Contacts of the helix formed by residues 233 - 249 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B GLU* 2.9 30.6 + - + +
203B GLY 5.8 0.4 - - - -
204B SER* 2.9 29.2 - - - -
206B ILE* 4.3 1.1 - - - -
232B ILE* 1.3 78.8 - - - +
234B GLN* 1.3 72.6 + - + +
235B ARG* 3.0 40.8 + - + +
236B ASP* 2.3 33.7 + - - +
237B ALA* 3.4 7.8 + - - +
125C LEU* 6.0 5.8 - - + +
128C GLU* 5.4 8.2 + - - -
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Residues in contact with GLN 234 (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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203B GLY 4.5 0.2 - - - +
204B SER* 2.7 18.3 + - - +
205B SER 3.0 28.8 + - - +
206B ILE* 4.1 11.4 - - + -
233B HIS* 1.3 82.1 + - + +
235B ARG* 1.3 57.2 + - - +
237B ALA* 3.8 0.7 - - - +
238B GLU* 2.9 67.7 + - + +
254B VAL* 5.6 0.9 - - + -
112C LEU 5.1 2.2 + - - -
113C VAL* 5.1 2.8 - - - +
114C THR* 3.3 22.8 - - - +
117C GLN* 2.5 33.9 + - - +
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Residues in contact with ARG 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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233B HIS* 3.0 34.7 - - + +
234B GLN* 1.3 79.6 - - - +
236B ASP* 1.3 72.7 + - - +
238B GLU* 4.5 7.0 - - - +
239B ASN* 2.9 49.9 + - - +
242B ARG* 5.2 0.7 + - - +
295B GLU 5.5 2.4 + - - -
296B HIS* 5.4 10.7 - - - +
132C ARG* 5.4 8.6 - - - +
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Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 4.8 1.2 - - - +
232B ILE* 4.9 5.8 - - + -
233B HIS* 2.3 52.0 + - - +
235B ARG* 1.3 83.6 - - - +
237B ALA* 1.3 57.8 + - - +
239B ASN* 3.6 5.3 - - - +
240B THR* 2.8 36.4 + - - +
261B ALA* 4.8 14.1 - - + -
265B ARG* 5.9 1.1 + - - -
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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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206B ILE* 4.0 14.8 - - + -
232B ILE* 4.7 1.9 - - + +
233B HIS 3.4 10.4 + - - +
234B GLN 3.8 7.2 - - - +
235B ARG 3.5 0.2 - - - -
236B ASP* 1.3 79.3 - - - +
238B GLU* 1.3 63.4 + - - +
241B MET* 3.1 25.5 + - - +
254B VAL* 3.4 28.9 - - + +
257B GLY* 3.5 4.9 - - - -
258B GLY* 3.7 22.6 - - - +
261B ALA* 5.3 0.2 - - - +
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Residues in contact with GLU 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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205B SER 4.7 0.9 - - - +
234B GLN* 2.9 49.4 + - + +
235B ARG* 4.5 4.6 - - - +
237B ALA* 1.3 74.1 - - - +
239B ASN* 1.3 63.2 + - - +
241B MET* 3.7 9.9 + - - +
242B ARG* 3.0 57.9 + - - +
254B VAL* 3.8 21.1 - - + +
291B VAL* 4.1 14.2 - - + +
295B GLU* 5.0 1.0 - - - +
112C LEU 5.1 6.9 - - - +
114C THR* 4.7 4.7 - - - +
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Residues in contact with ASN 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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235B ARG* 2.9 43.4 + - - +
236B ASP* 3.6 6.8 - - - +
237B ALA 3.2 0.2 - - - -
238B GLU* 1.3 79.1 - - - +
240B THR* 1.3 58.4 + - - +
242B ARG* 2.8 41.7 + - - +
243B GLU* 2.8 29.5 + - - +
294B GLU* 5.7 1.2 - - - +
295B GLU 4.8 7.0 + - - +
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Residues in contact with THR 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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19B MET* 4.3 13.9 - - + -
236B ASP* 2.8 24.5 + - - +
239B ASN* 1.3 71.4 - - - +
241B MET* 1.3 53.7 + - - +
243B GLU* 2.5 34.8 + - - +
244B LEU* 2.6 26.1 + - + +
257B GLY 3.3 23.1 - - - +
260B VAL* 4.1 13.2 - - + -
261B ALA* 3.4 25.1 - - + +
264B LEU* 4.9 4.4 - - + +
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Residues in contact with MET 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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237B ALA 3.1 16.7 + - - +
238B GLU* 3.8 12.3 - - - +
240B THR* 1.3 75.7 - - - +
242B ARG* 1.3 62.4 + - - +
