Contacts of the strand formed by residues 234 - 240 (chain A) in PDB entry 5BUK
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 THR 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A PHE* 3.5 4.5 - - - -
229A LEU* 2.8 34.6 + - + +
232A ILE* 2.7 40.5 + - + +
233A ASP* 1.3 74.4 - - - +
235A TRP* 1.3 63.3 + - - +
250A VAL* 3.9 24.2 - - + -
251A VAL 3.2 16.2 - - - +
252A THR* 2.9 19.4 + - - -
256A ARG* 4.1 0.5 - - - -
267A PHE* 4.8 1.5 - - + -
271A THR* 4.0 17.0 - - + +
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Residues in contact with TRP 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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199A GLN* 5.5 0.2 - - + -
226A ILE* 3.7 43.1 - - + -
227A HIS 3.2 9.2 - - - +
228A PHE* 4.3 10.3 - + + -
233A ASP 5.5 0.4 - - - -
234A THR* 1.3 75.4 - - - +
236A VAL* 1.3 67.3 + - - +
237A TRP* 3.7 28.0 - + + -
249A GLY 3.9 0.3 - - - +
250A VAL* 3.5 2.8 - - - -
251A VAL* 2.8 70.1 + - + +
296A ASP* 4.4 0.4 - - - -
320A ASP* 3.0 34.2 + - - -
321A PRO* 3.8 27.6 - - + -
322A ILE* 3.3 21.9 - - + +
376A TYR* 4.6 1.3 - - - +
377A TYR* 3.2 19.5 + + - -
501A FAD 5.1 2.5 - + - -
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Residues in contact with VAL 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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225A PHE 3.5 1.6 - - - +
226A ILE* 3.3 2.9 - - - -
227A HIS* 2.8 42.3 + - + +
229A LEU* 4.5 8.7 - - + -
235A TRP* 1.3 83.5 - - - +
237A TRP* 1.3 70.2 + - - +
248A VAL* 4.7 1.3 - - + -
249A GLY 3.3 9.4 - - - +
250A VAL* 4.1 6.5 - - + -
271A THR* 3.8 31.9 - - + +
272A LEU* 3.9 22.7 - - + -
274A SER* 5.8 0.4 - - - +
275A ARG* 3.8 25.7 + - - +
278A LEU* 5.1 0.9 - - + -
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Residues in contact with TRP 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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43A VAL* 3.7 25.1 - - + -
45A GLU* 4.8 1.3 - - - -
201A ALA* 4.2 2.0 - - + -
203A HIS* 3.4 37.0 - + + -
225A PHE 3.3 4.3 - - - +
226A ILE* 3.9 21.3 - - + -
235A TRP* 3.7 20.4 - + + -
236A VAL* 1.3 77.6 - - - +
238A GLN* 1.3 59.9 + - - +
239A ILE* 3.5 31.0 - - + +
247A SER* 3.1 35.1 + - - -
248A VAL* 3.3 12.1 - - - +
249A GLY* 2.9 38.5 + - - +
251A VAL* 3.5 24.2 - - + -
501A FAD 3.9 20.9 - + + -
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Residues in contact with GLN 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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209A PHE* 3.6 28.9 - - + -
211A ARG* 3.8 27.2 - - - +
214A LEU* 6.1 0.8 - - - +
221A SER 4.5 0.9 - - - +
223A PHE 4.0 3.0 - - - +
224A ILE* 3.5 6.4 - - - -
225A PHE* 2.9 59.5 + - + +
237A TRP* 1.3 73.6 - - - +
239A ILE* 1.3 61.7 + - - +
240A PRO* 4.3 0.7 - - + -
246A THR* 3.5 20.4 - - + -
247A SER 3.4 3.6 - - - -
248A VAL* 4.7 5.6 - - + +
278A LEU* 4.2 16.5 - - + +
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Residues in contact with ILE 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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45A GLU* 4.0 25.1 - - + +
46A SER* 3.9 12.8 - - - +
119A HIS* 3.7 21.5 - - + +
224A ILE* 3.6 30.7 - - + -
237A TRP* 3.5 28.5 - - + +
238A GLN* 1.3 78.0 - - - +
240A PRO* 1.3 77.4 - - - +
241A ILE* 4.4 1.3 - - + -
246A THR* 3.5 3.7 - - - -
247A SER* 2.7 45.9 + - - +
501A FAD 4.1 12.3 - - - +
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Residues in contact with PRO 240 (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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70A PRO* 4.0 11.4 - - + +
119A HIS* 3.1 58.9 - - + +
211A ARG* 3.5 46.2 - - - +
222A ASP* 3.6 20.9 - - - +
223A PHE 3.7 11.7 - - - +
238A GLN 4.1 0.9 - - - +
239A ILE* 1.3 87.3 - - - +
241A ILE* 1.3 60.7 + - - +
245A ILE 4.0 0.2 - - - +
246A THR* 4.5 0.2 - - - -
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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