Contacts of the helix formed by residues 352 - 362 (chain A) in PDB entry 4BHT
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 THR 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ASN* 3.4 35.2 - - + +
327A LEU 3.1 9.6 + - - +
328A ASP* 3.0 42.5 + - + +
351A THR* 1.3 73.2 - - - +
353A ILE* 1.3 64.0 + - - +
354A GLU* 3.6 3.8 + - - +
355A ALA* 3.1 19.1 + - - +
356A THR* 2.8 25.8 + - - -
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Residues in contact with ILE 353 (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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26A GLN* 4.5 26.0 - - + +
30A GLU* 4.6 22.4 - - + +
349A MET* 6.5 0.9 - - + -
351A THR 3.9 0.6 + - - +
352A THR* 1.3 73.2 - - - +
354A GLU* 1.3 57.0 + - - +
356A THR* 3.2 9.2 + - - -
357A GLU* 2.9 50.0 + - + +
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Residues in contact with GLU 354 (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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328A ASP* 4.7 3.3 - - - +
329A VAL* 3.3 30.3 - - + +
352A THR* 3.1 5.4 + - - +
353A ILE* 1.3 79.7 - - - +
355A ALA* 1.3 64.4 + - - +
357A GLU* 4.0 12.5 - - + +
358A LEU* 3.1 24.5 + - + +
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Residues in contact with ALA 355 (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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327A LEU* 3.4 19.7 - - + +
328A ASP 3.6 16.6 - - - -
329A VAL* 3.6 7.3 - - - +
332A ALA* 3.9 14.1 - - + +
351A THR* 3.5 10.1 - - + -
352A THR* 3.1 18.6 + - - +
354A GLU* 1.3 76.7 - - - +
356A THR* 1.3 63.8 + - - +
358A LEU* 3.4 3.7 + - - +
359A PHE* 3.1 27.7 + - - -
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Residues in contact with THR 356 (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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351A THR* 3.2 21.9 + - - +
352A THR 2.8 18.2 + - - -
353A ILE* 3.3 11.9 - - - -
355A ALA* 1.3 74.8 - - - +
357A GLU* 1.3 59.7 + - + +
359A PHE* 2.8 28.9 + - - +
360A GLN* 3.1 26.0 + - - +
366A PHE* 3.7 32.6 - - + -
426A VAL* 4.8 5.8 - - + -
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Residues in contact with GLU 357 (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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353A ILE* 2.9 38.6 + - + +
354A GLU* 4.0 11.8 - - + +
356A THR* 1.3 75.5 - - + +
358A LEU* 1.3 62.9 + - - +
360A GLN* 3.4 16.2 + - - +
361A GLN* 3.0 45.3 + - - +
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Residues in contact with LEU 358 (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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329A VAL* 4.1 8.1 - - + +
332A ALA* 4.1 14.4 - - + -
333A HIS* 3.3 44.2 - - + +
336A ILE* 3.6 18.8 - - + +
354A GLU* 3.1 18.1 + - + +
355A ALA* 3.6 5.2 - - - +
356A THR 3.1 0.4 - - - -
357A GLU* 1.3 79.9 - - - +
359A PHE* 1.3 61.4 + - - +
361A GLN* 3.5 17.3 + - + +
362A ALA* 3.1 23.0 + - + +
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Residues in contact with PHE 359 (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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327A LEU* 3.7 22.9 - - + -
332A ALA* 3.4 39.0 - - + -
335A LEU* 4.1 12.6 - - + -
336A ILE* 3.9 18.4 - - + -
340A VAL* 4.4 1.6 - - + -
343A VAL* 3.8 26.2 - - + -
351A THR* 3.9 10.3 - - + -
355A ALA 3.1 23.1 + - - -
356A THR* 2.8 12.9 + - - +
358A LEU* 1.3 68.2 - - - +
360A GLN* 1.3 62.9 + - - +
362A ALA 3.2 4.9 + - - -
364A VAL* 2.8 54.8 + - + +
366A PHE* 4.1 26.0 - + + -
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Residues in contact with GLN 360 (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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356A THR* 3.1 19.9 + - - +
357A GLU* 3.7 21.8 - - - +
359A PHE* 1.3 76.0 - - - +
361A GLN* 1.3 64.4 + - + +
363A GLY* 3.1 14.0 + - - -
364A VAL 4.4 4.9 - - - +
366A PHE* 4.6 17.9 + - + +
422A GLN* 5.2 1.2 - - - +
424A ASN* 3.5 34.0 + - - +
425A TYR 5.3 0.8 - - - +
426A VAL* 3.8 19.2 - - - +
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Residues in contact with GLN 361 (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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357A GLU* 3.0 35.1 + - - +
358A LEU* 3.9 20.9 - - + +
359A PHE 3.2 0.2 - - - -
360A GLN* 1.3 77.2 - - + +
362A ALA* 1.3 58.1 + - - +
363A GLY 3.3 0.9 - - - -
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Residues in contact with ALA 362 (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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336A ILE* 3.7 35.9 - - + -
358A LEU* 3.1 17.9 + - + +
359A PHE 3.2 4.0 + - - +
360A GLN 3.2 0.4 - - - -
361A GLN* 1.3 76.9 - - - +
363A GLY* 1.3 63.4 + - - +
364A VAL* 3.2 6.8 + - + +
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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