Contacts of the helix formed by residues 374 - 382 (chain A) in PDB entry 2JB2
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 GLY 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A SER* 6.4 0.2 - - - -
320A SER* 2.9 21.3 + - - -
373A SER* 1.3 72.3 - - - +
375A LYS* 1.3 64.8 + - - -
377A GLN* 3.0 11.4 + - - +
378A GLU* 3.0 21.2 + - - +
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Residues in contact with LYS 375 (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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373A SER 3.4 1.0 + - - -
374A GLY* 1.3 71.1 - - - -
376A ARG* 1.3 64.5 + - + +
378A GLU* 3.1 34.7 + - - +
379A ALA* 3.4 10.6 + - - +
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Residues in contact with ARG 376 (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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346A THR 3.0 27.1 + - - -
347A ASP* 3.5 17.9 + - - +
348A LYS 3.1 23.9 + - - -
349A ASP* 3.5 28.1 - - - +
351A SER* 3.1 22.6 + - - +
372A SER* 3.0 12.9 + - - -
373A SER 3.4 9.7 + - - +
374A GLY 3.2 1.2 - - - -
375A LYS* 1.3 84.9 - - + +
377A GLN* 1.3 56.2 + - - +
379A ALA* 3.8 5.7 - - - +
380A PHE* 3.3 20.3 - - - -
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Residues in contact with GLN 377 (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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320A SER* 3.1 22.4 - - - +
321A SER* 3.5 13.5 - - - -
322A GLY* 3.3 24.3 + - - +
370A TYR* 3.7 11.5 + - - -
372A SER* 2.8 37.1 + - - +
373A SER* 3.6 9.3 + - - -
374A GLY 3.0 5.8 + - - +
376A ARG* 1.3 76.3 - - - +
378A GLU* 1.3 58.9 + - - +
379A ALA 3.0 2.0 - - - -
380A PHE* 2.9 31.2 + - - +
381A GLU* 3.0 12.5 + - + +
388A ARG* 5.4 0.2 - - - -
414A GLY 4.3 1.2 + - - -
415A SER* 2.7 34.3 + - - +
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Residues in contact with GLU 378 (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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320A SER* 4.0 5.2 + - - +
374A GLY 3.0 21.1 + - - +
375A LYS* 3.1 22.0 + - - +
377A GLN* 1.3 75.5 - - - +
379A ALA* 1.3 61.6 + - - +
380A PHE 3.3 1.0 + - - -
381A GLU* 3.5 31.9 + - - +
382A SER* 4.4 6.9 + - - -
417A ARG* 4.0 19.3 + - - +
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Residues in contact with ALA 379 (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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349A ASP* 3.4 28.7 - - + +
375A LYS 3.4 8.1 + - - +
376A ARG 3.8 13.2 - - - +
378A GLU* 1.3 78.5 - - - +
380A PHE* 1.3 57.7 + - + +
382A SER 5.3 0.2 - - - -
383A LEU* 3.4 21.1 - - - +
391A LYS* 3.9 13.0 - - - +
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Residues in contact with PHE 380 (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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349A ASP* 3.7 19.1 - - + -
350A ILE* 3.9 20.0 - - + -
370A TYR* 3.3 50.3 - + - +
372A SER* 3.8 10.8 - - - -
376A ARG 3.3 27.4 - - - -
377A GLN* 2.9 16.1 + - - +
379A ALA* 1.3 74.7 - - - +
381A GLU* 1.3 67.8 + - - +
382A SER 3.3 2.9 - - - -
383A LEU* 3.1 15.5 + - + +
388A ARG* 3.0 34.0 + - + +
391A LYS* 3.6 40.2 - - + -
392A ALA 4.5 1.8 - - - -
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Residues in contact with GLU 381 (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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320A SER* 2.3 33.3 + - - +
377A GLN 3.0 14.8 + - - +
378A GLU* 3.5 17.2 + - - +
380A PHE* 1.3 76.9 - - - +
382A SER* 1.3 64.0 + - - +
383A LEU 3.3 0.6 - - - +
388A ARG* 3.1 16.0 + - - +
415A SER* 3.3 24.9 + - - +
417A ARG* 3.0 45.8 + - - +
418A ARG* 2.9 31.2 + - + +
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Residues in contact with SER 382 (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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378A GLU 4.4 6.5 + - - -
380A PHE 3.3 0.4 - - - -
381A GLU* 1.3 76.7 - - - +
383A LEU* 1.3 67.9 + - - +
384A THR* 3.9 1.9 + - - +
387A GLN* 4.6 1.4 - - - +
418A ARG* 3.2 26.4 + - - +
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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