Contacts of the helix formed by residues 363 - 371 (chain O) in PDB entry 1FQV
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 GLU 363 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361O ILE* 2.9 23.8 + - + +
362O PRO* 1.3 87.0 - - - +
364O THR* 1.3 66.4 + - + +
365O LEU 2.7 7.0 + - - -
366O LEU* 2.9 21.3 + - - +
387O THR* 3.9 21.3 - - - +
391O LEU* 5.3 0.5 - - - +
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Residues in contact with THR 364 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337O ASN* 3.2 48.1 - - + +
340O PHE* 3.3 4.2 - - - -
360O ILE* 3.6 9.2 - - - +
361O ILE* 2.5 42.9 + - + +
363O GLU* 1.3 77.2 - - + +
365O LEU* 1.3 53.3 + - - +
366O LEU 2.9 0.9 - - - -
367O GLU* 2.8 47.3 + - - +
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Residues in contact with LEU 365 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340O PHE* 4.2 5.2 - - + -
354O LEU* 4.9 2.7 - - + -
360O ILE* 4.0 24.0 - - + -
362O PRO* 3.3 22.9 - - + +
363O GLU 2.7 0.2 + - - -
364O THR* 1.3 80.7 + - - +
366O LEU* 1.3 61.7 + - - +
367O GLU 3.1 0.2 - - - -
368O LEU* 3.2 40.6 + - + +
377O LEU* 4.4 2.4 - - + +
379O VAL* 3.8 26.7 - - + -
382O ILE* 4.5 4.5 - - + -
383O VAL* 3.3 33.7 - - + -
391O LEU* 3.6 26.5 - - + +
395O LEU* 4.2 3.8 - - - +
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Residues in contact with LEU 366 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363O GLU 2.9 14.2 + - - +
364O THR 2.9 0.8 + - - -
365O LEU* 1.3 77.6 - - - +
367O GLU* 1.3 63.5 + - + +
369O GLY* 3.0 15.4 + - - -
370O GLU* 5.6 0.3 - - - +
391O LEU* 3.8 18.0 - - + +
394O ALA* 3.4 33.2 - - + -
395O LEU* 4.2 10.3 - - + +
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Residues in contact with GLU 367 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337O ASN* 3.1 32.2 + - - +
340O PHE* 3.8 18.2 - - + +
344O PHE* 3.5 12.4 - - + -
364O THR* 2.8 26.2 + - - +
366O LEU* 1.3 73.6 - - + +
368O LEU* 1.3 51.1 + - - +
369O GLY 2.7 16.2 + - - -
370O GLU* 2.8 34.4 + - + +
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Residues in contact with LEU 368 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340O PHE* 3.6 41.7 - - + -
343O PHE* 4.3 8.1 - - + -
344O PHE* 4.4 3.8 - - + -
352O LEU* 4.4 4.3 - - + -
354O LEU* 4.1 10.3 - - + -
365O LEU* 3.5 26.9 - - + +
366O LEU 3.1 1.8 - - - -
367O GLU* 1.3 75.3 - - - +
369O GLY* 1.3 57.8 + - - +
370O GLU 3.0 3.9 + - - +
371O ILE* 3.6 27.9 + - + +
374O LEU* 3.7 24.6 - - + +
377O LEU* 3.7 40.2 - - + -
395O LEU* 4.6 4.5 - - + -
397O HIS* 5.2 0.2 - - - -
398O LEU* 4.7 1.7 - - - +
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Residues in contact with GLY 369 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366O LEU 3.0 7.7 + - - -
367O GLU 2.7 3.6 + - - -
368O LEU* 1.3 78.4 - - - +
370O GLU* 1.3 67.6 + - - +
371O ILE 3.3 7.3 + - - +
372O PRO* 4.7 1.2 - - - +
395O LEU* 3.7 30.2 - - - +
397O HIS* 4.5 10.5 + - - -
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Residues in contact with GLU 370 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344O PHE* 3.2 35.9 - - + -
366O LEU 5.6 0.2 - - - +
367O GLU* 2.8 26.6 + - + +
369O GLY* 1.3 81.7 - - - +
371O ILE* 1.3 60.9 + - - +
372O PRO* 2.9 21.1 - - - +
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Residues in contact with ILE 371 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343O PHE* 3.6 34.1 - - + +
344O PHE* 3.4 27.8 - - + +
346O LEU 4.5 12.3 - - - +
349O LEU* 3.7 35.0 - - + +
352O LEU* 4.6 2.0 - - + -
368O LEU* 3.9 24.8 - - + +
369O GLY 3.3 6.7 - - - +
370O GLU* 1.3 75.1 - - - +
372O PRO* 1.3 68.2 - - + +
373O THR* 3.9 5.4 - - - +
374O LEU* 3.6 29.6 + - + +
397O HIS* 4.6 5.5 - - - -
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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