Contacts of the helix formed by residues 232 - 244 (chain X) in PDB entry 2QW0
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 ARG 232 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228X VAL* 5.5 0.4 - - - +
230X GLU* 3.3 38.0 + - - +
231X PHE* 1.3 81.7 - - - +
233X PRO* 1.4 62.5 - - + +
234X VAL 3.6 0.7 - - - -
235X ASP* 3.3 25.3 + - + +
236X ALA* 2.8 35.2 + - - +
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Residues in contact with PRO 233 (chain X).
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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231X PHE* 3.8 20.8 - - + +
232X ARG* 1.4 83.8 - - + +
234X VAL* 1.3 59.4 + - + +
236X ALA 3.3 1.6 + - - -
237X LEU* 3.1 25.1 + - - +
257X ALA* 4.0 30.5 - - + +
258X LEU* 3.5 13.6 - - + +
261X ALA* 4.0 20.2 - - + -
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Residues in contact with VAL 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X ARG* 5.1 0.2 - - - +
233X PRO* 1.3 75.7 - - + +
235X ASP* 1.3 66.6 + - - +
237X LEU* 3.2 5.6 + - - +
238X GLN* 3.0 37.8 + - - +
261X ALA* 4.0 20.9 - - + +
269X LEU* 4.8 14.8 - - + +
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Residues in contact with ASP 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228X VAL* 5.4 2.9 - - - +
230X GLU 4.9 7.6 - - - +
232X ARG* 3.3 34.5 + - + +
234X VAL* 1.3 76.5 - - - +
236X ALA* 1.3 58.9 + - - +
238X GLN* 3.1 17.0 + - - +
239X LEU* 2.9 48.5 + - - +
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Residues in contact with ALA 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X LEU* 4.1 16.0 - - + +
202X LEU* 4.5 5.8 - - + -
228X VAL* 5.9 1.8 - - + -
231X PHE* 4.2 14.8 - - + -
232X ARG 2.8 21.0 + - - +
233X PRO 3.7 4.7 - - - +
234X VAL 3.3 0.4 - - - -
235X ASP* 1.3 76.4 + - - +
237X LEU* 1.3 62.1 + - - +
239X LEU* 3.3 12.4 + - + +
240X VAL* 3.2 26.1 + - - +
258X LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X PRO 3.1 17.6 + - - +
234X VAL* 3.2 5.1 + - - +
236X ALA* 1.3 73.9 - - - +
238X GLN* 1.3 67.1 + - - +
240X VAL* 3.4 13.8 + - + +
241X GLN* 3.2 18.4 + - - +
248X LEU* 6.0 2.9 - - + -
258X LEU* 3.8 22.4 - - + +
261X ALA* 4.0 9.2 - - + -
262X ALA* 3.5 41.1 - - + +
269X LEU* 4.0 23.4 - - + +
271X LEU* 3.8 32.4 - - + +
274X LEU* 6.1 2.0 - - + -
296X LEU* 4.4 13.0 - - + -
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Residues in contact with GLN 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234X VAL* 3.0 25.8 + - + +
235X ASP* 3.1 18.5 + - - +
237X LEU* 1.3 76.7 - - - +
239X LEU* 1.3 54.3 + - + +
241X GLN* 3.1 8.9 + - - +
242X GLN* 2.7 40.6 + - + +
269X LEU* 3.8 21.3 - - + +
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Residues in contact with LEU 239 (chain X).
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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24X PRO* 3.7 34.8 - - + -
200X LEU* 4.3 14.6 - - + -
226X VAL* 4.5 5.6 - - + -
227X VAL 5.0 2.2 - - - +
228X VAL* 4.2 26.9 - - + -
235X ASP* 2.9 38.4 + - - +
236X ALA* 3.6 11.2 - - - +
237X LEU 3.3 0.4 - - - -
238X GLN* 1.3 73.1 - - + +
240X VAL* 1.3 59.9 + - - +
242X GLN* 4.4 13.2 - - - +
243X GLU* 2.7 41.3 + - + +
245X VAL* 4.0 2.9 - - - -
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Residues in contact with VAL 240 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X LEU* 4.4 4.0 - - + -
236X ALA 3.2 15.9 + - - +
237X LEU* 3.4 18.4 - - + +
238X GLN 3.3 0.2 - - - -
239X LEU* 1.3 73.0 - - - +
241X GLN* 1.3 57.9 + - - +
244X GLN* 3.0 25.1 + - - -
245X VAL* 3.1 32.8 + - + +
248X LEU* 4.3 18.8 - - + -
271X LEU* 3.9 25.1 - - + -
273X SER* 3.5 10.2 + - - +
274X LEU* 4.1 25.1 - - + -
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Residues in contact with GLN 241 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237X LEU 3.2 8.7 + - - +
238X GLN* 3.1 12.9 + - - +
240X VAL* 1.3 79.7 - - - +
242X GLN* 1.3 63.1 + - - +
244X GLN* 3.3 21.1 - - - +
268X SER 4.8 2.9 - - - +
269X LEU* 4.0 18.8 - - + +
270X LYS* 3.3 47.7 + - + +
273X SER* 5.3 0.2 - - - -
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Residues in contact with GLN 242 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X PRO* 3.8 18.8 - - - +
29X ARG* 5.4 0.4 - - - +
238X GLN* 2.7 23.0 + - + +
239X LEU* 4.1 9.7 - - - +
241X GLN* 1.3 76.5 - - + +
243X GLU* 1.3 87.5 + - - +
244X GLN* 3.4 4.0 + - - +
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Residues in contact with GLU 243 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X ALA* 4.1 7.4 - - - +
24X PRO* 4.0 20.4 - - + +
29X ARG* 3.0 31.8 + - - -
198X VAL* 3.5 14.1 - - + +
224X THR* 5.7 1.4 - - - +
226X VAL* 4.2 20.2 - - + +
239X LEU* 2.7 25.9 + - + +
242X GLN* 1.3 104.6 + - - +
244X GLN* 1.3 71.4 + - - +
245X VAL* 4.1 11.9 - - + -
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Residues in contact with GLN 244 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X HIS 4.9 0.2 - - - +
198X VAL* 3.1 20.4 - - + +
240X VAL 3.0 5.2 + - - +
241X GLN* 3.3 16.6 - - - +
242X GLN 3.4 4.1 - - - +
243X GLU* 1.3 80.3 - - - +
245X VAL* 1.3 65.3 + - - +
246X THR* 3.4 7.4 + - + +
273X SER* 3.3 25.8 + - - -
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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