Contacts of the helix formed by residues 367 - 375 (chain B) in PDB entry 1BHT
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 ALA 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B ILE* 4.3 5.6 - - + -
366B THR* 1.3 72.4 - - - +
368B ASP* 1.3 62.4 + - - +
370B CYS* 2.9 21.8 + - - +
371B ALA* 2.9 10.0 + - - +
387B PHE* 3.5 6.4 - - + -
389B PHE* 3.6 39.4 - - + -
419B TYR* 4.3 21.8 - - + +
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Residues in contact with ASP 368 (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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337B ASN* 3.4 35.0 - - + +
339B ILE* 3.6 18.9 - - - +
366B THR* 3.7 16.3 + - - +
367B ALA* 1.3 78.6 + - - +
369B GLN* 1.3 62.2 + - + +
371B ALA* 3.1 19.0 + - - +
372B ASN* 3.1 22.5 + - - +
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Residues in contact with GLN 369 (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 VAL* 3.5 20.4 - - + +
365B ASN* 2.8 42.1 + - - +
366B THR* 3.2 21.1 + - - +
367B ALA 3.1 0.2 - - - -
368B ASP* 1.3 78.5 - - + +
370B CYS* 1.3 63.9 + - - +
372B ASN* 4.5 4.4 - - - +
373B ARG* 3.4 21.7 + - - +
396B CYS* 4.8 0.7 - - - -
398B TRP* 4.6 1.3 - - - -
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Residues in contact with CYS 370 (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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366B THR 3.9 8.1 - - - -
367B ALA 2.9 9.0 + - - +
369B GLN* 1.3 77.9 - - - +
371B ALA* 1.3 63.3 + - - +
373B ARG 3.4 1.6 + - - -
374B CYS* 3.1 12.0 + - - +
387B PHE* 3.3 22.9 - - + -
389B PHE* 3.4 29.4 - - - -
396B CYS* 2.0 52.5 - - + -
398B TRP* 3.1 22.1 + - - +
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Residues in contact with ALA 371 (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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338B THR* 3.6 6.1 - - - +
339B ILE* 3.3 47.6 - - + +
342B PHE* 3.7 2.6 - - + -
367B ALA 2.9 5.0 + - - +
368B ASP 3.1 9.9 - - - +
370B CYS* 1.3 75.3 - - - +
372B ASN* 1.3 53.7 + - - +
374B CYS* 2.8 8.1 + - - +
375B THR* 2.7 34.3 + - - -
387B PHE* 3.4 14.3 - - + -
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Residues in contact with ASN 372 (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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336B ARG 3.5 25.5 + - - +
337B ASN* 3.5 4.1 - - - +
338B THR* 3.2 32.2 + - - -
368B ASP* 3.1 14.8 + - - +
369B GLN* 4.6 4.4 - - - +
371B ALA* 1.3 73.5 - - - +
373B ARG* 1.3 56.2 + - - +
375B THR* 4.2 3.1 - - - -
376B ARG* 2.7 62.5 + - - +
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Residues in contact with ARG 373 (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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360B LYS* 5.1 9.5 - - - +
362B LYS* 3.7 39.4 - - - +
364B VAL* 5.5 1.8 - - - +
369B GLN 3.4 18.0 + - - +
370B CYS 3.4 4.4 + - - +
371B ALA 3.2 0.8 - - - -
372B ASN* 1.3 78.1 - - - +
374B CYS* 1.3 58.5 + - - +
376B ARG* 5.1 0.2 - - - -
377B ASN 3.1 16.9 + - - -
378B LYS* 3.3 42.1 + - + +
379B GLY* 4.9 9.5 - - - -
380B LEU* 3.2 20.9 - - - +
398B TRP* 3.1 38.8 - - + -
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Residues in contact with CYS 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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142A ILE* 5.3 0.3 - - - +
342B PHE* 3.9 22.4 - - + -
370B CYS 3.1 11.5 + - - +
371B ALA 2.8 8.9 + - - +
373B ARG* 1.3 77.1 - - - +
375B THR* 1.3 65.5 + - - +
377B ASN* 3.1 11.1 + - - +
380B LEU* 4.2 0.9 - - - -
384B CYS* 2.0 75.7 - - - +
385B LYS 4.8 0.2 - - - -
386B ALA 4.4 6.7 - - - -
387B PHE* 4.2 9.0 - - + -
398B TRP* 4.0 4.7 - - + +
421B ASN* 5.1 1.5 + - - -
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Residues in contact with THR 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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142A ILE* 4.0 13.3 - - - +
338B THR* 2.6 41.7 + - + +
341B GLU* 5.0 8.0 - - + +
342B PHE* 3.1 17.1 - - - -
371B ALA 2.7 14.7 + - - -
372B ASN* 3.9 4.3 - - - -
374B CYS* 1.3 75.4 - - - +
376B ARG* 1.3 65.3 + - + +
421B ASN* 5.9 4.7 - - - +
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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