Contacts of the helix formed by residues 365 - 376 (chain A) in PDB entry 1OX4
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 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A GLY* 1.3 70.3 - - - +
366A ASP* 1.3 66.8 + - - +
368A VAL* 2.8 17.5 + - - +
369A TYR* 3.3 42.0 + - + +
440A ILE* 3.7 20.2 - - + +
441A LYS* 2.8 33.6 + - + +
801A SO4 3.1 23.3 + - - -
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Residues in contact with ASP 366 (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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333A ILE 4.5 1.1 - - - +
334A LYS* 3.1 37.5 - - - +
335A ASP 4.8 0.5 + - - -
363A ILE* 4.0 15.5 - - + +
364A GLY 3.4 0.8 - - - -
365A THR* 1.3 78.6 - - - +
367A ALA* 1.3 55.3 + - - +
369A TYR* 3.2 24.5 + - - +
370A ALA* 2.8 31.8 + - - +
386A PRO* 4.2 21.1 - - + +
387A ILE* 6.0 0.4 - - - -
801A SO4 4.3 4.4 + - - +
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 3.6 18.2 - - + +
364A GLY 3.0 16.0 + - - +
365A THR 3.0 0.6 + - - -
366A ASP* 1.3 78.6 - - - +
368A VAL* 1.3 55.6 + - + +
370A ALA* 3.5 1.9 + - - +
371A ALA* 3.0 22.7 + - - +
387A ILE* 4.2 9.4 - - - -
401A ILE* 3.8 31.4 - - + -
402A SER 5.3 0.2 - - - +
454A LEU* 3.4 13.2 - - + +
458A CYS* 3.7 10.1 - - - -
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY 4.1 8.1 - - - +
365A THR* 2.8 10.0 + - - +
367A ALA* 1.3 76.5 - - - +
369A TYR* 1.3 65.9 + - + +
371A ALA* 3.3 2.3 + - - +
372A GLU* 2.9 35.5 + - - +
438A CYS* 4.7 4.7 - - + -
439A THR 4.0 10.1 - - - +
440A ILE* 3.5 23.6 - - + -
447A ARG* 3.9 30.3 - - + -
449A LEU* 3.9 17.0 - - + -
454A LEU* 3.8 23.1 - - + -
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Residues in contact with TYR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 3.3 22.8 + - + +
366A ASP* 3.2 31.3 + - - +
368A VAL* 1.3 77.1 - - + +
370A ALA* 1.3 64.3 + - - +
372A GLU* 3.2 18.5 + - - +
373A LYS* 2.9 27.0 + - - +
440A ILE* 3.3 23.1 - - + +
441A LYS* 3.7 17.0 + - - -
447A ARG* 3.7 27.9 + - - -
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP 2.8 17.3 + - - +
367A ALA* 3.6 8.1 - - - +
369A TYR* 1.3 76.6 - - - +
371A ALA* 1.3 53.0 + - - +
373A LYS* 3.2 8.7 + - - +
374A TYR* 2.7 36.9 + - - +
385A SER* 3.9 23.3 - - - -
386A PRO* 5.7 0.4 - - + -
387A ILE* 4.3 5.8 - - + -
461A LEU* 3.8 20.8 - - + +
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Residues in contact with ALA 371 (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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367A ALA 3.0 7.5 + - - +
368A VAL 3.3 2.7 + - - +
370A ALA* 1.3 75.5 - - - +
372A GLU* 1.3 63.2 + - - +
374A TYR* 3.0 18.0 - - - +
375A TYR* 3.0 17.7 - - + -
449A LEU* 3.9 9.9 - - + -
454A LEU* 3.4 34.8 - - + +
457A ALA* 3.6 27.4 - - + -
458A CYS* 4.6 1.1 - - - -
461A LEU* 4.5 2.1 - - - +
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Residues in contact with GLU 372 (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 VAL* 2.9 25.0 + - - +
369A TYR* 3.5 16.7 - - - +
371A ALA* 1.3 75.0 - - - +
373A LYS* 1.3 63.3 + - - +
375A TYR* 3.2 16.7 + - - +
376A GLU* 3.2 25.1 + - - +
447A ARG* 3.0 52.7 + - - +
448A ASP 4.7 4.3 + - - -
449A LEU* 4.2 18.8 - - + +
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Residues in contact with LYS 373 (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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369A TYR* 2.9 18.3 + - - +
370A ALA* 3.6 7.0 - - - +
372A GLU* 1.3 75.3 - - - +
374A TYR* 1.3 63.7 + - - +
376A GLU* 2.9 30.6 + - + +
377A LEU* 3.0 27.8 + - + +
382A ASP* 3.3 30.0 + - - +
384A THR* 4.1 8.7 + - - +
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Residues in contact with TYR 374 (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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370A ALA 2.7 18.1 + - - +
371A ALA* 3.0 14.8 - - - +
373A LYS* 1.3 73.6 - - - +
375A TYR* 1.3 79.4 + + - +
377A LEU* 3.5 3.6 + - - -
379A ASN* 3.0 62.0 + - + +
380A ARG* 3.2 39.4 + - - +
381A GLY* 4.3 1.1 - - - -
456A ARG 5.4 0.2 - - - -
457A ALA* 3.6 24.7 - - + -
460A ALA* 3.7 29.4 - - + +
461A LEU* 3.8 23.3 - - + -
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Residues in contact with TYR 375 (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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371A ALA 3.0 27.1 + - - -
372A GLU* 3.9 6.5 - - - +
373A LYS 3.2 0.4 - - - -
374A TYR* 1.3 85.7 - + - +
376A GLU* 1.3 66.4 + - + +
377A LEU 3.2 0.2 - - - -
378A GLY* 3.0 13.3 + - - -
379A ASN* 3.2 25.6 + - - +
449A LEU* 4.2 12.6 - - + -
453A GLU* 2.4 57.4 + - + +
456A ARG* 4.3 5.4 - - - +
457A ALA* 3.7 17.5 + - + +
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Residues in contact with GLU 376 (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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372A GLU* 3.2 25.0 + - - +
373A LYS* 2.9 21.5 + - + +
375A TYR* 1.3 77.7 - - + +
377A LEU* 1.3 63.9 + - + +
378A GLY 3.1 3.2 + - - -
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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