Contacts of the helix formed by residues 379 - 388 (chain A) in PDB entry 5LZ6
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 GLN 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ARG* 3.3 25.2 + - - +
378A PRO* 1.3 91.2 - - - +
380A ILE* 1.3 61.1 + - - +
381A LYS 3.5 2.5 - - - -
382A ASP* 3.9 20.9 - - + +
383A PHE* 3.6 19.6 + - - +
491A VAL* 3.9 5.6 - - - +
26B LYS* 3.8 40.4 + - + +
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Residues in contact with ILE 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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378A PRO 2.6 19.0 + - - +
379A GLN* 1.3 71.9 - - - +
381A LYS* 1.3 80.8 + - + +
383A PHE* 3.4 1.9 + - - +
384A LYS* 3.1 52.0 + - - +
421A ALA* 4.1 4.3 - - + -
487A CYS 3.8 11.7 - - - +
488A HIS 3.4 32.5 - - - +
489A GLU 4.3 9.4 - - - +
490A GLU 4.0 10.8 - - - +
491A VAL* 3.5 18.2 - - + +
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLN 3.5 0.2 - - - -
380A ILE* 1.3 86.2 - - + +
382A ASP* 1.3 70.7 + - - +
384A LYS* 4.0 6.4 - - + +
385A GLU* 3.0 28.8 + - - +
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Residues in contact with ASP 382 (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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379A GLN* 3.9 28.1 - - + +
381A LYS* 1.3 80.8 + - - +
383A PHE* 1.3 63.3 + - - +
385A GLU* 3.9 7.6 - - - +
386A LYS* 3.1 25.1 + - - +
26B LYS* 6.4 0.2 - - - +
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Residues in contact with PHE 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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377A ARG* 3.3 20.0 - - - +
379A GLN 3.6 14.2 + - - +
380A ILE 3.4 9.2 + - - +
381A LYS 3.1 0.6 - - - -
382A ASP* 1.3 75.8 - - - +
384A LYS* 1.3 71.8 + - + +
386A LYS* 2.9 9.1 + - + +
387A ILE* 2.9 53.5 + - + +
419A GLU* 3.6 48.7 - - + -
420A PHE* 4.2 0.4 - - - -
421A ALA* 4.1 18.2 - - + -
491A VAL* 3.9 19.7 - - + -
521A TYR* 4.0 21.3 - - + -
522A TYR* 4.6 1.8 - - - -
523A ARG* 4.8 1.3 - - + -
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Residues in contact with LYS 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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380A ILE* 3.1 41.7 + - + +
381A LYS* 4.0 6.1 - - + +
383A PHE* 1.3 82.5 - - + +
385A GLU* 1.3 54.2 + - - +
387A ILE* 2.8 13.4 + - - +
388A GLN* 2.7 49.2 + - - +
421A ALA* 4.5 2.7 - - - -
422A THR 2.9 23.4 + - - -
423A ASP* 2.5 31.7 + - - +
424A ASN 5.2 0.2 - - - +
488A HIS 4.6 2.6 + - - -
521A TYR* 3.7 29.6 - - + +
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Residues in contact with GLU 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 LYS* 3.0 19.9 + - - +
382A ASP* 3.9 7.6 - - - +
384A LYS* 1.3 75.6 - - - +
386A LYS* 1.3 59.9 - - - +
388A GLN* 3.9 15.1 + - - +
389A GLN* 3.6 29.0 + - - +
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Residues in contact with LYS 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 ASP 3.1 16.6 + - - +
383A PHE* 2.9 8.3 + - + +
385A GLU* 1.3 76.2 - - - +
387A ILE* 1.3 65.6 + - + +
389A GLN* 3.7 23.7 - - - +
390A ASP* 5.8 0.2 - - - +
523A ARG* 3.9 18.4 + - - +
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Residues in contact with ILE 387 (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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383A PHE* 2.9 51.3 + - + +
384A LYS 2.8 7.4 + - - +
386A LYS* 1.3 75.2 - - + +
388A GLN* 1.3 51.6 + - - +
389A GLN 2.9 5.3 - - - -
390A ASP* 2.7 37.8 + - - +
393A SER* 3.4 35.4 - - - +
394A VAL* 4.1 1.3 - - + -
521A TYR* 3.9 18.6 - - + -
522A TYR 4.2 3.4 - - - +
523A ARG* 3.3 45.5 - - + +
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Residues in contact with GLN 388 (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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384A LYS* 2.7 33.0 + - - +
385A GLU* 4.3 11.0 - - - +
386A LYS 3.5 0.2 - - - -
387A ILE* 1.3 71.9 - - - +
389A GLN* 1.3 57.4 + - + +
390A ASP 2.9 15.0 + - - +
391A ALA* 5.3 0.3 - - - -
394A VAL* 4.6 5.8 - - + -
521A TYR* 3.6 33.3 + - + -
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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