Contacts of the helix formed by residues 396 - 405 (chain A) in PDB entry 2ILU
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 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLN* 4.6 2.7 - - - +
394A PHE* 3.3 10.1 - - - -
395A ASP* 1.3 85.7 - - + +
397A LEU* 1.3 70.0 + - - +
398A GLU* 3.2 12.3 + - - +
399A ASP* 2.4 38.0 + - - +
400A ALA 3.0 10.7 + - - -
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Residues in contact with LEU 397 (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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259A ILE* 4.8 0.7 - - + -
261A MET* 4.0 34.2 - - + +
394A PHE* 4.2 1.2 - - - -
396A THR* 1.3 73.8 - - - +
398A GLU* 1.3 65.1 + - - +
400A ALA* 3.0 9.5 + - + +
401A ILE* 2.8 55.4 + - + +
415A ILE* 4.1 21.1 - - + -
422A VAL* 3.9 34.8 - - + +
425A LYS* 3.9 25.8 - - + -
426A ALA* 4.7 0.2 - - + -
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Residues in contact with GLU 398 (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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396A THR* 3.2 9.7 - - - +
397A LEU* 1.3 82.4 + - - +
399A ASP* 1.3 62.0 + - - +
401A ILE* 4.0 7.6 - - + +
402A SER* 3.0 31.2 + - - -
425A LYS* 3.3 33.5 + - - +
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Residues in contact with ASP 399 (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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394A PHE* 4.4 3.6 - - + -
395A ASP* 3.9 14.4 + - - +
396A THR* 2.4 43.7 + - - +
398A GLU* 1.3 77.5 + - - +
400A ALA* 1.3 58.3 + - - +
402A SER* 3.1 7.2 + - - -
403A MET* 2.8 50.7 + - + +
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Residues in contact with ALA 400 (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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259A ILE* 3.6 23.8 - - + +
292A TYR* 4.8 4.8 - - + -
394A PHE* 3.5 39.7 - - + -
396A THR 3.0 2.2 + - - -
397A LEU* 3.5 9.4 - - + +
399A ASP* 1.3 79.6 - - - +
401A ILE* 1.3 56.4 + - - +
403A MET* 3.3 11.9 + - - +
404A ALA* 2.9 30.5 + - - +
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Residues in contact with ILE 401 (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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259A ILE* 4.2 10.8 - - + -
397A LEU* 2.8 52.5 + - + +
398A GLU* 4.0 7.0 - - + +
400A ALA* 1.3 72.5 - - - +
402A SER* 1.3 58.1 + - - +
404A ALA* 3.2 3.8 + - - +
405A ASN* 2.9 49.0 + - - +
425A LYS* 3.9 11.9 - - + +
426A ALA* 3.9 23.6 - - - -
429A GLY* 3.7 18.4 - - - +
430A LEU* 4.1 6.7 - - + +
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Residues in contact with SER 402 (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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398A GLU 3.0 21.0 + - - -
399A ASP* 3.5 5.6 - - - -
401A ILE* 1.3 78.8 - - - +
403A MET* 1.3 58.6 + - - +
405A ASN* 3.6 6.7 + - - +
406A ASP* 3.2 25.5 + - - +
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Residues in contact with MET 403 (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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290A ARG* 3.1 19.1 + - - -
292A TYR* 3.3 21.7 + - + -
375A GLN* 3.2 38.5 - - + +
392A VAL* 4.6 9.2 - - - -
393A ALA 4.8 1.8 - - - +
394A PHE* 3.5 28.5 - - + -
399A ASP* 2.8 45.4 + - + +
400A ALA* 3.7 4.0 - - - +
402A SER* 1.3 71.3 - - - +
404A ALA* 1.3 63.3 + - - +
406A ASP* 3.3 15.7 + - - +
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Residues in contact with ALA 404 (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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257A PRO* 3.9 19.5 - - + -
259A ILE* 4.4 8.1 - - + -
290A ARG* 3.0 27.6 + - - +
292A TYR* 4.3 6.2 - - + -
400A ALA 2.9 17.0 + - - +
401A ILE 3.7 4.0 - - - +
403A MET* 1.3 72.2 - - - +
405A ASN* 1.3 62.2 + - - +
406A ASP 3.0 5.2 + - - -
407A SER* 4.2 1.6 - - - -
430A LEU* 3.8 22.7 - - + -
432A PHE* 3.0 12.0 - - + -
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Residues in contact with ASN 405 (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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401A ILE* 2.9 29.9 + - - +
402A SER* 3.9 6.2 - - - +
404A ALA* 1.3 75.2 - - - +
406A ASP* 1.3 58.3 + - - +
407A SER 3.0 12.4 + - - +
429A GLY 2.8 24.5 + - - -
430A LEU* 3.4 4.3 - - - -
431A LYS* 2.5 57.2 + - + +
432A PHE* 3.6 7.4 - - - -
453A ARG* 4.0 12.5 + - - +
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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