Contacts of the helix formed by residues 374 - 382 (chain B) in PDB entry 2JB3
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B SER* 3.0 29.9 + - - -
373B SER* 1.3 70.4 - - - +
375B LYS* 1.3 65.9 + - - -
377B GLN 2.8 10.6 + - - -
378B GLU* 3.0 17.7 + - - +
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Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ASP* 6.0 0.4 - - - +
373B SER 3.4 1.2 + - - -
374B GLY* 1.3 70.1 - - - -
376B ARG* 1.3 69.4 + - + +
377B GLN 3.3 1.4 + - - -
378B GLU* 3.3 31.9 + - - +
379B ALA* 3.3 12.5 + - - +
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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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345B ASN* 6.1 1.0 - - - +
346B THR 2.9 27.7 + - - -
347B ASP* 3.5 18.4 - - - +
348B LYS 3.0 21.9 + - - -
349B ASP* 3.4 33.0 - - - +
351B SER* 3.1 22.6 + - - +
372B SER* 2.8 15.0 + - - -
373B SER 3.3 9.2 + - - +
374B GLY 3.1 1.0 - - - -
375B LYS* 1.3 85.6 - - + +
377B GLN* 1.3 57.7 + - - +
379B ALA* 4.0 4.8 - - - +
380B PHE* 3.3 16.3 - - - -
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Residues in contact with GLN 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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320B SER* 4.3 1.1 - - - +
321B SER* 3.6 12.6 - - - +
322B GLY* 3.4 33.6 + - - +
370B TYR* 3.7 12.0 + - - -
372B SER* 2.9 37.3 + - - +
373B SER* 3.6 6.9 + - - -
374B GLY 2.8 8.7 + - - +
376B ARG* 1.3 77.6 - - - +
378B GLU* 1.3 65.6 + - - +
379B ALA 3.0 1.6 - - - -
380B PHE* 2.9 25.4 + - - +
381B GLU* 2.9 18.0 + - - +
388B ARG* 5.4 0.2 - - - +
414B GLY 4.3 1.4 + - - -
415B SER* 2.6 37.3 + - - +
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Residues in contact with GLU 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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320B SER* 4.1 9.5 + - - +
374B GLY* 3.0 22.1 + - - +
375B LYS* 3.4 27.3 + - - +
377B GLN* 1.3 75.8 - - - +
379B ALA* 1.3 61.3 + - - +
380B PHE 3.4 0.9 + - - -
381B GLU* 3.6 20.9 + - - +
382B SER* 4.3 7.6 + - - -
417B ARG* 4.2 24.3 + - - +
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Residues in contact with ALA 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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349B ASP* 3.4 17.9 - - + +
375B LYS 3.3 11.0 + - - +
376B ARG 4.0 7.4 - - - +
377B GLN 3.0 0.2 - - - -
378B GLU* 1.3 80.5 - - - +
380B PHE* 1.3 56.8 + - + +
382B SER 5.3 0.2 - - - -
383B LEU* 3.4 21.4 - - - +
391B LYS* 3.3 26.3 - - - -
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Residues in contact with PHE 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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349B ASP* 3.6 20.6 - - + -
350B ILE* 3.9 21.1 - - + -
370B TYR* 3.4 50.3 - + + +
372B SER* 3.8 9.6 - - - -
376B ARG 3.3 27.8 - - - -
377B GLN* 2.9 12.7 + - - +
379B ALA* 1.3 76.0 - - - +
381B GLU* 1.3 69.1 + - - +
382B SER 3.2 2.9 - - - -
383B LEU* 3.0 19.7 + - + +
388B ARG* 3.0 32.5 + - + -
391B LYS* 3.4 37.9 - - + -
392B ALA 4.4 1.6 - - - -
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Residues in contact with GLU 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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320B SER* 2.9 32.1 - - - -
321B SER 4.9 0.2 + - - -
377B GLN* 2.9 13.0 + - - +
378B GLU* 3.6 15.4 + - - +
380B PHE* 1.3 77.0 - - - +
382B SER* 1.3 62.3 + - - +
383B LEU 3.9 0.3 - - - +
388B ARG* 3.0 20.0 + - - +
415B SER* 3.1 26.4 + - - +
417B ARG* 2.7 45.4 + - + +
418B ARG* 3.2 35.9 + - + +
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Residues in contact with SER 382 (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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378B GLU 4.3 7.5 + - - -
379B ALA 5.3 0.2 - - - -
380B PHE 3.2 0.6 - - - -
381B GLU* 1.3 78.1 + - - +
383B LEU* 1.3 66.6 + - - +
384B THR* 3.9 1.2 + - - +
387B GLN* 4.6 1.4 - - - +
418B ARG* 3.2 26.3 + - - +
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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