Contacts of the strand formed by residues 238 - 250 (chain A) in PDB entry 5BZZ
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 PHE 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A MET* 3.7 19.1 - - + -
200A PHE 3.4 16.2 - - - +
201A GLU* 3.9 32.1 - - + -
234A ARG* 3.4 8.0 - - - +
235A GLU* 2.9 48.3 + - + +
236A ASP* 6.1 0.4 - - + -
237A LYS* 1.3 87.8 - - + +
239A MET* 1.3 60.8 + - - +
240A TYR* 3.9 22.0 - - + -
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Residues in contact with MET 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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199A MET* 3.1 6.4 - - - +
200A PHE* 2.8 50.4 + - + +
203A ILE* 3.5 41.7 - - + -
210A THR* 4.3 4.3 - - - +
211A CYS* 4.0 21.5 - - - +
213A PRO* 3.9 23.8 - - - -
231A PRO* 4.0 22.0 - - + -
233A ARG 3.6 3.8 - - - -
234A ARG* 4.1 17.5 - - + +
237A LYS 4.1 0.4 + - - -
238A PHE* 1.3 75.0 - - - +
240A TYR* 1.3 64.4 + - - +
241A PHE* 4.0 12.9 - - + -
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Residues in contact with TYR 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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197A LYS* 4.6 24.2 - - + -
198A MET 3.6 3.8 - - - -
199A MET* 3.5 37.7 - - + -
231A PRO* 3.3 6.8 - - - +
232A THR* 2.8 30.6 + - - -
233A ARG* 2.8 57.1 + - + +
235A GLU* 3.4 42.1 + - + -
238A PHE* 3.9 14.5 - - + +
239A MET* 1.3 75.9 - - - +
241A PHE* 1.3 56.6 + - - +
242A GLU* 4.0 9.4 - - + +
346A TYR* 5.7 0.9 - - - -
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Residues in contact with PHE 241 (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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197A LYS* 3.1 4.3 - - - -
198A MET* 2.8 49.1 + - + +
200A PHE* 3.7 34.3 - + - -
213A PRO* 3.3 48.2 - - + -
215A PHE* 3.9 33.9 - + + -
227A SER* 5.5 0.7 - - - -
230A GLY 4.5 3.4 - - - -
231A PRO* 3.7 23.8 - - + -
232A THR* 3.6 4.0 - - - -
239A MET* 4.0 15.0 - - + -
240A TYR* 1.3 72.7 - - - +
242A GLU* 1.3 62.3 + - - +
243A PHE* 4.1 3.6 + - - -
257A PHE* 3.8 14.6 - + - -
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Residues in contact with GLU 242 (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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196A HIS 3.6 6.5 - - - +
197A LYS* 3.8 24.4 - - + +
215A PHE* 6.0 1.8 - - - -
225A TYR* 5.0 1.6 + - - -
232A THR* 2.9 47.2 + - + +
233A ARG* 3.2 31.5 + - - -
240A TYR* 4.3 7.6 - - + +
241A PHE* 1.3 75.7 - - - +
243A PHE* 1.3 67.2 + - - +
244A PRO* 3.6 6.1 - - - +
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Residues in contact with PHE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 3.2 61.7 - + - +
196A HIS 2.9 30.4 + - - +
197A LYS* 3.8 5.8 - - - -
198A MET* 4.6 1.8 - - + -
215A PHE* 3.6 24.0 - + - -
217A VAL* 4.3 1.1 - - + -
225A TYR* 3.4 46.7 - + + -
241A PHE 4.8 0.7 - - - -
242A GLU* 1.3 75.5 - - - +
244A PRO* 1.3 70.9 - - + +
245A GLN 3.2 21.8 + - - +
246A PRO* 4.6 1.4 - - - +
247A LEU* 3.6 22.2 - - + -
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Residues in contact with PRO 244 (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 TYR* 3.5 28.0 - - + +
242A GLU 3.7 6.5 - - - +
243A PHE* 1.3 85.0 - - + +
245A GLN* 1.3 80.4 + - - +
246A PRO* 4.8 0.5 - - - +
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Residues in contact with GLN 245 (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 TYR* 6.0 0.3 - - - -
243A PHE* 3.2 17.2 - - - +
244A PRO* 1.3 91.5 - - - +
246A PRO* 1.3 82.6 - - + +
247A LEU* 3.4 1.4 + - - +
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Residues in contact with PRO 246 (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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194A LEU* 3.9 27.9 - - + +
195A PHE 3.5 7.6 - - - +
196A HIS* 3.5 40.6 - - + +
243A PHE* 4.5 3.3 - - + +
244A PRO 4.8 0.2 - - - +
245A GLN* 1.3 92.6 - - + +
247A LEU* 1.3 60.4 + - - +
248A PRO* 3.4 11.1 - - - +
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Residues in contact with LEU 247 (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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194A LEU* 3.4 2.3 - - - -
195A PHE* 2.7 46.9 + - + +
217A VAL* 4.0 20.6 - - + -
224A ILE* 3.9 28.9 - - + +
225A TYR* 3.8 19.3 - - + -
243A PHE* 3.6 37.2 - - + -
245A GLN 3.4 1.7 + - - +
246A PRO* 1.3 72.4 - - - +
248A PRO* 1.3 86.1 - - + +
249A VAL* 3.3 8.0 + - + -
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Residues in contact with PRO 248 (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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193A LEU 3.6 7.0 - - - +
194A LEU* 3.8 14.4 - - + -
219A GLN* 4.2 1.6 - - - +
224A ILE* 3.7 14.2 - - - +
246A PRO 3.4 9.4 - - - +
247A LEU* 1.3 91.4 - - + +
249A VAL* 1.3 64.6 - - - +
350A THR* 6.0 0.4 - - + -
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Residues in contact with VAL 249 (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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191A VAL 4.1 0.5 - - - +
192A ALA* 3.7 1.4 - - - +
193A LEU* 2.8 54.2 + - + +
195A PHE* 4.0 17.7 - - + -
217A VAL* 4.9 0.2 - - + -
219A GLN* 3.5 3.6 - - - -
224A ILE* 4.0 15.3 - - + -
247A LEU* 3.8 15.5 - - + +
248A PRO* 1.3 80.6 - - - +
250A CYS* 1.3 65.2 + - - +
253A ILE* 3.9 20.2 - - + -
277A THR* 3.9 15.2 - - + +
347A PHE* 4.1 16.8 - - + -
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Residues in contact with CYS 250 (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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190A PRO* 3.8 28.0 - - - -
191A VAL 4.1 15.0 - - - -
192A ALA* 4.2 10.1 - - + -
219A GLN* 2.7 40.8 + - - +
249A VAL* 1.3 78.0 - - - +
251A GLY* 1.3 68.4 + - - +
252A ASP 3.5 0.7 + - - -
253A ILE* 3.7 2.7 - - - +
277A THR* 4.0 3.8 - - - -
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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