Contacts of the helix formed by residues 228 - 239 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ASN* 2.8 33.0 - - - +
93A VAL* 4.7 0.7 - - - -
181A LEU* 4.0 20.6 - - + -
182A ALA 2.9 27.8 + - - -
183A SER* 3.4 1.7 - - - -
187A HIS* 3.1 22.9 + - - -
226A LYS* 3.7 17.8 - - + +
227A ILE* 1.3 73.6 - - - +
229A VAL* 1.3 62.9 + - - +
230A LYS 3.7 1.1 - - - -
231A PRO* 3.7 9.9 - - - +
232A ILE* 2.8 33.6 + - + +
246A HIS* 4.5 2.2 - + - -
302A GLY* 3.2 32.2 - - - -
303A MET* 3.4 33.2 - - + -
324A GLU* 3.8 20.9 - - - -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.4 52.3 - - + +
90A ASN* 4.3 0.4 - - - +
93A VAL* 4.1 12.6 - - + -
99A PRO* 4.0 13.0 - - + -
130A ALA* 3.1 30.3 - - - +
227A ILE* 3.3 5.5 - - + +
228A TYR* 1.3 76.5 - - - +
230A LYS* 1.3 60.7 + - + +
232A ILE* 2.7 24.8 + - - +
233A LEU* 3.1 33.3 + - + +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.8 17.0 + - - +
129A GLN* 3.1 29.9 + - - +
130A ALA 4.4 8.1 - - - +
131A GLY* 4.0 12.2 - - - -
227A ILE* 5.2 0.4 + - - +
229A VAL* 1.3 78.2 - - + +
231A PRO* 1.3 70.9 - - + +
233A LEU* 3.4 7.7 + - + +
234A GLU* 2.6 40.8 + - - +
322A GLN* 4.8 0.9 - - + -
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 5.1 2.9 - - + -
227A ILE 4.8 2.9 - - - +
228A TYR* 3.7 11.9 - - - +
229A VAL 3.6 3.4 - - - +
230A LYS* 1.3 94.1 - - + +
232A ILE* 1.3 63.3 + - - +
234A GLU* 2.9 13.7 + - - +
235A LEU* 3.0 13.0 + - - +
319A LEU* 4.1 14.8 - - + +
322A GLN* 3.3 38.0 - - + +
324A GLU* 3.4 36.8 - - + +
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Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 3.3 29.8 - - + +
181A LEU* 3.9 21.8 - - + -
228A TYR 2.8 24.9 + - - +
229A VAL 2.7 11.9 + - - +
231A PRO* 1.3 75.7 - - - +
233A LEU* 1.3 58.2 + - - +
235A LEU* 3.4 24.7 - - + +
236A LEU* 3.0 22.8 - - + +
244A MET* 3.5 27.8 - - - -
303A MET* 3.3 33.4 - - - -
305A VAL* 5.8 0.9 - - + -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 3.7 9.9 - - + -
96A GLY 4.8 1.6 - - - +
97A ALA 3.4 29.2 - - - +
98A GLU* 4.1 26.5 - - + -
229A VAL* 3.1 29.2 + - + +
230A LYS* 4.0 10.5 - - + +
231A PRO 3.2 0.4 - - - -
232A ILE* 1.3 75.6 - - - +
234A GLU* 1.3 70.1 + - - +
236A LEU* 3.6 14.0 - - + +
237A LYS* 3.0 26.7 + - - +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LYS* 2.6 43.0 - - - +
231A PRO 2.9 4.9 + - - +
233A LEU* 1.3 82.0 - - - +
235A LEU* 1.3 70.0 + - - +
237A LYS* 3.2 7.2 + - - +
238A ASN* 3.1 25.2 + - - +
318A LEU* 4.1 5.8 - - + -
322A GLN* 3.2 35.4 - - - +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PRO 3.0 8.1 + - - +
232A ILE* 3.4 27.8 - - + +
234A GLU* 1.3 71.7 - - - +
236A LEU* 1.3 52.0 + - + +
238A ASN* 2.5 29.3 + - - +
239A HIS* 2.7 17.6 + - + -
241A VAL* 3.3 33.0 - - + -
244A MET* 5.8 2.0 - - - -
305A VAL* 4.9 12.3 - - + -
307A VAL* 5.2 2.5 - - + -
315A ILE* 4.0 23.3 - - + -
318A LEU* 3.3 22.6 - - + +
319A LEU* 3.4 37.5 - - + -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY* 4.0 32.8 - - - +
165A LYS 6.0 0.4 - - - +
167A VAL* 5.1 6.3 - - + -
232A ILE* 3.0 35.2 - - + +
233A LEU* 3.6 14.4 - - + +
235A LEU* 1.3 73.5 - - + +
237A LYS* 1.3 64.4 + - - +
238A ASN 3.1 0.6 + - - -
239A HIS 3.6 15.9 + - - +
241A VAL* 3.7 34.3 - - + +
244A MET* 4.4 11.7 - - + -
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU 3.0 14.7 + - - +
234A GLU* 3.5 14.6 - - - +
235A LEU 3.1 0.4 - - - -
236A LEU* 1.3 76.5 - - - +
238A ASN* 1.3 68.4 + - - +
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Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.1 10.8 + - - +
235A LEU 2.5 20.2 + - - +
237A LYS* 1.3 85.0 - - - +
239A HIS* 1.3 79.9 + - + +
318A LEU* 3.8 17.7 - - + +
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Residues in contact with HIS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU* 2.7 18.3 + - + +
236A LEU* 3.6 22.7 + - - +
237A LYS 3.8 0.4 - - - -
238A ASN* 1.3 95.6 + - + +
240A GLU* 1.3 64.3 + - - +
241A VAL* 3.6 4.3 + - - +
311A ASP* 4.3 19.1 - - + -
314A ASP* 4.0 21.6 + - + +
315A ILE* 4.0 46.3 - - + +
318A LEU* 4.0 17.9 - - + +
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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
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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