Contacts of the helix formed by residues 236 - 252 (chain B) in PDB entry 3TQI
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 GLY 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B LEU 3.2 1.4 + - - -
235B SER* 1.3 75.1 - - - +
237B GLY* 1.3 67.7 + - - +
238B VAL 3.6 0.9 + - - -
239B ASP* 3.9 7.4 + - - +
240B SER* 3.1 19.5 + - - -
265B LEU* 5.4 6.0 - - - +
269B GLU* 6.4 0.2 - - - +
402B PHE* 5.9 8.1 - - - -
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU 4.3 3.9 + - - +
236B GLY* 1.3 78.7 - - - +
238B VAL* 1.3 65.0 + - - -
240B SER* 3.2 1.2 + - - -
241B ALA* 3.0 22.8 + - - +
269B GLU* 5.4 1.0 + - - +
396B LEU* 5.0 3.8 - - - -
399B ARG* 3.4 29.6 - - - +
402B PHE* 6.0 5.2 - - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLY 3.6 0.8 + - - -
237B GLY* 1.3 71.8 - - - -
239B ASP* 1.3 66.8 + - - +
241B ALA* 3.4 1.0 + - - +
242B VAL* 3.0 25.6 + - + +
380B LYS* 4.8 12.8 - - - +
383B VAL* 4.1 17.5 - - + -
384B ARG* 4.5 10.1 - - + -
396B LEU* 3.3 31.6 - - + +
397B ILE* 3.4 38.1 - - + +
399B ARG* 4.4 15.0 - - + +
400B HIS 5.8 0.9 - - - +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLY 3.9 6.9 + - - +
237B GLY 3.4 0.4 - - - -
238B VAL* 1.3 76.8 - - - +
240B SER* 1.3 56.5 + - - +
243B THR* 2.6 33.3 + - - -
334B GLY* 3.4 28.2 - - - +
336B ILE* 3.9 20.8 - - - +
339B ASP* 5.2 1.9 - - - +
375B LEU* 3.3 12.7 - - + +
380B LYS* 3.6 27.2 - - - +
383B VAL* 4.1 8.3 - - - +
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 4.4 1.7 - - - +
233B GLY 3.3 22.9 + - - -
234B LEU* 3.7 13.9 - - - -
235B SER 3.1 18.0 + - - -
236B GLY* 3.1 12.1 + - - -
237B GLY 3.2 7.9 + - - -
239B ASP* 1.3 75.1 - - - +
241B ALA* 1.3 66.8 + - - +
243B THR* 3.0 10.0 + - - -
244B ALA* 2.9 24.2 + - - +
334B GLY* 4.5 6.4 + - - +
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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
----------------------------------------------------------
234B LEU* 5.0 2.4 + - - -
237B GLY 3.0 14.0 + - - +
238B VAL 3.4 4.2 + - - +
240B SER* 1.3 77.3 - - - +
242B VAL* 1.3 61.6 + - - +
244B ALA* 3.1 2.0 + - - -
245B THR* 2.9 28.4 + - - -
277B PHE* 3.5 27.0 - - + -
392B LEU* 3.8 18.8 - - + -
396B LEU* 3.9 19.3 - - + -
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 3.0 25.2 + - + +
241B ALA* 1.3 76.2 - - - +
243B THR* 1.3 63.4 + - - +
245B THR* 4.0 2.7 - - - -
246B LEU* 3.0 24.0 + - + +
375B LEU* 3.5 33.7 - - + -
383B VAL* 3.7 16.8 - - + +
386B LEU* 4.2 16.2 - - + -
387B GLY* 3.4 31.0 - - - -
390B LEU* 4.2 8.3 - - + +
392B LEU* 3.9 9.2 - - + -
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 4.1 13.7 - - + -
239B ASP 2.6 20.5 + - - -
240B SER* 3.0 9.7 + - - -
242B VAL* 1.3 77.8 - - - +
244B ALA* 1.3 58.4 + - - +
246B LEU* 3.6 5.1 - - - +
247B VAL* 3.0 40.2 + - + +
332B GLY* 4.4 1.8 - - - -
333B GLN 3.7 28.1 + - - +
334B GLY* 3.3 15.8 - - - -
374B PRO* 3.9 20.0 - - + -
375B LEU* 3.5 10.5 - - - +
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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
----------------------------------------------------------
232B VAL* 3.9 23.8 - - + -
234B LEU* 3.9 15.5 - - + -
240B SER 2.9 12.6 + - - +
241B ALA 3.6 7.0 - - - +
243B THR* 1.3 74.3 - - - +
245B THR* 1.3 59.4 + - - +
247B VAL* 3.5 0.5 + - - +
248B HIS* 2.8 29.7 + - - +
255B LEU* 3.3 6.3 - - - +
257B CYS* 4.5 7.4 - - - -
277B PHE* 3.6 19.5 - - + -
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Residues in contact with THR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ALA 2.9 17.2 + - - -
242B VAL* 4.0 3.4 - - - -
244B ALA* 1.3 75.8 - - - +
