Contacts of the helix formed by residues 382 - 396 (chain B) in PDB entry 2BEX
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 SER 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B ASP* 2.6 32.0 + - - +
380B ASP 5.2 0.7 - - - -
381B VAL* 1.3 75.7 - - - +
383B ASP* 1.3 65.6 + - - +
384B SER* 3.0 14.0 + - - -
385B SER* 3.1 14.6 + - - -
386B CYS 3.9 2.1 + - - -
408B CYS* 3.3 17.9 - - - -
409B LEU* 3.7 13.6 - - - +
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Residues in contact with ASP 383 (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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382B SER* 1.3 76.4 - - - +
384B SER* 1.3 62.0 + - - +
385B SER 3.2 1.0 + - - -
386B CYS* 3.2 23.9 + - - +
387B SER 4.4 0.3 + - - -
408B CYS 3.8 2.6 + - - +
409B LEU* 3.3 6.2 - - - -
410B GLY* 2.6 31.0 + - - -
412B ALA* 3.0 21.5 + - + +
413B GLY* 2.7 29.2 + - - +
416B GLN* 3.5 11.8 + - - +
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ASP* 3.7 16.7 + - - +
382B SER* 3.0 14.4 + - - -
383B ASP* 1.3 79.5 - - - +
385B SER* 1.3 58.5 + - - +
386B CYS 3.5 0.2 - - - -
387B SER* 3.9 12.8 + - - -
388B SER* 5.1 2.1 + - - -
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Residues in contact with SER 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ASP* 2.6 48.0 + - - +
357B VAL* 3.7 17.6 - - - +
358B ARG* 5.3 1.8 - - - -
381B VAL* 3.6 20.9 - - - +
382B SER 3.1 2.8 + - - -
384B SER* 1.3 74.1 - - - +
386B CYS* 1.3 61.7 + - - +
387B SER 3.2 2.7 - - - -
388B SER* 2.9 13.4 + - - -
389B LEU* 2.9 28.1 + - - +
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Residues in contact with CYS 386 (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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382B SER 4.0 10.5 - - - -
383B ASP 3.2 11.1 + - - +
385B SER* 1.3 76.9 - - - +
387B SER* 1.3 57.1 + - - +
389B LEU* 3.6 14.0 - - - +
390B ALA* 2.8 32.1 + - - +
409B LEU* 4.1 17.0 - - - -
413B GLY* 3.4 43.1 - - - +
414B ILE 4.5 0.4 - - - -
416B GLN* 3.8 5.5 - - + +
417B LEU* 3.9 19.1 - - + +
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ASP 4.4 0.8 + - - -
384B SER 3.9 12.5 + - - -
386B CYS* 1.3 76.9 - - - +
388B SER* 1.3 64.1 + - - +
390B ALA* 3.8 5.0 - - - +
391B ALA* 3.2 25.5 + - - +
416B GLN* 3.2 26.4 + - - +
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG* 3.9 25.9 + - - +
361B CYS* 3.8 19.7 - - - +
384B SER 5.1 2.6 + - - -
385B SER* 2.9 10.8 + - - -
387B SER* 1.3 83.6 + - - +
389B LEU* 1.3 64.8 + - - +
391B ALA* 3.2 7.2 + - - +
392B THR* 3.0 27.4 + - - -
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Residues in contact with LEU 389 (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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357B VAL* 4.1 13.5 - - + -
361B CYS* 3.5 22.2 - - - -
374B LEU* 5.6 2.9 - - + -
376B LEU* 4.6 13.9 - - + -
381B VAL* 4.6 4.3 - - + -
385B SER* 2.9 31.8 + - - +
386B CYS* 3.8 10.1 - - - +
388B SER* 1.3 77.4 - - - +
390B ALA* 1.3 62.5 + - - +
392B THR* 3.4 2.9 + - - -
393B LEU* 3.0 31.7 + - + +
402B LEU* 4.7 16.2 - - + -
404B LEU* 3.9 30.5 - - + -
417B LEU* 3.7 15.0 - - + -
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Residues in contact with ALA 390 (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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386B CYS 2.8 22.9 + - - +
