Contacts of the helix formed by residues 232 - 246 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.7 37.7 - - + -
10B ILE* 3.8 20.0 - - + -
22B ARG* 5.9 0.9 - - + -
26B LEU* 4.1 1.9 - - - +
35B GLU* 2.7 16.0 + - - +
231B GLU* 1.3 82.0 - - - +
233B SER* 1.3 66.9 + - - +
234B VAL* 3.1 14.4 + - - +
235B GLY 3.1 0.7 + - - -
236B LEU* 3.0 16.1 + - - +
258B LEU* 4.0 7.0 - - - -
261B LEU* 4.1 5.4 - - + -
264B ASP* 3.5 13.0 - - - -
265B VAL* 4.0 13.7 - - + +
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 1.3 74.0 - - - +
234B VAL* 1.3 57.3 + - - +
236B LEU* 3.8 9.0 - - - -
237B ALA* 2.9 30.7 + - - +
258B LEU* 3.3 6.5 - - - +
264B ASP* 2.5 32.8 + - - -
265B VAL* 5.0 0.2 - - - +
266B CYS* 3.8 17.3 - - - -
268B ASP 5.4 0.2 - - - -
269B PRO* 3.6 0.2 - - - +
270B LEU* 2.9 30.9 + - - +
282B VAL* 3.8 11.6 - - - +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.9 15.3 - - + -
33B TRP* 3.6 24.5 - - + +
34B GLY* 3.5 33.8 - - - +
35B GLU* 3.7 3.5 + - + +
57B ALA* 5.8 0.9 - - - +
62B TRP* 5.0 1.7 - - - -
232B THR* 3.0 10.6 + - - +
233B SER* 1.3 80.0 - - - +
235B GLY* 1.3 61.9 + - - +
237B ALA* 3.4 12.6 + - - +
238B ALA* 3.8 5.2 + - - +
265B VAL* 4.1 6.1 - - + -
266B CYS* 4.7 0.4 - - - -
282B VAL* 3.8 15.3 - - + -
284B VAL* 3.5 31.9 - - + -
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Residues in contact with GLY 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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35B GLU* 2.9 32.7 + - - -
204B VAL* 5.6 1.2 - - - +
205B GLN* 5.3 1.8 - - - -
231B GLU* 3.5 24.3 - - - +
232B THR 3.1 0.2 + - - -
234B VAL* 1.3 74.3 - - - +
236B LEU* 1.3 64.9 + - - +
238B ALA* 3.1 17.9 + - - +
239B GLY* 3.4 7.6 + - - -
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Residues in contact with LEU 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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228B SER* 3.4 33.0 - - - -
231B GLU* 3.7 22.0 - - - +
232B THR 3.0 17.7 + - - +
233B SER* 3.9 6.1 - - - +
235B GLY* 1.3 74.8 - - - +
237B ALA* 1.3 59.7 + - - +
239B GLY* 3.0 5.0 + - - +
240B VAL* 2.8 33.0 + - + +
255B LEU* 4.1 23.9 - - + +
257B THR* 3.6 8.7 - - - +
258B LEU* 3.7 35.7 - - + +
270B LEU* 4.0 17.9 - - + +
277B LEU* 5.7 0.7 - - + -
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Residues in contact with ALA 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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62B TRP* 3.8 17.5 - - + -
233B SER 2.9 18.1 + - - +
234B VAL 3.5 8.1 - - - +
235B GLY 3.2 0.2 - - - -
236B LEU* 1.3 75.8 - - - +
238B ALA* 1.3 57.7 + - - +
240B VAL* 3.4 5.6 + - - +
241B ALA* 2.9 27.2 + - - +
270B LEU* 3.6 8.9 - - + +
280B ARG 4.3 11.1 - - - +
282B VAL* 4.0 23.8 - - + +
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Residues in contact with ALA 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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53B ALA 5.9 0.7 - - - +
57B ALA* 4.9 6.1 - - + -
62B TRP* 3.5 32.2 - - + +
204B VAL* 3.6 24.9 - - + +
210B VAL* 3.5 7.6 - - - +
234B VAL 3.8 3.6 + - - +
235B GLY* 3.1 14.0 + - - +
236B LEU 3.1 0.6 - - - -
237B ALA* 1.3 77.6 - - - +
239B GLY* 1.3 63.5 + - - +
241B ALA* 3.2 3.5 + - - +
242B LEU 3.0 19.2 + - - -
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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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204B VAL* 3.6 16.5 - - - +
226B VAL* 3.6 11.3 - - - +
227B SER 5.7 1.1 - - - -
228B SER* 6.4 0.4 - - - -
235B GLY 3.4 5.5 + - - -
236B LEU 3.0 7.1 + - - -
238B ALA* 1.3 80.8 - - - +
240B VAL* 1.3 60.9 + - - +
