Contacts of the helix formed by residues 393 - 403 (chain F) in PDB entry 5ZR1
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 ARG 393 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337F ARG* 3.9 33.6 - - - +
387F ASP* 3.3 21.1 - - - +
389F PHE* 3.8 8.0 - - - +
392F ILE* 1.3 79.9 - - - +
394F TYR* 1.3 62.6 + - - +
395F ASP* 3.9 16.6 - - - +
396F GLU* 3.7 40.0 + - + +
397F ILE* 3.3 25.5 + - - +
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Residues in contact with TYR 394 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B LEU* 4.0 2.3 - - - +
296B ILE* 4.3 13.5 - - + +
495C GLU 3.8 16.4 - - - -
496C GLN* 3.3 31.6 - - - -
497C VAL 2.5 23.4 + - - -
498C LEU 4.1 3.4 - - - -
499C PRO* 3.3 37.8 - - + +
500C SER* 5.5 2.7 - - - +
387F ASP* 3.9 8.7 + - - +
389F PHE* 3.7 26.6 - + + -
393F ARG* 1.3 73.8 - - - +
395F ASP* 1.3 73.1 + - - +
396F GLU 3.2 0.2 - - - -
397F ILE* 4.1 2.5 - - + -
398F ILE* 3.1 46.4 + - + +
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Residues in contact with ASP 395 (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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296B ILE* 5.5 3.6 - - - +
393F ARG* 3.5 11.7 - - + +
394F TYR* 1.3 90.9 - - - +
396F GLU* 1.3 59.2 + - + +
398F ILE* 4.0 6.3 - - - +
399F PHE* 3.3 30.7 - - + -
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Residues in contact with GLU 396 (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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337F ARG* 5.4 3.5 + - - -
392F ILE* 3.7 25.6 - - + +
393F ARG* 3.7 44.3 + - - +
394F TYR 3.2 0.8 - - - -
395F ASP* 1.3 80.5 - - + +
397F ILE* 1.3 60.4 + - - +
398F ILE 3.5 0.7 - - - -
399F PHE* 4.1 3.5 + - - +
400F ARG* 3.6 24.0 + - - +
407F GLN* 5.7 2.3 - - - +
408F THR* 4.5 27.3 - - + +
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Residues in contact with ILE 397 (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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496C GLN* 3.7 39.9 - - + +
389F PHE* 3.4 27.4 - - + +
390F ASP* 4.1 6.7 - - - +
392F ILE* 3.7 19.3 - - + -
393F ARG 3.3 19.5 + - - +
394F TYR* 3.3 10.0 + - - +
396F GLU* 1.3 77.3 - - - +
398F ILE* 1.3 62.9 + - - +
399F PHE 3.3 0.7 - - - -
400F ARG* 3.3 12.3 + - + -
401F LYS* 2.9 37.6 + - + +
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Residues in contact with ILE 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 4.0 16.4 - - + -
296B ILE* 4.2 20.9 - - + -
481B SER 6.1 0.2 - - - +
496C GLN 3.5 19.5 - - - +
497C VAL* 3.8 19.5 - - + +
394F TYR* 3.1 38.6 + - + +
395F ASP* 4.0 7.4 - - - +
397F ILE* 1.3 79.9 - - - +
399F PHE* 1.3 77.2 + - + +
401F LYS* 3.4 8.9 + - + -
402F LEU* 3.0 38.5 + - + +
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Residues in contact with PHE 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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296B ILE* 3.6 38.1 - - + -
299B LYS* 3.9 28.7 - - + -
300B MET* 4.3 12.1 - - - -
395F ASP* 3.3 27.8 - - + +
396F GLU 4.1 4.1 + - - +
398F ILE* 1.3 80.5 - - + +
400F ARG* 1.3 60.8 + - - +
402F LEU* 4.0 9.2 - - + -
403F GLY 3.4 0.3 + - - -
404F SER* 2.9 54.8 + - - +
406F LEU* 5.9 1.6 - - + -
407F GLN* 3.7 13.2 - - + +
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Residues in contact with ARG 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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472C SER* 4.4 19.9 + - - +
473C GLY 5.4 3.8 - - - +
477C GLN* 4.1 15.7 + - - +
392F ILE* 3.4 42.2 - - - +
396F GLU* 3.6 17.3 + - - +
397F ILE* 3.3 18.3 + - + +
398F ILE 3.2 0.4 - - - -
399F PHE* 1.3 78.5 - - - +
401F LYS* 1.3 62.8 + - + +
403F GLY* 3.6 9.5 + - - -
407F GLN* 3.3 22.8 + - + +
408F THR* 4.7 22.0 + - - +
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Residues in contact with LYS 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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479B ASP* 3.5 31.8 + - - +
477C GLN* 4.5 13.8 - - - +
486C ASN* 5.6 5.1 + - - +
489C ASP* 5.2 8.3 + - - +
490C ASN* 2.6 33.1 + - - +
496C GLN* 3.7 34.8 - - + +
497C VAL* 3.8 17.9 - - - +
397F ILE* 2.9 30.3 + - + +
398F ILE* 3.9 9.2 - - + +
400F ARG* 1.3 77.3 - - + +
402F LEU* 1.3 62.7 + - - +
403F GLY* 3.2 1.7 + - - -
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Residues in contact with LEU 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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293B LEU* 6.0 1.6 - - + -
296B ILE* 4.3 16.8 - - + -
297B GLN* 3.5 39.9 - - + +
300B MET* 3.8 35.7 - - + +
304B TYR* 4.8 3.7 + - - +
478B HIS* 3.4 26.9 - - - +
479B ASP 3.4 22.4 + - - +
480B ILE* 4.0 7.0 - - + -
481B SER 5.7 0.2 - - - +
398F ILE* 3.0 30.6 + - + +
399F PHE* 4.3 9.4 - - + -
400F ARG 3.5 0.2 - - - -
401F LYS* 1.3 75.7 - - - +
403F GLY* 1.3 60.4 - - - +
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Residues in contact with GLY 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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300B MET* 4.2 0.9 - - - -
303B GLN* 3.8 10.4 + - - -
477B PHE 5.9 0.4 - - - -
478B HIS* 4.2 5.0 + - - -
323C TYR* 4.3 2.4 + - - -
474C LEU* 3.3 20.2 - - - +
477C GLN* 4.5 11.7 - - - -
478C SER* 4.1 9.0 + - - -
399F PHE 3.4 4.5 + - - -
400F ARG* 3.6 8.0 + - - -
401F LYS 3.2 5.3 - - - -
402F LEU* 1.3 80.2 - - - +
404F SER* 1.3 66.1 + - - +
405F MET 3.7 1.4 + - - -
407F GLN* 5.5 0.7 - - - -
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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