Contacts of the helix formed by residues 233 - 249 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 6.0 2.7 + - - -
201D GLU* 3.7 24.8 + - + +
204D SER* 3.7 16.9 + - - -
231D ASP 4.2 1.2 + - - -
232D ILE* 1.3 72.2 - - - +
234D GLN* 1.3 62.0 + - + +
235D ARG* 3.0 37.5 + - + +
236D ASP* 2.7 46.1 + - - +
237D ALA* 2.9 9.7 + - - +
265D ARG* 5.2 1.8 - - - +
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Residues in contact with GLN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 5.6 0.6 - - - +
114A THR* 3.6 5.3 + - - +
117A GLN* 3.1 25.1 + - - +
125A LEU* 6.0 1.4 - - - +
204D SER* 3.1 26.8 + - - +
205D SER* 2.8 51.7 + - - +
206D ILE* 4.7 6.1 - - + -
232D ILE 3.3 4.6 + - - -
233D HIS* 1.3 73.4 - - + +
235D ARG* 1.3 57.7 + - - +
237D ALA* 3.3 9.3 + - - +
238D GLU* 2.8 45.2 + - - +
254D VAL* 4.7 2.3 - - + +
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.5 11.5 - - - +
233D HIS* 3.0 23.6 + - + +
234D GLN* 1.3 75.0 + - - +
236D ASP* 1.3 61.6 + - - +
237D ALA 3.0 1.5 + - - -
238D GLU* 3.1 7.5 + - - -
239D ASN* 2.7 55.3 + - - +
295D GLU* 3.4 46.9 + - - +
296D HIS* 2.9 50.7 - - + +
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Residues in contact with ASP 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ILE* 4.9 1.1 - - + -
233D HIS* 2.7 33.5 + - + +
235D ARG* 1.3 76.5 - - - +
237D ALA* 1.3 54.6 + - - +
239D ASN* 4.7 4.3 - - - -
240D THR* 2.9 35.9 + - - +
257D GLY 4.3 0.5 - - - +
261D ALA* 4.4 15.2 - - + +
265D ARG* 4.3 12.3 + - - +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ILE* 4.3 8.3 - - + -
232D ILE* 4.3 5.3 - - + +
233D HIS 2.9 10.7 + - - +
234D GLN* 3.4 12.8 - - - +
236D ASP* 1.3 75.5 - - - +
238D GLU* 1.3 55.5 + - - +
240D THR 3.2 1.0 + - - -
241D MET* 2.7 35.9 + - - +
254D VAL* 4.0 17.9 - - + +
257D GLY* 3.8 5.1 - - - -
258D GLY* 3.7 30.7 - - - +
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Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 4.5 6.8 - - - +
205D SER 5.4 0.3 - - - +
234D GLN* 2.8 39.3 + - - +
235D ARG* 3.6 11.9 - - - +
237D ALA* 1.3 71.3 - - - +
239D ASN* 1.3 62.9 + - - +
241D MET* 3.2 9.2 - - - +
242D ARG* 3.1 48.0 + - - +
254D VAL* 4.0 11.3 - - + +
291D VAL* 3.5 28.7 - - + +
295D GLU* 2.5 30.1 - - - +
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Residues in contact with ASN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ARG* 2.7 57.1 + - - +
236D ASP* 4.4 4.2 - - - +
238D GLU* 1.3 73.9 - - - +
240D THR* 1.3 59.3 + - - +
242D ARG* 2.7 39.1 + - - +
243D GLU* 3.1 29.4 + - - +
294D GLU* 6.1 0.8 - - - +
295D GLU 4.6 0.2 - - - +
296D HIS* 3.5 20.7 - - - +
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Residues in contact with THR 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D MET* 3.9 12.4 - - + +
236D ASP* 2.9 23.7 + - - +
239D ASN* 1.3 76.6 - - - +
241D MET* 1.3 66.9 + - - +
243D GLU* 4.0 8.4 + - - +
244D LEU* 3.3 22.9 + - + +
257D GLY 3.4 20.9 - - - +
260D VAL* 3.7 29.6 - - + -
261D ALA* 4.0 10.9 - - - +
264D LEU* 5.6 1.1 - - + -
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Residues in contact with MET 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ALA 2.7 15.7 + - - +
238D GLU* 3.2 18.2 - - + +
240D THR* 1.3 79.2 - - - +
242D ARG* 1.3 63.7 + - + +
244D LEU* 3.2 17.4 + - - +
245D ALA 3.9 2.9 + - - -
250D ILE 4.8 1.0 - - - +