387B SER* 3.8 6.5 - - - +
389B LEU* 1.3 73.1 - - - +
391B ALA* 1.3 63.5 + - - +
393B LEU* 3.3 12.9 + - - +
394B LEU* 3.5 5.1 + - - +
416B GLN* 3.5 24.0 - - + +
417B LEU* 4.1 2.4 - - - +
420B SER* 2.7 38.1 + - - +
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Residues in contact with ALA 391 (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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387B SER 3.2 16.2 + - - +
388B SER* 3.5 8.1 - - - +
389B LEU 3.2 0.2 - - - -
390B ALA* 1.3 79.2 - - - +
392B THR* 1.3 63.5 + - - +
394B LEU* 3.0 11.5 + - - +
395B ALA* 3.0 23.1 + - - +
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Residues in contact with THR 392 (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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361B CYS* 2.9 39.9 + - - +
364B LEU* 3.6 28.7 - - + -
365B GLY* 3.6 25.5 - - - +
388B SER 3.0 8.0 + - - -
389B LEU* 3.9 4.3 - - - -
391B ALA* 1.3 70.8 - - - +
393B LEU* 1.3 58.4 + - - +
394B LEU 3.0 5.4 - - - -
395B ALA* 4.2 6.7 - - - +
396B ASN* 2.8 34.8 + - + +
399B LEU* 6.1 1.6 - - + -
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Residues in contact with LEU 393 (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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389B LEU* 3.0 27.0 + - + +
390B ALA* 3.5 14.8 - - - +
391B ALA 3.2 0.2 - - - -
392B THR* 1.3 75.8 - - - +
394B LEU* 1.3 58.4 + - - +
396B ASN* 3.4 13.1 - - - +
397B HIS* 5.6 0.3 - - - -
399B LEU* 4.1 28.5 - - + -
402B LEU* 4.5 15.5 - - + -
417B LEU* 4.3 15.0 - - + +
420B SER* 4.1 9.6 - - - -
421B VAL* 3.9 22.2 - - + -
426B CYS* 3.9 28.8 - - - +
428B LEU* 4.3 20.9 - - + -
431B LEU* 5.9 1.1 - - + -
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Residues in contact with LEU 394 (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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390B ALA 3.6 3.8 - - - +
391B ALA* 3.0 9.1 + - - +
392B THR 3.0 0.4 - - - -
393B LEU* 1.3 85.1 - - - +
395B ALA* 1.3 61.4 + - - +
396B ASN 3.5 0.9 - - - -
397B HIS* 3.4 19.8 + - - -
419B GLU 5.5 0.4 - - - +
420B SER* 3.6 47.3 - - - +
423B GLN* 4.1 19.3 - - + -
425B GLY 5.9 0.4 - - - -
426B CYS* 4.5 7.0 - - + +
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Residues in contact with ALA 395 (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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365B GLY* 3.4 33.1 - - - +
366B GLN 5.0 2.1 - - - +
367B PRO* 5.7 2.1 - - - +
391B ALA 3.0 15.1 + - - +
392B THR* 4.1 1.6 - - - +
394B LEU* 1.3 77.7 - - - +
396B ASN* 1.3 60.0 + - - +
397B HIS* 3.6 17.3 + - - -
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Residues in contact with ASN 396 (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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364B LEU* 2.9 38.2 - - + +
365B GLY* 4.3 0.6 - - - -
366B GLN 5.4 0.2 - - - -
369B SER* 2.8 25.8 + - - -
392B THR* 2.8 21.1 + - + +
393B LEU* 3.4 20.7 - - - +
395B ALA* 1.3 75.2 - - - +
397B HIS* 1.3 64.1 + - - +
398B SER* 2.8 23.2 + - - +
399B LEU* 2.9 34.7 + - - +
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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