Contacts of the helix formed by residues 397 - 406 (chain F) in PDB entry 4XLR
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 THR 397 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387F ARG* 4.1 8.7 - - - +
395F GLU 4.0 2.4 + - - -
396F HIS* 1.3 75.3 - - - +
398F LEU* 1.3 74.7 + - - +
399F GLU* 3.6 13.0 + - + +
400F GLU* 2.9 44.0 + - + +
401F VAL* 3.1 12.1 + - - +
42P T 3.3 38.5 + - - +
43P G 3.4 13.9 + - - -
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Residues in contact with LEU 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387F ARG* 3.2 37.7 - - - +
397F THR* 1.3 76.1 + - - +
399F GLU* 1.3 57.8 + - + +
402F GLY* 2.9 27.4 + - - -
409F ARG* 3.3 54.4 - - + +
412F ILE* 4.0 10.0 - - + +
413F ARG* 3.6 28.9 - - + +
416F GLU* 5.7 0.7 - - + -
42P T 5.7 0.4 - - + -
43P G 3.1 33.2 - - + +
44P T 4.4 11.0 - - + +
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Residues in contact with GLU 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397F THR* 3.1 13.4 + - + +
398F LEU* 1.3 78.1 - - - +
400F GLU* 1.3 57.4 + - + +
402F GLY* 3.6 1.3 + - - -
403F ALA* 2.9 28.1 + - - +
409F ARG* 2.8 47.8 + - - +
42P T 3.4 41.6 - - + +
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Residues in contact with GLU 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395F GLU 4.9 2.1 - - - +
396F HIS* 3.4 42.5 + - + +
397F THR* 2.9 31.8 + - + +
399F GLU* 1.3 76.7 - - + +
401F VAL* 1.3 60.0 + - - +
403F ALA* 2.9 9.7 + - - +
404F TYR* 2.9 24.8 + - - +
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Residues in contact with VAL 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F VAL* 3.6 44.9 - - + +
386F LEU* 3.8 22.4 - - + -
387F ARG* 4.4 10.3 - - + -
396F HIS* 3.6 18.4 - - + +
397F THR 3.1 16.5 + - - +
400F GLU* 1.3 71.2 - - - +
402F GLY* 1.3 61.0 + - - +
404F TYR* 3.0 29.7 + - + +
405F PHE* 3.0 13.9 + - - +
412F ILE* 3.7 16.9 - - + +
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Residues in contact with GLY 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398F LEU 2.9 18.9 + - - -
399F GLU* 3.8 1.8 - - - -
401F VAL* 1.3 78.2 - - - +
403F ALA* 1.3 55.2 + - - +
404F TYR 3.1 0.2 - - - -
406F GLY* 3.0 22.2 + - - -
407F VAL* 2.8 32.4 + - - +
408F THR 4.6 2.0 - - - -
409F ARG 4.7 0.7 - - - -
412F ILE* 3.5 11.1 - - - +
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Residues in contact with ALA 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399F GLU 2.9 18.8 + - - +
400F GLU* 2.9 10.9 + - - +
402F GLY* 1.3 75.8 - - - +
404F TYR* 1.3 61.7 + - - +
406F GLY* 4.3 4.1 + - - -
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Residues in contact with TYR 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F MET* 4.1 25.0 - - + +
383F VAL* 5.0 1.1 - - + -
386F LEU* 5.0 9.9 - - + -
400F GLU 2.9 9.4 + - - +
401F VAL* 3.0 22.6 + - + +
403F ALA* 1.3 81.8 - - - +
405F PHE* 1.3 107.5 + + - +
406F GLY* 3.2 2.3 + - - -
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Residues in contact with PHE 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378F GLU 5.2 0.4 - - - -
379F ARG* 3.4 60.7 + - + +
382F MET* 4.7 7.0 - - + -
383F VAL* 3.5 27.4 - - + -
401F VAL 3.0 9.6 + - - +
404F TYR* 1.3 116.3 - + - +
406F GLY* 1.3 61.9 + - - +
407F VAL* 3.2 23.6 + - + +
412F ILE* 5.1 0.4 - - + -
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Residues in contact with GLY 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F GLY 3.0 10.0 + - - -
403F ALA* 4.3 3.1 - - - -
404F TYR 3.2 5.4 + - - +
405F PHE* 1.3 79.0 - - - +
407F VAL* 1.3 59.9 + - - +
2O T 4.6 2.6 + - - -
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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