246B LEU* 1.3 59.0 + - - +
248B HIS* 3.4 10.4 - - + +
249B LYS* 2.9 39.6 + - + +
277B PHE* 3.7 9.5 - - - -
281B LEU* 5.3 11.6 - - + +
390B LEU* 3.8 35.2 - - + +
392B LEU* 3.6 25.3 - - + +
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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
----------------------------------------------------------
214B ILE* 4.3 22.7 - - + +
217B SER* 3.3 26.9 - - - +
218B ILE* 4.3 7.6 - - + +
221B ILE* 4.0 8.1 - - + +
242B VAL 3.0 15.9 + - - +
243B THR* 3.6 4.3 - - - +
245B THR* 1.3 79.1 - - - +
247B VAL* 1.3 62.3 + - + +
249B LYS* 3.5 5.8 + - - +
250B ALA* 3.2 20.8 + - - +
374B PRO* 3.6 22.2 - - + -
375B LEU* 4.2 15.9 - - + -
386B LEU* 4.5 12.3 - - + -
390B LEU* 3.5 31.4 - - + +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 4.0 26.5 - - + -
230B VAL* 4.4 13.9 - - + -
232B VAL* 4.3 11.0 - - + -
243B THR* 3.0 28.5 + - + +
244B ALA 3.8 3.1 - - - +
246B LEU* 1.3 73.9 - - - +
248B HIS* 1.3 65.3 + - - +
250B ALA* 2.9 12.4 + - - +
251B ILE* 2.9 39.5 + - + +
255B LEU* 3.8 21.8 - - + -
332B GLY* 5.8 0.2 - - - -
372B ILE* 5.3 6.3 - - + -
374B PRO* 4.9 4.5 - - + -
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Residues in contact with HIS 248 (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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244B ALA 2.8 19.4 + - - +
245B THR* 3.4 11.7 + - - +
247B VAL* 1.3 77.1 - - - +
249B LYS* 1.3 63.9 + - - +
252B GLY* 2.9 43.5 + - - +
255B LEU* 3.4 24.2 - - + -
277B PHE* 6.3 0.4 - - + -
281B LEU* 3.8 33.5 - - + +
282B GLY* 5.6 0.4 - - - -
283B ALA* 4.6 19.2 + - + -
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Residues in contact with LYS 249 (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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214B ILE* 5.7 0.2 - - + -
218B ILE* 4.3 22.3 - - + +
222B GLN* 4.9 1.6 + - - -
245B THR* 2.9 25.4 + - + +
246B LEU* 3.8 6.5 - - - +
248B HIS* 1.3 82.9 - - - +
250B ALA* 1.3 61.6 + - - +
252B GLY 4.7 0.7 + - - -
389B GLU 5.4 1.4 + - - -
390B LEU* 3.9 44.9 + - + +
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Residues in contact with ALA 250 (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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218B ILE* 3.8 28.5 - - + +
221B ILE* 3.8 30.3 - - + -
222B GLN* 3.1 22.5 + - + +
246B LEU 3.2 12.8 + - - +
247B VAL 2.9 8.8 + - - +
249B LYS* 1.3 78.4 - - - +
251B ILE* 1.3 63.9 + - + +
252B GLY 3.9 0.2 - - - -
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Residues in contact with ILE 251 (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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221B ILE* 4.1 5.2 - - + -
222B GLN* 4.8 5.6 - - + -
225B VAL* 3.7 23.1 - - + -
226B GLY 4.6 2.2 - - - +
228B GLU 4.4 0.2 - - - +
230B VAL* 3.6 31.6 - - + -
247B VAL* 2.9 28.4 + - + +
250B ALA* 1.3 90.3 - - + +
252B GLY* 1.3 64.7 + - - +
253B ASP* 3.2 1.2 + - - +
254B GLN* 3.0 52.8 + - + +
255B LEU 3.7 11.4 - - - +
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Residues in contact with GLY 252 (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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248B HIS* 2.9 33.8 + - - -
249B LYS 4.7 0.8 + - - -
250B ALA 3.9 0.6 - - - -
251B ILE* 1.3 74.3 - - - +
253B ASP* 1.3 62.9 + - - -
254B GLN 3.0 5.4 + - - -
255B LEU* 3.1 21.3 + - - +
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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
------------------------------------------------------------
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