242B LEU* 3.3 3.8 + - - +
243B ALA* 3.0 19.8 + - - +
255B LEU* 3.8 20.4 - - - -
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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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70B VAL* 4.0 11.4 - - + +
236B LEU 2.8 22.1 + - - +
237B ALA* 3.6 7.4 - - - +
239B GLY* 1.3 75.7 - - - +
241B ALA* 1.3 58.3 + - - +
243B ALA* 3.3 3.3 + - - +
244B ALA* 2.8 27.5 + - - +
255B LEU* 3.8 13.2 - - + -
270B LEU* 4.6 8.1 - - + -
277B LEU* 3.7 32.3 - - + -
278B PRO 3.7 20.2 - - - +
279B VAL* 3.7 25.4 - - + -
280B ARG 4.9 2.2 - - - +
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Residues in contact with ALA 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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62B TRP* 3.4 47.8 - - + -
63B PRO 4.9 3.8 - - - +
65B PRO* 5.4 1.5 - - - +
210B VAL* 4.3 3.7 - - + +
237B ALA 2.9 10.4 + - - +
238B ALA 3.2 9.4 + - - +
240B VAL* 1.3 77.8 - - - +
242B LEU* 1.3 61.4 + - - +
244B ALA* 3.4 6.9 + - - +
245B ALA* 3.1 24.6 + - - +
279B VAL* 5.1 5.8 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 4.0 14.8 - - + +
204B VAL* 3.8 19.7 - - + +
210B VAL* 3.7 19.2 - - + +
213B ALA* 3.6 35.4 - - + -
214B LEU* 3.7 25.8 - - + +
226B VAL* 3.8 26.7 - - + -
238B ALA 3.0 12.0 + - - +
239B GLY 3.6 6.7 - - - +
240B VAL 3.3 0.2 - - - -
241B ALA* 1.3 72.9 - - - +
243B ALA* 1.3 66.7 + - - +
245B ALA* 3.1 11.3 + - - +
246B LEU* 3.2 20.1 + - + +
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Residues in contact with ALA 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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67B ARG* 3.0 20.3 + - - -
70B VAL* 3.8 17.9 - - + -
226B VAL* 3.9 12.3 - - + +
239B GLY 3.0 13.0 + - - +
240B VAL 3.6 7.4 - - - +
242B LEU* 1.3 78.1 - - - +
244B ALA* 1.3 58.3 + - - +
245B ALA 3.4 0.5 + - - -
246B LEU* 3.5 2.7 + - - -
249B LEU* 3.4 16.6 - - + +
253B CYS* 4.1 26.2 - - - -
255B LEU* 4.4 4.3 - - + -
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Residues in contact with ALA 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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65B PRO* 3.5 23.1 - - + -
66B VAL* 2.7 39.1 + - - +
67B ARG* 3.5 16.3 + - + +
70B VAL* 3.9 1.5 - - + +
240B VAL 2.8 16.9 + - - +
241B ALA 3.8 4.7 - - - +
242B LEU 3.2 0.2 - - - -
243B ALA* 1.3 77.7 - - - +
245B ALA* 1.3 53.1 + - - +
246B LEU 3.5 0.2 - - - -
279B VAL* 3.6 25.1 - - + -
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Residues in contact with ALA 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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63B PRO* 4.3 13.0 - - + +
64B ALA 4.0 19.3 - - - +
65B PRO* 4.8 0.4 - - + -
66B VAL* 4.3 10.5 - - - +
210B VAL* 4.9 1.6 - - + -
214B LEU* 4.0 28.8 - - + +
241B ALA 3.1 13.7 + - - +
242B LEU* 3.1 6.4 + - - +
244B ALA* 1.3 76.4 - - - +
246B LEU* 1.3 65.3 + - - +
247B PRO* 3.8 2.8 - - - +
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Residues in contact with LEU 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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66B VAL* 3.5 4.7 - - - +
67B ARG* 2.8 18.7 + - - -
202B LEU* 4.5 6.5 - - + -
214B LEU* 3.6 19.5 - - + -
217B ALA* 4.0 24.2 - - + -
224B VAL* 3.7 24.2 - - + +
226B VAL* 3.7 24.7 - - + -
242B LEU* 3.2 13.4 + - + +
243B ALA 3.8 6.1 - - - +
244B ALA 3.5 1.2 - - - -
245B ALA* 1.3 80.2 - - - +
247B PRO* 1.3 80.5 - - + +
248B GLU 4.2 4.7 - - - +
249B LEU* 3.7 26.2 - - + -
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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