Contacts of the helix formed by residues 288 - 302 (chain A) in PDB entry 4JJ7
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 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LYS* 3.7 24.0 - - + +
286A ASP 5.4 0.2 - - - +
287A CYS* 1.3 76.5 - - - +
289A VAL* 1.3 65.7 + - - +
290A GLU* 3.6 6.5 + - - +
291A GLN* 3.0 37.9 + - - +
292A ILE* 2.9 21.0 + - - +
325A GLY* 4.0 1.3 - - - -
326A THR* 3.6 13.9 - - - +
327A ASP* 3.5 32.1 - - + +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 1.3 72.1 - - - +
290A GLU* 1.3 64.2 + - - +
292A ILE* 3.1 11.5 + - + +
293A TYR* 3.0 55.7 + - + +
325A GLY* 3.5 11.4 - - - +
327A ASP* 3.2 5.2 + - - +
329A GLN* 3.2 47.1 - - + +
330A GLU 3.9 15.3 - - - +
331A ALA* 4.0 9.2 - - + +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 3.3 6.7 + - - +
289A VAL* 1.3 79.2 - - - +
291A GLN* 1.3 60.1 + - + +
293A TYR* 3.3 9.8 + - - +
294A GLU* 3.0 27.7 + - + +
327A ASP* 5.1 2.3 + - - +
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 4.5 8.8 + - - +
286A ASP 3.6 7.8 - - - +
287A CYS* 3.4 16.2 - - + -
288A THR* 3.0 46.4 + - - +
290A GLU* 1.3 76.4 - - + +
292A ILE* 1.3 64.4 + - - +
294A GLU* 3.2 15.4 + - - +
295A ILE* 3.0 31.1 + - + +
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.7 35.9 - - + -
241A ASN* 4.3 5.6 - - - +
287A CYS* 3.6 23.8 - - + +
288A THR 2.9 21.6 + - - +
289A VAL* 3.5 11.9 - - + +
291A GLN* 1.3 76.2 - - - +
293A TYR* 1.3 65.0 + - + +
295A ILE* 3.1 10.2 + - - +
296A LEU* 2.9 26.3 + - + +
314A ILE* 5.4 1.3 - - + -
323A ILE* 3.8 26.5 - - + -
325A GLY* 4.6 2.0 - - - -
331A ALA* 5.5 0.9 - - + -
336A LEU* 3.9 28.0 - - + -
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Residues in contact with TYR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 3.0 36.2 + - + +
290A GLU* 3.8 9.6 - - - +
292A ILE* 1.3 76.5 - - + +
294A GLU* 1.3 58.2 + - - +
296A LEU* 3.4 8.4 + - + +
297A LYS* 2.9 30.0 + - - +
330A GLU 4.3 1.0 + - - -
331A ALA* 3.5 23.6 - - + +
332A PRO* 3.7 12.0 - - - +
335A GLU* 3.7 23.6 - - + +
336A LEU* 3.8 29.2 - - + -
339A GLN* 5.8 4.7 - - + +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU* 3.0 15.6 + - + +
291A GLN* 3.5 18.5 - - - +
292A ILE 3.2 0.2 - - - -
293A TYR* 1.3 78.5 - - - +
295A ILE* 1.3 65.8 + - - +
297A LYS* 3.3 7.9 + - + +
298A ILE* 3.1 39.0 + - + +
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Residues in contact with ILE 295 (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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237A LEU* 4.3 11.4 - - + -
239A ILE* 5.0 8.5 - - + -
284A HIS* 3.6 52.7 - - + +
287A CYS* 3.7 24.2 - - - -
291A GLN* 3.0 23.7 + - + +
292A ILE* 3.1 8.5 + - - +
294A GLU* 1.3 78.4 - - + +
296A LEU* 1.3 67.1 + - + +
298A ILE* 3.2 13.8 + - + +
299A TYR* 3.1 34.2 + - + -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 3.9 23.6 - - + -
239A ILE* 4.5 9.2 - - + -
292A ILE* 2.9 23.1 + - + +
293A TYR* 3.9 7.4 - - + +
295A ILE* 1.3 75.7 - - + +
297A LYS* 1.3 53.0 + - - +
299A TYR* 3.2 1.9 + - - -
300A GLN* 2.7 36.2 + - - +
312A CYS* 4.1 15.7 - - - -
314A ILE* 5.9 0.9 - - + -
336A LEU* 3.7 53.6 - - + +
339A GLN* 4.4 13.5 - - + -
340A PHE* 3.5 22.8 - - + -
355A PHE* 5.8 0.4 - - + -
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Residues in contact with LYS 297 (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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293A TYR 2.9 17.6 + - - +
294A GLU* 3.6 8.1 - - + +
295A ILE 3.2 0.2 - - - -
296A LEU* 1.3 73.3 - - - +
298A ILE* 1.3 66.3 + - + +
300A GLN* 2.7 39.6 + - - +
301A LEU* 3.0 49.2 + - + +
339A GLN* 5.2 9.8 + - - +
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Residues in contact with ILE 298 (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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284A HIS* 6.5 0.7 - - + -
294A GLU* 3.1 36.2 + - + +
295A ILE* 3.2 14.8 + - + +
297A LYS* 1.3 77.6 - - + +
299A TYR* 1.3 69.3 + - + +
301A LEU* 3.4 5.7 + - - +
302A MET* 3.1 43.1 + - + +
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A TYR* 3.8 32.3 - + - -
237A LEU* 3.7 37.7 - - + -
282A LYS* 3.2 28.6 - - + +
284A HIS* 4.5 10.3 + + - -
295A ILE* 3.1 25.5 + - + +
296A LEU 3.9 4.9 - - - +
298A ILE* 1.3 85.6 - - + +
300A GLN* 1.3 63.3 + - - +
301A LEU 3.1 0.4 - - - -
302A MET* 3.3 28.8 + - + +
304A HIS* 2.8 27.6 + + - -
310A PHE* 4.2 10.1 - + + -
340A PHE* 3.8 17.0 - - + -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU 2.7 22.0 + - - +
297A LYS* 2.7 42.7 + - - +
299A TYR* 1.3 72.7 - - - +
301A LEU* 1.3 79.1 + - - +
302A MET 3.6 1.4 + - - +
339A GLN* 3.2 35.2 - - + +
340A PHE* 3.6 11.8 - - + -
344A LYS* 2.9 36.9 + - - +
345A CYS* 3.5 20.0 - - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 3.0 45.2 + - + +
298A ILE* 3.8 5.6 - - - +
300A GLN* 1.3 95.6 - - - +
302A MET* 1.3 65.2 + - - +
303A ASP 3.8 0.5 + - - -
344A LYS 5.5 0.2 - - - +
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Residues in contact with MET 302 (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 TYR* 3.9 28.3 - - + +
298A ILE* 3.1 31.7 + - + +
299A TYR* 3.3 44.0 + - + +
300A GLN 4.0 3.6 - - - +
301A LEU* 1.3 82.3 - - - +
303A ASP* 1.3 67.5 + - - +
304A HIS* 3.2 24.4 + - + +
347A SER* 3.5 5.0 + - - -
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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