Contacts of the helix formed by residues 228 - 239 (chain B) in PDB entry 2BTU
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 TYR 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B ASN* 3.1 19.5 - - - +
93B VAL* 4.8 2.5 - - - -
181B LEU* 4.0 18.8 - - + -
182B ALA 3.4 17.5 + - - -
183B SER* 3.6 1.0 - - - -
187B HIS* 3.2 17.8 + + - -
226B LYS* 3.5 22.2 - - + +
227B ILE* 1.3 72.4 - - - +
229B VAL* 1.3 68.0 + - - +
230B LYS 3.4 2.2 - - - -
231B PRO* 3.4 9.3 - - + +
232B ILE* 3.1 22.9 + - + +
246B HIS* 4.9 1.1 - + - -
302B GLY* 3.2 34.0 - - - -
303B MET* 3.3 38.1 - - + -
324B GLU* 3.2 39.0 - - + -
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Residues in contact with VAL 229 (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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89B VAL* 3.3 53.6 - - + +
90B ASN* 4.1 2.7 - - - +
93B VAL* 3.9 15.8 - - + +
99B PRO* 3.3 22.9 - - + -
130B ALA* 3.2 25.1 - - + +
227B ILE* 3.4 12.3 - - + +
228B TYR* 1.3 79.7 - - - +
230B LYS* 1.3 68.7 + - + +
232B ILE* 3.8 1.6 - - - +
233B LEU* 3.2 27.0 + - + +
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Residues in contact with LYS 230 (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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128B ARG 3.9 11.2 + - - -
129B GLN* 2.8 31.7 + - - +
130B ALA 5.1 2.7 - - - +
131B GLY* 4.1 15.3 - - - +
227B ILE* 5.4 0.2 - - - +
229B VAL* 1.3 83.8 - - + +
231B PRO* 1.3 70.7 - - + +
233B LEU* 3.1 11.1 + - + +
234B GLU* 2.8 39.3 - - - +
322B GLN* 6.1 0.4 - - + -
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Residues in contact with PRO 231 (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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227B ILE 4.8 3.1 - - - +
228B TYR* 3.4 17.3 - - + +
230B LYS* 1.3 96.5 - - + +
232B ILE* 1.3 61.1 + - - +
234B GLU* 3.6 1.6 + - - +
235B LEU* 3.0 21.3 + - - +
319B LEU* 4.1 12.4 - - + +
322B GLN* 3.4 46.5 - - + +
324B GLU* 3.9 29.6 - - + +
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.7 28.5 - - + +
181B LEU* 5.6 6.5 - - + -
228B TYR* 3.1 22.0 + - + +
229B VAL 3.8 2.7 - - - +
231B PRO* 1.3 76.7 - - - +
233B LEU* 1.3 53.8 + - - +
235B LEU* 2.7 20.1 + - + +
236B LEU* 2.6 58.0 + - + -
244B MET* 4.0 16.4 - - - -
303B MET* 4.1 25.1 - - - -
305B VAL* 5.7 1.6 - - + -
319B LEU* 4.9 2.0 - - + +
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Residues in contact with LEU 233 (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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93B VAL* 4.0 18.2 - - + -
96B GLY 4.8 3.6 - - - +
97B ALA 4.2 10.8 - - - +
98B GLU* 4.3 33.2 - - + +
99B PRO* 4.7 0.7 - - + -
229B VAL* 3.2 25.6 + - + +
230B LYS* 3.1 12.5 + - + +
232B ILE* 1.3 81.8 - - + +
234B GLU* 1.3 66.4 + - - +
236B LEU* 3.4 11.7 + - + +
237B LYS* 2.9 27.9 + - - +
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Residues in contact with GLU 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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230B LYS* 2.8 43.8 - - - +
231B PRO* 3.9 7.9 - - + -
233B LEU* 1.3 79.3 - - - +
235B LEU* 1.3 62.5 + - - +
237B LYS* 3.6 7.1 - - - +
238B ASN* 2.5 34.1 + - - +
318B LEU* 3.9 4.5 - - + +
322B GLN* 4.0 24.0 + - - +
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Residues in contact with LEU 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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231B PRO 3.0 14.2 + - - +
232B ILE* 2.7 22.8 + - + +
234B GLU* 1.3 74.9 - - - +
236B LEU* 1.3 53.3 + - - -
238B ASN 3.0 1.7 + - - -
239B HIS* 2.5 63.8 + - + +
241B VAL* 3.7 22.9 - - + -
244B MET* 5.7 0.7 - - - -
305B VAL* 4.7 18.6 - - + -
315B ILE* 4.0 18.8 - - + -
318B LEU* 3.9 11.4 - - + +
319B LEU* 4.2 28.9 - - + -
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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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96B GLY* 3.7 27.8 - - - +
165B LYS 5.2 4.9 - - - +
167B VAL* 3.9 23.8 - - + -
232B ILE* 2.6 42.7 + - + +
233B LEU* 3.9 11.2 - - + +
235B LEU* 1.3 73.1 - - - +
237B LYS* 1.3 61.0 + - - +
238B ASN 3.3 0.9 + - - -
239B HIS 3.3 17.5 + - - +
241B VAL* 4.1 22.7 - - + +
244B MET* 4.0 4.7 - - + -
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Residues in contact with LYS 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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233B LEU 2.9 18.0 + - - +
234B GLU* 3.6 12.3 - - - +
235B LEU 3.1 0.2 - - - -
236B LEU* 1.3 75.7 - - - +
238B ASN* 1.3 64.8 + - - +
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Residues in contact with ASN 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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234B GLU* 2.5 27.3 - - - +
235B LEU 3.0 1.0 + - - -
236B LEU 4.3 0.4 - - - -
237B LYS* 1.3 86.4 + - - +
239B HIS* 1.3 75.6 + - + +
318B LEU* 3.7 25.5 - - + +
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Residues in contact with HIS 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 LEU* 2.5 29.4 + - + +
236B LEU* 3.3 20.8 - - - +
238B ASN* 1.3 84.5 + - + +
240B GLU* 1.3 66.5 + - - +
241B VAL* 3.4 7.1 + - + +
311B ASP* 4.2 20.0 - - + +
314B ASP* 4.5 11.3 - - + +
315B ILE* 3.6 41.7 + - + +
318B LEU* 3.7 28.8 - - + +
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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