Contacts of the helix formed by residues 349 - 358 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272D TYR* 3.1 39.9 + - + -
273D TYR* 2.8 32.4 + - - +
346D LYS* 3.3 13.3 + - - +
347D LYS 3.1 1.0 - - - -
348D GLU* 1.3 85.8 - - - +
350D VAL* 1.3 57.8 + - - +
351D PRO* 3.3 2.2 - - - -
352D LEU* 3.0 11.9 + - + +
353D LEU* 2.8 34.6 + - + +
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Residues in contact with VAL 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D LYS 4.0 1.7 + - - +
347D LYS* 3.1 17.0 + - - +
349D ASP* 1.3 76.7 - - - +
351D PRO* 1.3 66.1 - - + +
353D LEU* 4.2 10.5 - - + +
354D ALA* 2.7 30.1 + - - +
376D GLU* 3.5 41.5 - - + +
379D PHE* 3.9 15.5 - - + -
380D LEU* 3.9 13.0 - - + -
383D PHE* 3.8 30.7 - - + -
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Residues in contact with PRO 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D LYS 3.9 3.6 - - - +
348D GLU 3.4 16.8 - - - +
349D ASP 3.5 1.1 - - - -
350D VAL* 1.3 94.1 - - + +
352D LEU* 1.3 56.1 + - - +
355D ASP* 3.1 8.7 + - - +
372D GLN* 2.9 25.5 + - - -
376D GLU* 2.9 26.5 - - - +
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Residues in contact with LEU 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D GLN* 6.2 0.2 - - + -
272D TYR* 4.1 37.7 - - + +
349D ASP* 3.0 13.4 + - + +
351D PRO* 1.3 78.2 - - - +
353D LEU* 1.3 74.5 + - + +
355D ASP* 3.2 4.8 + - - +
356D HIS* 2.9 55.0 + - + +
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Residues in contact with LEU 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D GLN* 3.4 32.1 - - + +
269D LEU* 3.9 23.6 - - + +
272D TYR* 3.9 31.9 - - + -
273D TYR* 4.1 15.5 - - + +
345D ALA* 5.6 1.6 - - + -
346D LYS 4.9 2.2 - - - +
349D ASP* 2.8 28.7 + - + +
350D VAL* 3.8 10.5 - - + +
352D LEU* 1.3 81.2 - - + +
354D ALA* 1.3 58.7 + - - +
356D HIS* 5.1 0.4 - - - -
357D ALA* 2.9 29.1 + - - +
379D PHE* 3.8 21.7 - - + -
383D PHE* 6.2 0.7 - - + -
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Residues in contact with ALA 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D VAL 2.7 21.5 + - - +
353D LEU* 1.3 72.6 - - - +
355D ASP* 1.3 64.0 + - - +
357D ALA* 3.2 2.5 + - - +
358D LEU* 3.1 27.6 + - - +
372D GLN* 3.5 9.0 - - - +
375D VAL* 3.7 25.8 - - + +
376D GLU* 3.4 31.2 - - + +
379D PHE* 3.7 3.9 - - + -
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Residues in contact with ASP 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D PRO 3.1 9.9 + - - +
352D LEU* 3.2 7.4 + - - +
354D ALA* 1.3 79.0 - - - +
356D HIS* 1.3 73.1 + - + +
358D LEU* 3.5 6.9 + - - +
359D LYS* 3.0 51.0 + - - +
372D GLN* 2.8 32.0 + - - +
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Residues in contact with HIS 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D VAL* 3.3 30.4 - - + +
268D GLN* 3.2 26.6 + - - +
352D LEU* 2.9 49.9 + - + +
353D LEU 4.2 0.9 - - - +
355D ASP* 1.3 89.2 + - + +
357D ALA* 1.3 67.4 + - - +
358D LEU 3.2 0.4 - - - -
359D LYS* 3.0 26.7 + - + +
360D ASP* 3.0 10.7 + - - -
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Residues in contact with ALA 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D ALA* 3.4 40.4 - - + +
265D MET* 4.1 16.8 - - + -
268D GLN* 3.6 3.3 - - + +
353D LEU 2.9 20.3 + - - +
354D ALA* 3.2 10.7 + - - +
356D HIS* 1.3 76.1 - - - +
358D LEU* 1.3 58.2 + - + +
360D ASP* 3.1 23.0 + - - +
363D ALA* 3.5 2.6 - - - +
375D VAL* 4.3 5.4 - - + -
379D PHE* 4.3 0.4 - - + -
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Residues in contact with LEU 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D TYR* 3.6 33.0 - - + +
354D ALA 3.1 11.3 + - - +
355D ASP 3.8 9.4 - - - +
356D HIS 3.2 0.2 - - - -
357D ALA* 1.3 80.9 - - - +
359D LYS* 1.3 59.0 + - + +
360D ASP 3.3 1.3 + - - +
363D ALA* 4.0 13.7 - - + +
369D GLN* 5.7 2.2 - - - +
370D GLY 4.1 8.5 - - - +
371D ASP* 3.5 7.6 - - - +
372D GLN* 3.3 42.0 - - + +
375D VAL* 4.1 11.4 - - + -
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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