Contacts of the helix formed by residues 376 - 386 (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 GLU 376 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526C LYS* 4.5 6.3 - - - +
530C GLU* 5.2 9.1 - - - +
305F GLU* 3.0 26.4 - - - +
372F LEU 3.5 13.9 - - - +
373F ILE* 3.5 26.4 + - - +
374F ILE 3.5 3.7 - - - +
375F GLY* 1.3 82.5 - - - +
377F LYS* 1.3 65.1 + - - +
378F TRP* 2.6 42.4 + - + +
379F PHE* 3.6 4.1 + - + +
380F ARG* 3.3 21.3 + - - +
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Residues in contact with LYS 377 (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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515C LYS 3.6 21.8 + - - -
516C ILE* 4.5 17.7 + - - +
526C LYS* 5.5 1.0 - - - +
375F GLY 3.9 0.6 + - - -
376F GLU* 1.3 73.1 - - - +
378F TRP* 1.3 64.4 + - + +
380F ARG* 3.4 33.8 + - - +
381F ASP* 2.9 58.4 + - - +
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Residues in contact with TRP 378 (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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298F VAL* 5.5 1.8 - - - -
301F LYS* 3.7 64.8 + - + +
302F ILE* 5.2 2.0 - - + -
305F GLU* 3.9 13.8 + - + +
323F LEU* 4.2 15.5 - - + -
327F CYS* 4.1 23.3 - - - -
373F ILE* 4.1 25.4 - - + -
376F GLU* 2.6 35.3 + - + -
377F LYS* 1.3 82.5 - - + +
379F PHE* 1.3 74.7 + + + +
381F ASP* 3.5 7.1 + - - +
382F LEU* 2.9 34.9 + - + +
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Residues in contact with PHE 379 (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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495C GLU* 5.9 0.9 - - - -
326F ASN* 4.4 12.8 - - + -
327F CYS* 5.2 1.6 - - - -
330F ILE* 3.6 22.0 - - + -
370F LYS* 3.3 28.9 - - + -
373F ILE* 3.2 55.0 - - + +
374F ILE* 4.3 15.9 - - + -
376F GLU* 3.6 5.5 + - + +
377F LYS 3.3 0.6 - - - -
378F TRP* 1.3 100.7 - + + +
380F ARG* 1.3 64.8 + - - +
382F LEU* 3.6 9.6 + - + +
383F GLN* 3.2 48.1 + - - +
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Residues in contact with ARG 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C LEU 5.2 3.0 + - - -
493C SER 4.9 1.2 + - - -
494C TRP* 3.4 49.2 - - - +
495C GLU* 3.2 34.3 - - + +
518C ALA* 4.5 10.9 - - - +
523C GLN* 5.0 6.1 - - - +
526C LYS* 5.5 4.0 - - - +
374F ILE 5.8 1.3 + - - +
375F GLY* 4.0 19.6 + - - -
376F GLU 3.3 9.8 + - - +
377F LYS* 3.4 39.9 + - - +
379F PHE* 1.3 77.2 - - - +
381F ASP* 1.3 63.2 + - - +
383F GLN* 3.0 5.5 + - - +
384F ILE* 2.9 46.2 + - + +
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Residues in contact with ASP 381 (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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515C LYS 4.9 3.8 - - - +
377F LYS* 2.9 51.7 + - - +
378F TRP* 3.7 6.9 - - - +
380F ARG* 1.3 76.5 + - - +
382F LEU* 1.3 63.4 + - - +
384F ILE* 3.9 19.5 - - - +
385F ARG* 3.3 26.0 + - - +
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Residues in contact with LEU 382 (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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298F VAL* 3.8 24.9 - - + -
327F CYS* 3.7 34.5 - - + -
330F ILE* 3.7 25.1 - - + +
331F VAL* 4.3 3.4 - - + -
378F TRP* 2.9 29.7 + - + +
379F PHE* 3.7 10.5 - - + +
380F ARG 3.2 0.2 - - - -
381F ASP* 1.3 79.3 - - - +
383F GLN* 1.3 60.6 + - - +
385F ARG* 4.9 2.0 - - - +
386F TYR* 3.3 47.9 + - + +
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Residues in contact with GLN 383 (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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495C GLU* 2.9 26.9 - - + +
496C GLN* 4.0 7.8 - - - +
330F ILE* 3.8 27.1 - - + +
370F LYS* 3.6 10.7 - - - +
374F ILE* 5.3 2.4 - - - +
379F PHE* 3.2 43.7 + - - +
380F ARG* 3.0 8.9 + - - +
382F LEU* 1.3 76.0 - - - +
384F ILE* 1.3 61.5 + - - +
387F ASP* 3.1 19.3 + - - -
388F ASP 3.1 10.3 + - - +
389F PHE* 3.8 19.9 - - + +
390F ASP* 4.1 20.0 + - - +
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Residues in contact with ILE 384 (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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494C TRP* 5.7 5.6 - - + -
495C GLU* 4.4 17.3 - - + -
500C SER* 3.3 35.9 - - - +
515C LYS* 5.5 7.9 - - - +
380F ARG* 2.9 39.0 + - + +
381F ASP* 4.0 17.7 - - - +
382F LEU 3.4 0.2 - - - -
383F GLN* 1.3 77.0 - - - +
385F ARG* 1.3 65.6 + - - +
387F ASP* 3.5 14.7 + - - +
389F PHE* 4.1 11.7 - - + -
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Residues in contact with ARG 385 (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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297F GLU* 4.8 29.2 + - - +
381F ASP 3.3 18.5 + - - +
382F LEU* 4.2 3.1 - - - +
384F ILE* 1.3 83.7 - - - +
386F TYR* 1.3 84.8 + - + +
387F ASP* 3.2 3.6 + - - +
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Residues in contact with TYR 386 (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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295F PRO* 3.6 23.7 - - - +
298F VAL* 4.6 2.7 - - + -
330F ILE* 3.5 20.9 - - + +
331F VAL* 3.6 41.3 - - + +
333F ASN* 3.2 17.1 + - - +
382F LEU* 3.3 42.2 + - + +
385F ARG* 1.3 101.3 + - + +
387F ASP* 1.3 68.8 + - - +
388F ASP 3.5 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