Contacts of the helix formed by residues 233 - 249 (chain C) in PDB entry 2BHT
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 HIS 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C GLU* 3.0 29.5 + - + +
203C GLY* 5.5 3.6 - - - -
204C SER* 2.8 27.8 + - - -
232C ILE* 1.3 77.3 - - - +
234C GLN* 1.3 70.1 + - + +
235C ARG* 3.0 62.0 + - + +
236C ASP* 3.2 7.4 + - + +
237C ALA* 3.0 20.5 + - - +
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Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLY 5.1 0.2 - - - +
204C SER* 3.1 13.2 + - - +
205C SER* 2.6 52.9 + - - +
206C ILE* 3.3 24.4 - - + +
233C HIS* 1.3 73.2 - - + +
235C ARG* 1.3 52.4 + - - +
237C ALA* 2.9 5.2 + - - +
238C GLU* 2.6 65.8 + - + +
254C VAL* 5.2 0.7 - - + -
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Residues in contact with ARG 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C HIS* 3.0 39.2 + - + +
234C GLN* 1.3 78.1 - - - +
236C ASP* 1.3 54.5 + - + +
238C GLU* 3.1 15.8 - - - +
239C ASN* 2.7 48.2 + - - +
242C ARG* 4.1 1.1 + - - +
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Residues in contact with ASP 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ILE* 4.9 3.1 - - + -
233C HIS* 3.2 9.3 + - + +
235C ARG* 1.3 77.8 - - + +
237C ALA* 1.3 62.4 + - - +
238C GLU 3.3 0.2 - - - -
239C ASN* 3.3 25.8 + - - +
240C THR* 3.0 38.8 + - - -
261C ALA* 4.1 8.6 - - - +
265C ARG* 4.9 7.9 + - - +
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Residues in contact with ALA 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ILE* 5.0 2.9 - - + -
232C ILE* 3.9 13.5 - - + +
233C HIS 3.0 14.0 + - - +
234C GLN* 2.9 11.3 + - - +
236C ASP* 1.3 77.8 - - - +
238C GLU* 1.3 56.3 + - - +
240C THR* 3.4 0.7 + - - -
241C MET* 2.8 27.2 + - - +
254C VAL* 4.0 15.7 - - + +
257C GLY* 3.5 9.3 - - - -
258C GLY* 3.8 30.1 - - - +
261C ALA* 4.8 0.2 - - - -
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Residues in contact with GLU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLN* 2.6 57.4 + - - +
235C ARG* 3.1 15.1 - - - +
237C ALA* 1.3 70.5 - - - +
239C ASN* 1.3 63.1 + - - +
241C MET* 3.2 18.2 - - + +
242C ARG* 3.0 40.3 + - - +
254C VAL* 3.8 17.5 - - + +
291C VAL* 4.3 17.0 - - + +
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Residues in contact with ASN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C ARG* 2.7 34.4 + - - +
236C ASP* 3.3 29.5 + - - +
237C ALA 3.4 0.4 - - - -
238C GLU* 1.3 72.7 - - - +
240C THR* 1.3 57.9 + - - +
242C ARG* 2.5 32.3 + - - +
243C GLU* 2.9 30.1 + - - +
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Residues in contact with THR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C MET* 5.3 3.5 - - - +
236C ASP* 3.0 27.7 + - - -
237C ALA 3.8 1.1 - - - -
239C ASN* 1.3 73.7 - - - +
241C MET* 1.3 61.4 + - - +
243C GLU* 3.9 8.4 - - - +
244C LEU* 2.8 31.3 + - - +
257C GLY* 3.1 23.8 - - - +
260C VAL* 3.3 16.8 - - + -
261C ALA* 3.2 28.6 - - - +
264C LEU* 5.0 2.2 - - + +
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Residues in contact with MET 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ALA 2.8 15.6 + - - +
238C GLU* 3.2 21.8 - - + +
