Contacts of the helix formed by residues 386 - 394 (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 PRO 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A ILE 4.7 1.3 - - - +
334A LYS* 4.8 2.5 - - - -
335A ASP* 5.1 9.0 - - - +
346A ALA* 3.5 28.7 - - + -
363A ILE* 4.4 22.2 - - + -
366A ASP* 4.2 33.0 - - + +
370A ALA* 5.7 0.2 - - + -
384A THR 3.9 3.1 - - - +
385A SER* 1.3 86.9 - - - +
387A ILE* 1.3 62.0 + - + +
389A THR* 3.5 9.0 - - - +
390A ILE* 2.9 33.4 + - + +
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 4.6 13.5 - - + -
366A ASP 6.0 0.4 - - - -
367A ALA* 4.2 12.6 - - - -
370A ALA* 4.3 11.9 - - + -
385A SER* 3.0 8.7 - - - +
386A PRO* 1.3 79.9 - - + +
388A GLU* 1.3 49.9 + - - +
391A SER* 2.6 40.0 + - - -
399A VAL* 4.2 9.8 - - + +
401A ILE* 3.5 30.1 - - + -
458A CYS* 3.6 25.1 - - + +
461A LEU* 3.5 26.5 - - + +
462A GLY 4.0 0.4 - - - -
463A ALA* 3.6 25.8 - - - +
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Residues in contact with GLU 388 (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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381A GLY* 3.5 14.2 - - - -
382A ASP* 3.8 4.7 + - - +
383A GLY* 2.7 41.9 + - - +
384A THR 3.4 0.3 + - - -
385A SER* 2.7 38.0 + - - +
387A ILE* 1.3 74.1 - - - +
389A THR* 1.3 64.1 + - - +
391A SER* 3.7 0.4 - - - -
392A LYS* 3.0 47.6 + - - +
461A LEU* 3.4 38.9 - - + +
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Residues in contact with THR 389 (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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346A ALA* 4.7 0.7 - - - +
347A LEU* 3.8 30.4 + - + +
383A GLY 3.9 17.5 - - - +
384A THR* 4.3 9.0 - - - +
385A SER 3.0 12.3 + - - +
386A PRO* 3.2 15.1 + - - +
388A GLU* 1.3 75.0 - - - +
390A ILE* 1.3 73.5 + - - +
392A LYS* 4.1 4.3 - - - +
393A ALA* 3.3 23.9 + - - +
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Residues in contact with ILE 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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333A ILE* 4.1 17.0 - - + -
346A ALA 4.3 4.5 - - - +
347A LEU* 4.2 19.7 - - - +
350A ALA* 3.8 19.5 - - + -
354A PHE* 4.1 26.5 - - + -
361A VAL* 4.1 12.6 - - + -
363A ILE* 4.5 5.2 - - + -
386A PRO* 2.9 29.9 + - + +
389A THR* 1.3 84.9 + - - +
391A SER* 1.3 60.7 + - - +
393A ALA 3.3 0.7 + - - -
394A TYR* 2.8 34.8 + - + +
398A ALA* 4.9 0.2 - - + -
399A VAL* 3.7 18.4 - - + -
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Residues in contact with SER 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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52A ASN* 5.7 0.2 - - - +
387A ILE 2.6 23.5 + - - -
388A GLU 3.3 4.7 + - - -
390A ILE* 1.3 77.7 - - - +
392A LYS* 1.3 63.3 + - - +
395A GLY* 2.6 38.4 + - - -
396A ALA* 3.8 5.7 + - - -
399A VAL* 3.7 8.5 - - - +
461A LEU 3.6 3.1 + - - -
462A GLY* 3.2 38.8 - - - -
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Residues in contact with LYS 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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52A ASN* 3.6 23.4 + - - +
55A HIS* 4.9 1.0 - - - -
383A GLY* 3.9 26.2 + - - +
388A GLU* 3.0 40.2 + - - +
389A THR* 4.1 4.9 - - - +
391A SER* 1.3 80.1 - - - +
393A ALA* 1.3 61.1 + - - +
461A LEU 5.5 1.8 - - - -
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Residues in contact with ALA 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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51A GLY* 3.9 1.9 - - - -
52A ASN 3.5 14.0 + - - -
55A HIS* 3.2 36.6 - - + +
347A LEU* 3.9 15.5 - - + -
389A THR 3.3 16.7 + - - +
392A LYS* 1.3 80.4 - - - +
394A TYR* 1.3 77.8 + - + +
395A GLY 3.7 0.2 - - - -
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Residues in contact with TYR 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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11A SER* 3.8 17.4 + - - -
12A GLY* 3.7 30.0 + - - -
50A VAL* 4.6 15.3 - - + +
51A GLY* 3.3 18.5 + - - -
55A HIS* 6.3 0.2 - - - -
347A LEU* 3.9 15.9 - - + -
351A SER* 2.6 37.9 + - - -
354A PHE* 3.5 35.4 - + - -
355A ARG* 5.7 0.3 - - - +
390A ILE* 2.8 25.6 + - + +
393A ALA* 1.3 82.7 - - + +
395A GLY* 1.3 58.3 + - - +
397A GLN* 3.2 17.5 + - - +
398A ALA* 3.7 21.3 - - + +
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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