Contacts of the helix formed by residues 232 - 246 (chain A) in PDB entry 2QVH
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.7 33.2 - - + -
10A ILE* 3.9 20.2 - - + -
22A ARG* 6.1 0.4 - - + -
26A LEU* 4.1 1.4 - - - +
35A GLU* 2.6 25.6 + - - +
231A GLU* 1.3 79.4 - - - +
233A SER* 1.3 65.2 + - - +
234A VAL* 3.0 19.6 + - - +
235A GLY 3.1 0.9 + - - -
236A LEU* 2.9 15.9 + - - +
258A LEU* 4.0 6.5 - - - -
261A LEU* 4.4 4.7 - - + -
264A ASP* 3.4 13.0 - - - -
265A VAL* 3.8 11.5 - - + +
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A THR* 1.3 74.8 - - - +
234A VAL* 1.3 56.0 + - - +
236A LEU* 3.8 9.6 - - - -
237A ALA* 2.9 30.7 + - - +
258A LEU* 3.3 8.0 - - - +
264A ASP* 2.4 31.0 + - - -
266A CYS* 3.7 16.6 - - - -
269A PRO* 4.5 0.2 - - - -
270A LEU* 2.9 32.2 + - - +
282A VAL* 3.7 10.9 - - - +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.8 13.0 - - + -
33A TRP* 3.7 23.3 - - + +
34A GLY* 3.5 32.9 - - - +
35A GLU* 3.7 2.6 + - + +
57A ALA* 5.8 0.9 - - - +
62A TRP* 4.9 2.3 - - - -
232A THR* 3.0 12.8 - - - +
233A SER* 1.3 79.6 - - - +
235A GLY* 1.3 62.3 + - - +
237A ALA* 3.4 12.8 + - - +
238A ALA* 3.8 5.4 + - - +
265A VAL* 4.0 7.9 - - + -
266A CYS* 4.5 0.4 - - - -
282A VAL* 3.7 15.9 - - + +
284A VAL* 3.7 30.5 - - + -
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Residues in contact with GLY 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.0 23.4 + - - -
204A VAL* 5.6 0.9 - - - +
205A GLN* 5.4 2.0 - - - -
231A GLU* 3.5 31.7 - - - +
232A THR 3.1 0.4 + - - -
234A VAL* 1.3 73.7 - - - +
236A LEU* 1.3 65.4 + - - +
238A ALA* 3.1 17.8 + - - +
239A GLY* 3.4 7.6 + - - -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A SER* 3.4 32.8 - - - -
231A GLU* 3.7 21.5 - - - +
232A THR 2.9 14.6 + - - +
233A SER* 3.9 6.5 - - - +
235A GLY* 1.3 77.4 - - - +
237A ALA* 1.3 56.8 + - - +
239A GLY* 3.0 3.4 + - - +
240A VAL* 2.8 33.2 + - + +
255A LEU* 4.2 24.3 - - + +
257A THR* 3.6 8.7 - - - +
258A LEU* 3.7 39.5 - - + +
270A LEU* 3.9 17.0 - - + +
277A LEU* 5.9 0.7 - - + -
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.8 17.5 - - + -
233A SER 2.9 18.1 + - - +
234A VAL 3.5 7.9 - - - +
235A GLY 3.2 0.4 - - - -
236A LEU* 1.3 76.8 - - - +
238A ALA* 1.3 56.8 + - - +
240A VAL* 3.6 5.6 - - - +
241A ALA* 2.9 28.1 + - - +
270A LEU* 3.5 14.6 - - + +
280A ARG 4.0 17.0 - - - +
281A ARG* 4.9 0.4 - - - -
282A VAL* 4.1 12.6 - - + +
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 5.9 0.4 - - - +
57A ALA* 4.9 5.6 - - + -
62A TRP* 3.5 34.6 - - + +
204A VAL* 3.6 29.1 - - + +
210A VAL* 3.6 2.9 - - - +
234A VAL 3.8 2.6 + - - +
235A GLY* 3.1 13.2 + - - +
237A ALA* 1.3 76.6 - - - +
239A GLY* 1.3 62.3 + - - +
241A ALA* 3.2 3.2 + - - +
242A LEU 2.9 23.6 + - - -
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Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 3.6 16.9 - - - +
226A VAL* 3.6 11.8 - - - +
227A SER 5.7 1.1 - - - -