252D CYS* 3.0 26.1 + - - +
253D GLY* 3.2 12.3 - - - +
254D VAL* 3.3 32.3 - - - -
257D GLY* 3.7 8.1 - - - -
286D TYR* 5.5 0.7 - - - -
291D VAL* 3.6 43.1 - - + +
292D PHE* 3.6 33.9 - - + -
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Residues in contact with ARG 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA 4.2 4.7 - - - +
238D GLU* 3.1 30.9 + - - +
239D ASN* 2.7 39.3 - - - +
241D MET* 1.3 81.3 - - + +
243D GLU* 1.3 62.6 + - - +
244D LEU 3.0 1.8 + - - -
245D ALA* 3.5 2.4 + - - +
246D VAL* 3.5 23.6 + - + +
291D VAL* 2.7 27.6 + - - +
292D PHE* 3.0 44.0 - - + +
293D GLY 3.2 16.8 + - - -
294D GLU* 4.2 5.6 - - - +
295D GLU* 2.5 44.3 + - - +
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Residues in contact with GLU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D MET* 3.5 22.0 - - + +
239D ASN 3.1 20.2 + - - +
240D THR* 4.0 8.2 + - - +
241D MET 3.3 0.4 - - - -
242D ARG* 1.3 76.6 - - - +
244D LEU* 1.3 57.2 + - - +
246D VAL* 3.7 6.3 - - + -
247D ARG* 2.5 82.2 + - + +
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.1 16.6 - - + -
19D MET* 4.0 14.6 - - + -
29D LEU* 3.9 26.7 - - + -
240D THR* 3.3 21.4 + - + +
241D MET 3.2 8.0 + - - +
242D ARG 3.0 1.2 - - - -
243D GLU* 1.3 76.2 - - - +
245D ALA* 1.3 59.9 + - - +
248D GLU* 2.7 32.8 + - + +
249D GLY 3.0 4.9 + - - -
250D ILE* 3.3 21.9 + - + +
252D CYS* 4.0 20.4 - - - -
257D GLY* 4.4 4.0 - - - -
260D VAL* 3.5 32.1 - - + -
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Residues in contact with ALA 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 3.2 8.7 - - - +
105C ALA 3.3 23.1 - - - +
106C TYR* 3.6 19.3 - - + -
241D MET 3.9 1.0 + - - -
242D ARG 3.5 4.1 + - - +
243D GLU 3.5 0.2 - - - -
244D LEU* 1.3 76.5 - - - +
246D VAL* 1.3 58.8 + - - +
249D GLY* 3.0 21.2 + - - -
250D ILE 3.0 25.0 + - - +
251D PHE* 4.1 15.3 - - + -
292D PHE* 4.8 4.7 - - + -
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Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 3.4 19.9 - - - +
104C ARG 5.3 0.4 - - - +
105C ALA 3.9 12.1 - - - +
106C TYR 4.0 16.3 - - - +
107C GLY* 4.2 9.0 - - - +
18D ARG* 5.1 0.2 + - - -
242D ARG* 3.5 15.2 + - + +
243D GLU* 3.3 10.5 + - + +
244D LEU 3.1 0.4 - - - -
245D ALA* 1.3 79.3 - - - +
247D ARG* 1.3 72.5 + - + +
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA 4.2 0.4 - - - -
18D ARG* 2.6 75.7 + - - +
19D MET* 3.8 16.4 - - + +
243D GLU* 2.5 64.2 + - + +
246D VAL* 1.3 80.7 - - + +
248D GLU* 1.3 68.8 + - + +
249D GLY 3.6 0.2 - - - -
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 4.7 1.3 - - - -
82C LEU* 3.4 22.3 - - - +
15D LYS 4.6 2.6 - - - +
16D LEU* 3.6 23.4 - - + +
17D GLN* 3.1 25.8 + - - +
18D ARG* 2.6 47.6 + - - +
19D MET* 3.0 23.3 + - - +
244D LEU* 2.7 15.7 + - + +
247D ARG* 1.3 74.1 - - - +
249D GLY* 1.3 62.4 + - - +
250D ILE* 3.0 27.5 + - + +
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Residues in contact with GLY 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.6 13.5 - - - +
78C MET* 3.8 10.3 - - - +
81C ALA* 3.5 15.5 - - - +
82C LEU* 4.6 1.6 - - - -
106C TYR* 2.9 27.5 + - - -
244D LEU 3.0 0.2 + - - -
245D ALA* 3.0 21.6 + - - -
247D ARG 3.6 1.4 - - - -
248D GLU* 1.3 78.2 - - - +
250D ILE* 1.3 58.2 + - - +
251D PHE 3.7 0.9 + - - -
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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