244B LEU* 3.9 8.9 - - - +
245B ALA* 3.4 21.8 + - - +
250B ILE 4.3 1.9 - - - +
252B CYS* 3.2 32.2 - - - +
253B GLY* 3.8 7.9 - - - +
254B VAL* 3.6 23.3 - - + -
257B GLY* 3.6 18.8 - - - +
291B VAL* 3.3 42.0 - - + +
292B PHE* 3.6 29.1 - - + -
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 4.9 0.3 - - - +
235B ARG 5.2 0.6 + - - -
238B GLU* 3.0 48.8 + - - +
239B ASN* 2.8 36.5 + - - +
241B MET* 1.3 82.7 - - + +
243B GLU* 1.3 59.5 + - + +
245B ALA* 3.4 10.9 + - - +
246B VAL* 3.5 18.0 + - - +
291B VAL* 2.9 34.7 + - - +
292B PHE* 4.9 13.5 - - + +
293B GLY 3.5 4.1 + - - +
294B GLU* 4.0 34.0 - - + +
295B GLU* 2.6 43.2 + - - +
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 2.9 30.9 - - + +
239B ASN* 2.8 28.0 + - - +
240B THR* 2.5 21.9 + - - +
242B ARG* 1.3 69.0 - - + +
244B LEU* 1.3 65.4 + - - +
245B ALA 3.1 2.2 - - - -
246B VAL* 4.7 2.0 - - - +
247B ARG* 3.0 37.5 + - + +
264B LEU* 5.5 1.6 - - - +
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Residues in contact with LEU 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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16B LEU* 4.0 27.6 - - + -
19B MET* 4.0 14.4 - - - -
29B LEU* 4.4 2.7 - - + -
240B THR* 2.6 29.8 + - + +
241B MET* 3.9 4.7 - - - +
242B ARG 3.3 0.2 - - - -
243B GLU* 1.3 72.7 - - - +
245B ALA* 1.3 55.4 + - - +
248B GLU* 3.3 12.1 + - + +
249B GLY 3.2 6.8 + - - -
250B ILE* 2.8 50.7 + - + +
252B CYS* 4.0 20.0 - - - -
256B SER 4.3 4.7 - - - +
257B GLY* 4.4 2.7 - - - -
260B VAL* 3.3 34.8 - - + -
279B ILE* 4.6 1.1 - - + -
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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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81A ALA* 3.9 1.9 - - - +
105A ALA* 3.6 24.2 - - + +
106A TYR* 3.6 14.8 - - + -
241B MET 3.4 9.2 + - - +
242B ARG* 3.6 10.1 - - - +
243B GLU 3.1 0.6 - - - -
244B LEU* 1.3 77.5 - - - +
246B VAL* 1.3 62.2 + - - +
249B GLY* 3.2 20.1 + - - -
250B ILE 2.9 17.7 + - - +
251B PHE* 4.6 8.1 - - + -
292B PHE* 4.7 10.5 - - + -
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Residues in contact with VAL 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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81A ALA* 3.4 21.3 - - - +
104A ARG 5.0 0.4 - - - +
105A ALA 3.0 24.9 - - - +
106A TYR 3.9 10.7 - - - +
107A GLY* 3.9 18.2 - - - +
242B ARG 3.5 12.9 + - - +
243B GLU* 4.7 2.0 - - - +
245B ALA* 1.3 76.9 - - - +
247B ARG* 1.3 65.4 + - + +
294B GLU* 5.2 9.2 - - - +
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Residues in contact with ARG 247 (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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81A ALA 4.6 3.4 - - - -
18B ARG* 2.8 87.4 + - - +
19B MET* 4.2 15.9 - - + -
243B GLU* 3.0 22.3 + - + +
246B VAL* 1.3 85.3 + - + +
248B GLU* 1.3 60.0 + - - +
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Residues in contact with GLU 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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81A ALA* 4.7 3.4 - - - -
82A LEU* 3.1 24.1 - - - +
15B LYS 4.5 1.4 - - - +
16B LEU* 3.5 13.8 - - - +
17B GLN* 2.7 29.2 + - - +
18B ARG 2.7 26.5 + - - -
19B MET* 2.7 42.0 + - - +
244B LEU* 3.3 18.1 + - + +
247B ARG* 1.3 82.2 - - - +
249B GLY* 1.3 63.1 + - - +
250B ILE* 3.5 18.5 + - + +
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Residues in contact with GLY 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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4A LEU* 3.2 22.4 - - - +
78A MET* 3.9 4.5 - - - +
81A ALA* 3.9 16.4 - - - +
82A LEU* 4.2 9.4 - - - -
106A TYR* 3.8 19.2 + - - -
244B LEU 3.2 1.8 + - - -
245B ALA 3.2 14.2 + - - -
247B ARG 3.8 0.2 - - - -
248B GLU* 1.3 79.2 - - - +
250B ILE* 1.3 59.6 + - - +
251B PHE 3.9 1.0 + - - -
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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