Contacts of the helix formed by residues 379 - 386 (chain A) in PDB entry 1Z6T
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 ILE 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LEU* 4.2 15.3 - - + -
376A ARG* 3.1 49.8 + - + +
378A ASP* 1.3 84.5 + - - +
380A LYS* 1.3 63.7 + - - +
381A ASP 3.3 3.1 - - - -
382A TYR* 3.2 19.9 + - + +
383A TYR 3.1 17.3 + - - -
414A ILE* 4.3 15.7 - - + +
417A GLU* 3.8 29.6 - - + +
418A PHE* 3.5 32.4 - - + -
421A LYS* 5.9 2.2 - - - -
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A VAL* 3.6 14.7 - - + +
373A GLU* 2.8 56.2 + - - +
375A LEU* 3.3 35.4 - - + +
376A ARG 3.5 3.9 + - - +
377A GLU* 3.1 43.1 + - - +
379A ILE* 1.3 76.4 - - - +
381A ASP* 1.3 65.3 + - - +
383A TYR* 3.3 4.0 + - - +
384A THR* 3.1 25.6 + - - -
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Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU 4.8 3.8 + - - +
378A ASP 5.3 0.9 - - - +
379A ILE 3.3 1.0 - - - +
380A LYS* 1.3 80.0 - - - +
382A TYR* 1.3 69.8 + - + +
384A THR* 3.2 11.5 + - - +
385A ASP* 3.0 27.3 + - - +
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Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASP 3.5 25.6 - - - -
379A ILE* 3.2 13.6 + - + +
381A ASP* 1.3 79.5 - - + +
383A TYR* 1.3 61.5 + - - +
385A ASP* 3.1 18.9 + - - +
386A LEU* 3.5 3.6 + - - +
404A TRP* 3.3 67.8 + + + +
406A MET* 3.8 18.5 - - - +
410A GLU* 4.8 2.1 + - - -
414A ILE* 3.8 26.9 - - + -
418A PHE* 4.2 8.3 - - + -
459A LYS* 5.7 1.6 - - - -
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A MET* 3.5 16.2 - - + +
372A VAL* 3.7 36.3 - - + -
375A LEU* 3.8 16.2 - - + -
379A ILE 3.1 6.7 + - - -
380A LYS 3.7 6.7 - - - +
381A ASP 3.2 0.4 - - - -
382A TYR* 1.3 73.0 - - - +
384A THR* 1.3 67.7 + - - +
386A LEU* 3.0 38.1 + - + +
387A SER* 3.9 2.6 + - - -
418A PHE* 3.7 31.3 - + + -
423A LEU* 2.5 46.9 + - + +
424A LEU* 4.9 0.2 - - + -
437A LEU* 3.7 9.7 - - + +
445A LEU* 3.7 28.6 - - + +
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Residues in contact with THR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A VAL* 5.8 2.9 - - - +
380A LYS 3.1 15.7 + - - -
381A ASP* 3.2 16.9 + - - +
383A TYR* 1.3 76.1 - - - +
385A ASP* 1.3 63.8 + - - +
387A SER* 2.8 29.4 + - - -
445A LEU* 5.3 0.7 - - - -
448A LYS* 4.5 9.7 + - - -
449A ASN* 3.9 20.5 + - - +
452A GLN* 3.6 35.2 - - - +
456A LEU* 3.6 11.7 - - + +
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Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ASP* 3.0 16.7 + - - +
382A TYR* 3.1 13.0 + - - +
384A THR* 1.3 78.3 - - - +
386A LEU* 1.3 58.0 + - - +
387A SER 3.0 5.7 + - - -
388A ILE* 3.2 27.7 + - - +
403A LEU* 3.9 11.1 - - + +
404A TRP* 2.7 30.0 + - + +
456A LEU* 3.1 25.9 - - - +
459A LYS* 2.8 33.0 + - - +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A TYR 3.7 8.1 - - - +
383A TYR* 3.0 35.9 + - + +
385A ASP* 1.3 76.2 - - + +
387A SER* 1.3 60.0 + - - +
388A ILE* 3.0 3.6 - - - +
389A LEU* 3.0 40.1 + - + +
400A LEU* 3.7 33.0 - - + -
403A LEU* 5.4 0.9 - - + -
404A TRP* 3.9 11.9 - - + -
415A LEU* 4.4 2.7 - - + -
418A PHE* 4.1 19.3 - - + -
424A LEU* 4.2 21.3 - - + -
437A LEU* 3.8 13.3 - - + +
445A LEU* 4.3 4.0 - - + -
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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