 4.9 2.2 - - + -
231F PRO 2.9 15.0 + - - +
232F ALA* 3.2 11.9 - - - +
234F ALA* 1.3 78.0 - - - +
236F VAL* 1.3 63.1 + - - +
238F GLU* 3.7 7.6 + - - +
239F LYS* 3.5 14.6 + - - +
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Residues in contact with VAL 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F VAL* 4.2 25.1 - - + +
206F ALA* 3.8 20.6 - - + +
207F ILE* 4.5 4.7 - - + -
210F CYS* 5.2 0.7 - - - -
224F PRO* 4.4 14.4 - - + -
225F THR* 3.5 24.9 - - + -
232F ALA 3.1 15.8 + - - +
233F MSE 3.2 5.4 + - - +
235F HIS* 1.3 74.2 - - - +
237F ARG* 1.3 67.7 + - - +
239F LYS* 3.0 6.0 + - - -
240F VAL* 3.0 41.9 + - + +
244F ILE* 4.8 2.9 - - + -
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Residues in contact with ARG 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F MSE 2.9 17.6 + - - +
234F ALA 3.6 3.0 + - - +
236F VAL* 1.3 77.7 - - - +
238F GLU* 1.3 86.7 + - - +
239F LYS 3.2 0.9 + - - -
240F VAL* 3.4 7.6 + - - +
242F ILE 5.2 1.0 - - - +
244F ILE* 3.8 21.7 - - + +
263F ARG* 2.8 35.2 + - - +
264F ALA* 3.8 16.3 - - - +
265F ALA* 3.8 9.0 - - - +
266F ASP* 3.5 32.2 + - - +
235H HIS* 3.2 32.1 + - - +
239H LYS* 3.1 34.9 + - - +
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Residues in contact with GLU 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ARG* 5.9 1.0 + - - -
238A GLU* 5.9 3.6 - - - +
234F ALA* 2.9 34.9 + - - +
235F HIS* 4.1 6.7 - - - +
237F ARG* 1.3 100.1 + - - +
239F LYS* 1.3 57.5 + - - +
262F GLN 5.1 3.6 - - - +
239H LYS* 2.9 19.4 + - - +
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Residues in contact with LYS 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ARG* 2.9 36.6 + - - +
238A GLU* 3.1 22.7 + - - +
239A LYS 3.9 2.4 + - - -
240A VAL 2.7 29.2 + - - +
241A GLY* 4.8 7.0 - - - +
242A ILE 6.4 0.4 - - - -
207F ILE* 3.7 42.0 - - + -
235F HIS 3.5 11.5 + - - +
236F VAL 3.0 7.6 + - - +
238F GLU* 1.3 81.8 + - - +
240F VAL* 1.3 62.1 + - - +
241F GLY 4.1 0.3 + - - -
239H LYS* 3.8 2.1 + - - -
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Residues in contact with VAL 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F ILE* 3.7 29.2 - - + +
210F CYS* 3.5 33.2 - - + -
236F VAL* 3.0 22.6 + - + +
237F ARG 3.4 4.8 - - - +
239F LYS* 1.3 78.1 - - - +
241F GLY* 1.3 60.8 + - - +
242F ILE 3.4 20.9 - - - +
244F ILE* 3.9 20.9 - - + -
239H LYS* 2.7 28.0 + - - +
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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