228A SER* 6.3 0.4 - - - -
235A GLY 3.4 6.3 + - - -
236A LEU* 3.0 8.0 + - - -
238A ALA* 1.3 80.0 - - - +
240A VAL* 1.3 61.0 + - - +
242A LEU* 3.2 4.0 + - - +
243A ALA* 3.0 19.6 + - - +
255A LEU* 3.8 19.1 - - - -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.9 12.3 - - + +
236A LEU* 2.8 19.3 + - + +
237A ALA* 3.6 9.6 - - - +
239A GLY* 1.3 77.6 - - - +
241A ALA* 1.3 56.4 + - - +
243A ALA* 3.3 2.3 + - - +
244A ALA* 2.8 28.6 + - - +
255A LEU* 3.8 21.5 - - + +
270A LEU* 4.4 10.1 - - + -
277A LEU* 3.9 22.9 - - + -
278A PRO 3.8 15.3 - - - +
279A VAL* 3.8 29.8 - - + -
280A ARG 4.9 2.0 - - - +
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.4 41.7 - - + -
63A PRO 4.9 3.8 - - - +
65A PRO* 5.3 1.5 - - - +
210A VAL* 4.3 4.3 - - + +
237A ALA 2.9 17.5 + - - +
238A ALA 3.2 6.5 + - - +
240A VAL* 1.3 78.6 - - - +
242A LEU* 1.3 61.2 - - - +
244A ALA* 3.4 6.7 + - - +
245A ALA* 3.1 24.8 + - - +
279A VAL* 5.1 6.3 - - + -
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 3.9 16.6 - - + +
204A VAL* 3.7 20.2 - - + +
210A VAL* 3.7 33.6 - - + +
213A ALA* 3.5 26.5 - - + -
214A LEU* 3.7 20.0 - - + +
226A VAL* 3.9 24.2 - - + -
238A ALA 2.9 13.5 + - - +
239A GLY 3.2 7.4 + - - +
241A ALA* 1.3 73.2 - - - +
243A ALA* 1.3 65.6 + - - +
245A ALA* 3.0 11.1 + - - -
246A LEU* 3.2 19.1 + - + +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 2.8 21.1 + - - -
70A VAL* 3.9 15.0 - - + -
226A VAL* 3.9 12.8 - - + -
239A GLY 3.0 16.4 + - - +
240A VAL 3.7 4.3 - - - +
242A LEU* 1.3 77.8 - - - +
244A ALA* 1.3 57.3 + - - +
245A ALA 3.5 0.3 + - - -
246A LEU* 3.7 5.1 + - - -
249A LEU* 3.2 15.9 - - + +
253A CYS* 3.9 27.6 - - - -
255A LEU* 4.4 5.2 - - + -
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO* 3.5 17.5 - - + -
66A VAL* 2.7 39.4 + - - +
67A ARG* 3.5 16.8 + - + +
70A VAL* 4.1 1.6 - - + -
240A VAL 2.8 17.9 + - - +
241A ALA 3.7 3.6 - - - +
242A LEU 3.1 0.2 - - - -
243A ALA* 1.3 77.0 - - - +
245A ALA* 1.3 53.4 + - - +
279A VAL* 3.4 31.0 - - + -
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Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PRO* 4.4 11.4 - - + +
64A ALA 4.1 19.1 - - - +
65A PRO* 4.4 0.9 - - + -
66A VAL* 4.3 10.4 - - - +
210A VAL* 4.7 1.3 - - + -
214A LEU* 4.0 29.3 - - + +
241A ALA 3.1 14.9 + - - +
242A LEU* 3.0 6.5 + - - +
244A ALA* 1.3 78.6 - - - +
246A LEU* 1.3 63.7 + - - +
247A PRO* 3.7 2.9 - - - +
11B PRO* 5.3 6.6 - - - +
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.4 4.0 - - - +
67A ARG* 2.7 26.7 + - - -
202A LEU* 4.4 6.7 - - + -
214A LEU* 3.7 18.2 - - + -
217A ALA* 4.2 17.5 - - + -
224A VAL* 3.8 29.2 - - + -
226A VAL* 3.6 25.8 - - + -
242A LEU* 3.2 13.4 + - + +
243A ALA 4.0 5.2 - - - +
244A ALA 3.5 1.0 - - - -
245A ALA* 1.3 80.0 - - - +
247A PRO* 1.3 76.3 - - + +
248A GLU 4.1 10.5 - - - +
249A LEU* 3.6 23.6 - - + -
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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