Contacts of the helix formed by residues 386 - 398 (chain A) in PDB entry 2EBT
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 LYS 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A HIS* 3.7 8.0 - - - -
384A TYR* 3.0 8.5 + - + +
385A THR* 1.3 87.3 - - - +
387A SER* 1.3 62.8 + - - +
388A SER* 3.3 13.6 + - - +
389A HIS* 3.2 51.5 + - + +
390A LEU* 3.5 22.0 + - - +
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Residues in contact with SER 387 (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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368A GLU* 5.9 1.8 - - - -
373A HIS* 4.3 19.7 + - - -
386A LYS* 1.3 72.3 - - - +
388A SER* 1.3 64.3 + - - +
390A LEU* 4.2 7.3 - - - +
391A LYS* 3.3 36.7 + - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LYS* 3.9 23.4 + - - +
387A SER* 1.3 82.3 + - - +
389A HIS* 1.3 72.5 + - - +
391A LYS* 3.6 9.4 + - - +
392A ALA* 3.4 19.2 + - - +
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Residues in contact with HIS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A TYR* 4.5 22.3 - + + +
386A LYS* 3.2 40.7 + - + +
387A SER 3.6 0.2 - - - -
388A SER* 1.3 85.5 + - - +
390A LEU* 1.3 66.4 + - - +
392A ALA* 3.2 10.6 + - + +
393A HIS* 3.1 18.9 + - - +
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Residues in contact with LEU 390 (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 HIS* 4.2 26.2 - - + +
374A TYR 5.1 5.2 - - - +
375A CYS* 4.3 25.6 - - + +
376A ASP 6.1 0.2 - - - +
384A TYR* 4.6 17.4 - - + +
386A LYS 3.5 17.3 + - - +
387A SER* 4.2 7.0 - - - +
389A HIS* 1.3 75.3 - - - +
391A LYS* 1.3 60.7 + - + +
393A HIS* 2.6 41.8 + - + +
394A LEU* 2.9 30.4 + - + +
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Residues in contact with LYS 391 (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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387A SER* 3.3 23.7 + - - +
388A SER* 3.6 11.1 + - - +
390A LEU* 1.3 81.7 - - + +
392A ALA* 1.3 62.6 + - - +
394A LEU* 3.5 16.3 + - + +
395A ARG* 3.4 25.0 + - - +
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Residues in contact with ALA 392 (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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388A SER 3.4 8.8 + - - +
389A HIS* 3.2 14.3 + - + +
390A LEU 3.0 0.8 - - - -
391A LYS* 1.3 79.0 - - - +
393A HIS* 1.3 63.3 + - - +
395A ARG* 3.1 39.3 - - - +
396A THR* 4.3 3.1 + - - +
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Residues in contact with HIS 393 (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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100A ZN 2.0 36.6 - - - -
375A CYS* 3.5 11.0 - - + -
380A CYS* 3.5 8.5 - - - -
382A LYS* 4.1 14.3 - - + +
384A TYR* 4.1 27.4 + + + +
389A HIS 3.1 10.2 + - - +
390A LEU* 2.6 26.2 + - + +
392A ALA* 1.3 67.4 - - - +
394A LEU* 1.3 66.0 + - - +
395A ARG 3.0 2.0 - - - -
396A THR* 2.5 49.8 + - - +
397A HIS* 3.2 7.8 + + - -
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Residues in contact with LEU 394 (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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375A CYS* 4.3 10.3 - - - -
376A ASP* 5.2 9.4 - - + +
377A TYR* 5.2 5.4 - - + -
390A LEU* 2.9 39.9 + - + +
391A LYS* 3.7 17.3 - - + +
393A HIS* 1.3 81.4 - - + +
395A ARG* 1.3 54.9 + - - +
397A HIS* 2.6 47.9 + - + +
398A THR* 3.0 18.2 + - + +
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Residues in contact with ARG 395 (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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391A LYS* 3.4 11.6 + - - +
392A ALA* 3.1 33.5 - - - +
393A HIS 2.9 0.2 + - - -
394A LEU* 1.3 77.0 - - - +
396A THR* 1.3 55.3 + - + +
398A THR* 2.5 35.3 - - + +
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Residues in contact with THR 396 (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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392A ALA 4.8 3.6 - - - +
393A HIS* 2.5 41.9 + - - +
394A LEU 2.7 4.2 + - - -
395A ARG* 1.3 75.4 - - + +
397A HIS* 1.3 70.5 + - - +
398A THR 4.2 2.4 - - - +
399A GLY* 5.5 0.5 - - - -
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Residues in contact with HIS 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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100A ZN 2.0 37.8 - - - -
375A CYS* 3.6 6.6 - - - -
377A TYR* 3.3 65.9 + + + -
380A CYS* 3.8 9.0 - - + -
393A HIS* 3.2 14.9 + + - -
394A LEU* 2.6 22.8 + - + +
396A THR* 1.3 82.0 + - - +
398A THR* 1.3 58.2 + - + +
399A GLY 3.7 2.1 + - - -
401A LYS* 5.9 1.4 + - - -
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Residues in contact with THR 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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394A LEU* 3.0 23.8 + - + +
395A ARG* 2.5 35.1 - - + +
396A THR 4.2 2.0 - - - +
397A HIS* 1.3 74.4 - - + +
399A GLY* 1.3 60.5 + - - +
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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