Contacts of the helix formed by residues 368 - 378 (chain B) in PDB entry 5O9Z
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 SER 368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B ARG 3.7 22.9 - - - -
343B LEU* 4.4 7.9 - - - +
344B TRP 4.3 4.9 - - - -
347B ILE* 2.6 19.8 + - - +
348B TYR* 4.6 0.6 - - - +
349B PHE* 4.8 15.5 - - - -
356B PHE* 5.6 2.5 - - - -
366B GLN 3.7 0.8 + - - -
367B ARG* 1.3 73.0 - - - +
369B PHE* 1.3 57.4 + - - +
371B GLU* 5.0 1.8 - - - -
372B PHE* 2.9 40.9 + - - +
373B ILE* 3.5 0.3 + - - +
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Residues in contact with PHE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B TYR* 5.7 7.9 - - + -
343B LEU 3.9 12.4 + - - +
344B TRP 4.2 1.8 + - - -
345B GLY* 3.7 27.6 - - - +
346B ASP 5.2 0.2 - - - +
367B ARG* 3.2 2.7 - - + +
368B SER* 1.3 77.5 - - - +
370B VAL* 1.3 53.6 + - - +
373B ILE* 2.6 37.3 + - + +
374B LEU* 2.7 16.2 + - - +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO* 4.7 20.1 - - + +
272B THR* 5.4 3.4 - - - +
275B TYR* 5.7 5.4 - - + -
366B GLN* 4.6 7.6 - - + -
367B ARG* 3.3 23.8 + - + +
369B PHE* 1.3 77.8 - - - +
371B GLU* 1.3 51.5 + - - +
374B LEU* 2.9 18.3 + - - +
375B GLU* 2.7 32.1 + - - +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PRO* 5.2 4.6 - - + +
366B GLN* 5.1 11.4 - - + +
367B ARG 3.1 13.1 + - - +
368B SER* 5.0 1.3 - - - -
370B VAL* 1.3 77.9 - - - +
372B PHE* 1.3 61.1 + - + +
375B GLU* 2.5 41.9 + - + +
376B PRO* 3.3 1.6 - - - +
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Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PRO* 4.9 20.2 - - + +
387A PHE* 5.7 0.5 + - - +
323B PHE* 5.9 3.5 - - - +
343B LEU* 5.8 6.3 - - + -
368B SER* 2.9 26.2 + - - +
371B GLU* 1.3 77.4 - - + +
373B ILE* 1.3 55.7 + - - +
376B PRO* 3.3 18.7 - - - +
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LEU* 5.5 3.4 - - + +
368B SER 3.5 0.4 + - - +
369B PHE* 2.6 31.4 + - + +
372B PHE* 1.3 79.3 - - + +
374B LEU* 1.3 60.4 + - - +
375B GLU 3.3 0.2 - - - -
376B PRO* 3.2 15.4 - - - +
377B LEU* 3.7 9.9 + - - +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B PRO* 3.7 30.8 - - + +
369B PHE 2.7 11.9 + - - +
370B VAL* 2.9 14.6 + - - +
373B ILE* 1.3 73.2 - - + +
375B GLU* 1.3 64.7 + - - +
376B PRO 3.5 0.2 - - - -
377B LEU* 3.7 6.2 - - - +
378B TYR* 3.2 28.5 + - + +
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PRO* 5.9 3.4 - - + -
390A ASP* 5.0 8.5 - - + +
271B PRO* 6.0 1.6 - - - -
370B VAL 2.7 8.8 + - - +
371B GLU* 2.5 33.6 + - + +
374B LEU* 1.3 73.1 - - - +
376B PRO* 1.3 60.9 - - + +
378B TYR* 4.8 0.6 - - - +
379B LYS* 3.2 26.7 + - - +
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Residues in contact with PRO 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PRO* 5.2 9.4 - - + -
387A PHE* 4.8 22.0 - - + +
388A LEU 5.6 1.8 - - - +
389A LYS 5.1 10.8 - - - +
390A ASP* 5.9 0.7 - - + -
371B GLU 3.3 10.3 - - - +
372B PHE* 3.3 19.1 - - - +
373B ILE 3.2 13.2 - - - +
375B GLU* 1.3 90.9 - - + +
377B LEU* 1.3 61.1 + - + +
379B LYS* 4.1 4.7 - - + +
380B ILE* 3.3 22.2 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B ILE 3.9 9.9 - - - +
374B LEU* 3.7 10.8 - - - +
375B GLU 3.2 1.0 - - - -
376B PRO* 1.3 79.1 - - - +
378B TYR* 1.3 66.9 + - - +
380B ILE* 3.2 5.7 + - - +
381B LEU* 3.0 23.8 + - - +
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Residues in contact with TYR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ILE* 5.3 17.2 - - + +
271B PRO* 5.3 11.7 - - + -
374B LEU* 3.2 12.3 + - + +
375B GLU* 4.8 0.9 - - - +
377B LEU* 1.3 78.9 - - - +
379B LYS* 1.3 57.2 + - - +
381B LEU* 3.9 6.6 - - - +
382B ALA* 3.0 31.9 + - - +
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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