240C THR* 1.3 77.2 - - - +
242C ARG* 1.3 63.9 + - - +
244C LEU* 3.2 26.9 - - - +
245C ALA* 3.3 6.4 + - - +
250C ILE 4.4 1.0 - - - +
252C CYS* 3.1 30.3 - - - +
253C GLY* 3.3 28.0 - - - +
254C VAL* 3.7 11.9 - - + -
257C GLY* 4.1 2.0 - - - -
286C TYR* 5.2 0.2 - - - -
291C VAL* 3.3 46.0 - - + +
292C PHE* 3.5 18.5 - - + -
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Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ARG* 4.1 1.6 + - - +
238C GLU* 3.0 28.8 + - - +
239C ASN* 2.5 49.1 + - - +
241C MET* 1.3 79.2 - - + +
243C GLU* 1.3 59.2 + - - +
245C ALA* 3.4 5.7 + - - +
246C VAL* 3.0 27.4 + - - +
290C GLY 5.5 0.6 + - - -
291C VAL* 2.8 41.5 + - - +
292C PHE* 3.9 27.8 - - + +
105D ALA* 4.3 2.4 - - - +
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C MET* 3.0 31.5 - - + +
239C ASN 2.9 16.1 + - - +
240C THR* 4.3 7.6 - - - +
241C MET 3.2 0.2 - - - -
242C ARG* 1.3 75.0 - - - +
244C LEU* 1.3 59.5 + - - +
246C VAL* 2.8 24.2 - - - +
247C ARG* 2.7 61.2 + - + +
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.9 5.2 - - + -
19C MET* 3.3 17.6 - - + +
29C LEU* 3.7 20.4 - - + -
240C THR 2.8 26.5 + - - +
241C MET* 3.2 10.7 + - - +
243C GLU* 1.3 75.1 - - - +
245C ALA* 1.3 67.0 + - - +
248C GLU* 3.0 8.3 + - + -
249C GLY 2.9 18.5 + - - -
250C ILE* 2.9 43.4 + - + +
252C CYS* 3.9 18.2 - - - -
257C GLY* 4.0 12.6 - - - +
260C VAL* 4.2 21.1 - - + -
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Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C MET 3.3 6.2 + - - +
242C ARG* 3.6 10.1 - - - +
243C GLU 3.3 0.4 - - - -
244C LEU* 1.3 75.6 - - - +
246C VAL* 1.3 58.4 + - - +
249C GLY* 2.8 27.5 + - - -
250C ILE 3.0 18.8 + - - +
251C PHE* 4.6 12.8 - - + +
292C PHE* 4.6 2.5 - - + -
81D ALA* 3.7 3.8 - - - +
105D ALA* 3.1 33.2 - - + +
106D TYR* 4.0 8.4 - - + +
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ARG 3.0 12.8 - - - +
243C GLU* 2.8 27.8 - - + +
245C ALA* 1.3 73.1 - - - +
247C ARG* 1.3 69.0 + - + +
81D ALA* 2.9 30.7 - - - +
104D ARG 5.4 0.2 - - - +
105D ALA 3.8 14.4 - - - +
106D TYR 3.9 18.5 - - - +
107D GLY* 4.3 7.0 - - - +
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 2.5 57.2 + - + +
19C MET* 2.9 46.4 - - + +
243C GLU* 2.7 59.5 + - + +
246C VAL* 1.3 80.4 - - + +
248C GLU* 1.3 59.1 + - - +
81D ALA 3.4 1.9 - - - +
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LYS 4.5 1.4 - - - +
16C LEU* 3.7 20.7 - - + +
17C GLN* 3.1 27.7 + - - +
18C ARG* 2.5 42.6 + - - +
19C MET* 3.2 31.3 + - + +
244C LEU* 3.0 10.0 + - + +
247C ARG* 1.3 76.9 - - - +
249C GLY* 1.3 56.0 + - - +
250C ILE* 3.1 20.5 + - + +
4D LEU* 4.4 0.7 - - - +
81D ALA* 4.6 1.8 - - - -
82D LEU* 2.7 34.9 - - - +
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Residues in contact with GLY 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ALA* 2.8 22.9 + - - -
246C VAL 3.6 2.6 + - - -
248C GLU* 1.3 77.8 - - - +
250C ILE* 1.3 61.7 + - - +
251C PHE 3.4 3.8 + - - -
4D LEU* 3.7 16.0 - - - +
78D MET* 3.9 1.4 - - - +
81D ALA* 3.7 14.4 - - - -
82D LEU* 4.4 6.5 - - - -
106D TYR* 3.6 20.1 + - - -
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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