Contacts of the helix formed by residues 373 - 381 (chain B) in PDB entry 4BEJ
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 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B TYR* 3.2 25.1 + - - -
369B ILE* 3.9 14.7 - - - +
372B GLU* 1.3 80.9 - - - +
374B PHE* 1.3 69.3 + - - +
375B GLY 2.9 3.0 + - - -
376B ARG* 3.1 21.9 + - + +
377B THR* 3.1 28.5 + - + +
434B LEU* 4.6 16.8 - - + -
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Residues in contact with PHE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ILE* 2.9 22.5 + - + +
370B PHE 3.8 5.6 - - - +
373B THR* 1.3 74.3 - - - +
375B GLY* 1.3 57.4 + - - +
377B THR* 2.5 25.7 + - - -
378B LEU* 3.2 41.1 + - + +
427B PRO 3.3 26.5 - - - -
428B SER* 3.5 27.4 - - - -
431B CYS* 3.5 31.2 - - + -
434B LEU* 5.9 2.9 - - + -
637B GLN* 4.3 9.0 - - + -
640B VAL* 3.9 24.7 - - + -
641B PRO* 4.0 20.0 - - + -
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Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B PHE 4.0 8.9 + - - -
371B HIS 5.2 4.7 - - - -
372B GLU 4.5 2.0 - - - -
373B THR* 2.9 2.6 - - - +
374B PHE* 1.3 76.7 - - - +
376B ARG* 1.3 64.6 + - - +
377B THR 3.1 2.0 - - - -
378B LEU* 3.9 0.3 - - - +
379B GLU* 2.9 33.2 + - - +
637B GLN* 3.8 25.0 + - - -
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B TYR* 4.5 8.3 + - - -
372B GLU* 3.1 66.6 + - - +
373B THR* 3.1 17.4 + - + +
375B GLY* 1.3 75.2 - - - +
377B THR* 1.3 61.2 + - + +
379B GLU* 3.1 25.9 - - - +
380B SER* 2.9 27.1 + - - +
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Residues in contact with THR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B THR* 3.1 25.6 - - + +
374B PHE* 2.5 34.3 + - - -
376B ARG* 1.3 75.6 - - + +
378B LEU* 1.3 60.9 + - - +
380B SER* 2.7 31.5 + - - -
381B VAL* 3.2 10.4 + - - +
427B PRO* 4.6 8.5 - - - +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B PHE* 3.2 33.8 + - + +
375B GLY 4.0 2.5 - - - +
377B THR* 1.3 81.0 + - - +
379B GLU* 1.3 62.4 + - - +
381B VAL* 3.0 23.3 + - + +
424B LEU* 3.7 28.7 - - + +
427B PRO* 3.6 31.0 - - + -
428B SER* 4.8 0.4 - - - +
633B ARG* 3.3 20.4 - - + +
636B ILE* 4.1 8.3 - - + -
637B GLN* 3.6 48.9 - - + +
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B GLY 2.9 17.5 + - - +
376B ARG* 3.1 36.7 - - - +
378B LEU* 1.3 77.4 - - - +
380B SER* 1.3 63.3 + - - +
381B VAL 3.1 7.2 + - - +
633B ARG* 3.7 29.5 + - - +
637B GLN* 4.5 8.0 + - - +
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ARG* 2.9 18.5 + - - +
377B THR* 2.7 17.8 + - - -
379B GLU* 1.3 77.1 + - - +
381B VAL* 1.3 63.9 + - - +
382B ASP* 3.3 5.2 + - - +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B THR 3.2 10.7 + - - +
378B LEU* 3.0 26.3 + - + +
379B GLU 3.7 8.0 - - - +
380B SER* 1.3 77.9 - - - +
382B ASP* 1.3 61.4 + - - +
383B PRO* 3.7 5.7 - - - +
423B ARG* 3.2 39.5 - - + +
424B LEU* 4.6 12.8 - - + -
427B PRO* 4.9 11.4 - - + -
629B PHE* 3.8 22.3 - - + -
633B ARG* 4.4 4.0 + - - -
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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