Contacts of the helix formed by residues 349 - 358 (chain A) in PDB entry 3OX4
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 ASP 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A TYR* 2.8 32.6 + - + +
346A LYS* 2.7 48.9 + - - +
348A GLU* 1.3 78.6 - - - +
350A VAL* 1.3 63.6 + - - +
351A PRO 3.4 2.0 - - - -
352A LEU* 3.2 15.3 + - + +
353A LEU* 3.0 32.5 + - + +
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Residues in contact with VAL 350 (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 LYS 3.8 0.2 + - - -
347A LYS* 3.0 23.1 - - - +
349A ASP* 1.3 76.6 - - - +
351A PRO* 1.3 63.8 - - + +
353A LEU* 3.0 10.3 + - + +
354A ALA* 2.7 33.1 + - - +
376A GLU* 3.1 45.3 - - + +
379A PHE* 3.6 11.7 - - + -
380A LEU* 3.4 25.6 - - + -
383A PHE* 4.1 15.7 - - + -
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Residues in contact with PRO 351 (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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347A LYS 4.1 4.0 - - - +
348A GLU* 3.8 12.1 - - - +
349A ASP 3.6 3.4 - - - -
350A VAL* 1.3 94.0 - - + +
352A LEU* 1.3 58.8 - - - +
355A ASP* 3.3 11.4 + - - +
372A GLN* 3.1 18.8 + - - +
376A GLU* 3.5 32.8 - - - +
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Residues in contact with LEU 352 (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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272A TYR* 5.3 13.2 - - + -
273A TYR* 5.1 11.0 - - + +
349A ASP* 3.2 15.8 + - - +
350A VAL 3.2 0.6 - - - -
351A PRO* 1.3 77.5 - - - +
353A LEU* 1.3 69.2 + - + +
355A ASP* 3.4 4.9 + - + +
356A HIS* 2.9 63.7 + - + +
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Residues in contact with LEU 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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268A GLN* 3.6 41.2 - - + +
269A LEU* 3.6 22.7 - - + -
272A TYR* 4.6 8.1 - - + -
273A TYR* 3.7 19.5 - - + +
345A ALA* 5.5 4.3 - - + -
346A LYS 5.1 2.0 - - - +
349A ASP* 3.0 38.0 + - + +
350A VAL* 3.5 9.2 - - + +
352A LEU* 1.3 80.6 - - + +
354A ALA* 1.3 57.8 + - - +
356A HIS* 3.5 2.1 + - - -
357A ALA* 2.9 30.1 + - - +
379A PHE* 3.6 23.1 - - + -
383A PHE* 5.7 2.5 - - + -
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Residues in contact with ALA 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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350A VAL 2.7 19.9 + - - +
353A LEU* 1.3 70.4 - - - +
355A ASP* 1.3 64.6 + - - +
357A ALA* 3.5 1.4 - - - +
358A LEU* 3.1 29.6 + - - +
372A GLN* 3.4 19.5 - - - +
375A VAL* 3.5 29.5 - - + +
376A GLU* 3.5 19.5 - - + +
379A PHE* 3.6 3.3 - - + -
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Residues in contact with ASP 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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351A PRO 3.3 15.0 + - - +
352A LEU* 3.7 6.9 - - + +
353A LEU 3.3 0.2 - - - -
354A ALA* 1.3 79.4 - - - +
356A HIS* 1.3 66.5 + - - +
358A LEU* 3.6 6.4 + - - +
359A LYS* 2.8 61.5 + - - +
372A GLN* 3.5 20.8 - - - +
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Residues in contact with HIS 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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268A GLN* 3.2 30.8 + - + +
272A TYR* 3.0 34.9 + + + +
352A LEU* 2.9 52.7 + - + +
353A LEU 4.0 1.3 - - - +
355A ASP* 1.3 78.4 + - - +
357A ALA* 1.3 64.1 + - - +
359A LYS* 3.3 33.9 + - - +
360A ASP* 3.2 15.8 + - - -
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Residues in contact with ALA 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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261A TYR* 6.3 0.2 - - - -
264A ALA* 3.7 24.7 - - + +
265A MET* 4.0 21.3 - - + -
268A GLN* 3.8 4.0 - - + -
353A LEU 2.9 19.5 + - - +
354A ALA* 3.5 9.9 - - - +
356A HIS* 1.3 74.6 - - - +
358A LEU* 1.3 62.8 + - - +
359A LYS 3.0 4.7 - - - -
360A ASP* 3.0 20.3 + - - +
363A ALA* 3.6 8.9 - - - +
375A VAL* 4.1 5.6 - - + -
379A PHE* 4.3 0.9 - - + -
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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
----------------------------------------------------------
261A TYR* 3.6 17.0 - - + +
354A ALA 3.1 16.7 + - - +
355A ASP* 4.0 6.5 - - - +
356A HIS 3.4 0.2 - - - -
357A ALA* 1.3 77.7 - - - +
359A LYS* 1.3 60.5 + - + +
360A ASP 4.2 0.5 - - - +
363A ALA* 4.0 14.3 - - + +
369A GLN* 6.0 0.4 - - - +
370A GLY 3.2 22.9 - - - +
371A ASP* 3.7 4.5 - - - -
372A GLN* 3.7 37.2 - - + +
375A VAL* 3.4 20.6 - - + -
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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