Contacts of the helix formed by residues 366 - 374 (chain B) in PDB entry 2O8F
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 TYR 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365B TRP* 1.3 73.6 - - - +
367B HIS* 1.3 61.5 + - - +
369B THR* 2.6 32.0 + - - -
370B LEU* 3.7 26.4 - - + +
402B PHE* 3.7 23.1 - + - -
405B SER* 6.1 0.5 - - - -
406B CYS* 6.0 0.3 - - - -
414B TRP* 6.1 0.2 - - - -
437B HIS* 3.9 22.2 - + - -
455B ASN* 3.3 28.9 + - - +
456B TRP* 3.7 16.4 - + + +
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Residues in contact with HIS 367 (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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365B TRP* 3.7 24.5 - - + +
366B TYR* 1.3 74.9 + - - +
368B GLU* 1.3 68.8 + - + +
369B THR 3.1 5.6 - - - -
370B LEU* 3.1 36.8 + - + +
373B LEU* 3.5 31.3 - - + +
414B TRP* 5.0 1.1 - - + -
437B HIS* 3.4 47.7 + - + +
438B MET* 3.9 15.0 + - + +
441B LEU* 3.5 32.0 - - + +
457B ALA* 3.9 7.8 + - + +
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Residues in contact with GLU 368 (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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363B THR 5.2 0.5 - - - +
364B VAL* 3.4 27.6 - - + +
365B TRP* 3.2 40.3 + - + +
367B HIS* 1.3 94.4 - - + +
369B THR* 1.3 60.5 + - - +
370B LEU 3.3 0.7 - - - -
373B LEU* 5.6 0.2 - - - -
374B LYS* 3.4 25.5 + - - +
441B LEU* 3.8 15.8 - - - +
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Residues in contact with THR 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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364B VAL* 4.3 14.4 - - + +
365B TRP 3.7 14.6 - - - +
366B TYR* 2.6 29.5 + - - +
368B GLU* 1.3 78.0 - - - +
370B LEU* 1.3 66.0 + - - +
371B GLU* 3.3 20.2 + - - +
374B LYS* 5.0 3.1 - - - +
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Residues in contact with LEU 370 (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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366B TYR* 3.7 27.1 - - + +
367B HIS* 3.1 27.7 + - + +
369B THR* 1.3 79.4 - - - +
371B GLU* 1.3 66.4 + - - +
372B TRP* 3.5 38.4 - - + +
373B LEU* 3.3 20.4 + - + +
374B LYS* 3.6 12.0 + - - +
402B PHE* 3.8 30.1 - - + -
414B TRP* 4.1 13.5 - - + -
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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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369B THR* 3.4 15.2 - - - +
370B LEU* 1.3 67.3 - - - +
372B TRP* 1.3 64.3 + - + +
373B LEU 2.9 10.3 + - - -
374B LYS* 3.2 37.7 + - - +
377B LYS* 3.1 50.3 + - + +
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Residues in contact with TRP 372 (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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370B LEU* 3.7 22.3 - - + +
371B GLU* 1.3 80.3 - - + +
373B LEU* 1.3 64.8 + - + +
377B LYS* 4.4 10.7 - - - +
378B ARG* 3.8 18.3 - - - -
379B ARG 4.5 1.0 + - - -
396B LEU* 3.8 22.7 - - + +
397B TYR* 3.5 22.9 - - + +
398B VAL* 3.8 9.9 - - + -
399B PRO* 3.5 33.2 - - + +
402B PHE* 3.5 45.6 - + - +
414B TRP* 3.5 39.5 - + - -
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Residues in contact with LEU 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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367B HIS* 3.5 39.0 - - + +
370B LEU* 3.3 17.9 + - + +
371B GLU 3.0 1.2 - - - -
372B TRP* 1.3 87.3 - - + +
374B LYS* 1.3 65.3 + - + +
378B ARG* 3.2 26.6 + - - +
396B LEU* 4.0 14.1 - - + -
414B TRP* 4.6 7.6 - - + -
421B PHE* 3.8 31.9 - - + -
438B MET* 3.8 25.1 - - + -
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Residues in contact with LYS 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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368B GLU* 3.4 26.5 + - - +
369B THR* 5.0 2.7 - - - +
370B LEU 3.8 11.9 - - - +
371B GLU* 3.2 33.9 + - - +
373B LEU* 1.3 77.9 - - + +
375B GLU* 1.3 51.2 + - - +
376B GLU* 3.0 32.2 + - + +
377B LYS* 2.8 11.9 + - + -
378B ARG* 2.8 30.2 + - - +
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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