Contacts of the helix formed by residues 386 - 395 (chain A) in PDB entry 1Z59
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 ASP 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A ARG* 2.9 43.9 + - - +
379A LEU* 3.8 2.9 - - - +
382A ASP 3.8 1.2 + - - -
383A GLU 3.2 14.6 + - - +
384A LYS 3.4 1.2 - - - +
385A SER* 1.3 80.5 - - - +
387A VAL* 1.3 67.9 + - - +
388A ILE* 2.9 33.7 + - - +
389A TRP* 3.2 11.2 + - - +
390A LYS* 3.2 12.5 + - - +
429A SER* 3.4 3.8 - - - -
430A ILE* 2.9 39.4 + - - +
432A GLU* 5.3 0.7 - - - -
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Residues in contact with VAL 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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385A SER 3.8 1.4 + - - -
386A ASP* 1.3 79.3 + - - +
388A ILE* 1.3 65.2 + - + +
390A LYS* 3.3 5.7 + - + +
391A VAL* 3.0 24.1 + - + +
430A ILE* 3.1 28.8 + - + +
431A ALA 3.6 19.1 - - - +
432A GLU* 3.8 21.2 - - + +
436A ILE* 5.2 2.0 - - + -
437A GLU* 3.7 46.4 - - + +
440A ILE* 4.0 17.7 - - + -
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Residues in contact with ILE 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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370A VAL* 4.1 13.5 - - + -
371A LEU 5.1 0.9 - - - +
372A ARG* 3.9 34.8 - - + -
373A TYR 4.7 3.1 - - - +
386A ASP* 2.9 20.2 + - - +
387A VAL* 1.3 73.9 - - + +
389A TRP* 1.3 62.5 + - - +
391A VAL* 3.4 5.7 + - - +
392A VAL* 3.1 26.2 + - + +
413A VAL* 3.9 53.8 - - + +
415A LEU* 5.6 1.6 - - + +
430A ILE* 4.0 18.2 - - + -
440A ILE* 4.0 18.2 - - + -
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Residues in contact with TRP 389 (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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367A GLU* 4.1 26.9 - - + -
368A PRO 5.2 3.6 - - - -
370A VAL* 4.0 38.1 - - + -
372A ARG* 4.9 2.8 - - - +
383A GLU* 3.0 62.8 - - + +
384A LYS* 3.6 48.2 - - + +
386A ASP* 3.2 8.5 + - + +
388A ILE* 1.3 81.0 - - - +
390A LYS* 1.3 59.2 + - - +
392A VAL* 3.5 5.1 + - + +
393A GLU* 3.0 53.9 + - + +
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Residues in contact with LYS 390 (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 6.1 0.4 - - - +
386A ASP 3.2 9.7 + - - +
387A VAL* 3.3 8.5 + - - +
389A TRP* 1.3 80.1 - - - +
391A VAL* 1.3 65.1 + - - +
393A GLU* 3.5 7.4 + - - +
394A GLU* 3.1 58.5 + - + +
432A GLU* 3.7 32.8 - - + +
437A GLU* 2.8 35.1 + - - +
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Residues in contact with VAL 391 (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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387A VAL* 3.0 23.3 + - + +
388A ILE 3.8 4.0 - - - +
390A LYS* 1.3 75.0 - - + +
392A VAL* 1.3 65.5 + - + +
394A GLU* 3.3 8.4 + - - +
395A LEU* 3.3 22.2 + - + +
437A GLU* 3.8 39.0 - - + +
440A ILE* 4.1 16.8 - - + -
441A LYS* 3.8 37.0 - - + +
444A LEU* 4.1 14.8 - - + -
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Residues in contact with VAL 392 (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 PRO* 4.0 23.3 - - + +
370A VAL* 3.8 28.7 - - + -
388A ILE* 3.1 29.7 + - + +
389A TRP 4.0 2.9 - - - +
391A VAL* 1.3 78.1 - - + +
393A GLU* 1.3 63.5 + - - +
394A GLU 3.4 0.5 + - - -
395A LEU* 3.5 8.5 + - - +
397A TRP* 3.7 24.7 + - + -
411A VAL* 4.0 23.6 - - + -
413A VAL* 5.1 3.1 - - + -
444A LEU* 4.1 17.5 - - + -
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Residues in contact with GLU 393 (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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367A GLU* 5.5 2.6 - - - +
389A TRP* 3.0 44.0 + - + +
390A LYS* 3.9 6.7 - - - +
392A VAL* 1.3 76.0 - - - +
394A GLU* 1.3 62.8 + - + +
395A LEU 3.6 5.9 + - - +
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Residues in contact with GLU 394 (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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390A LYS* 3.1 58.6 + - + +
391A VAL* 3.8 6.6 - - - +
392A VAL 3.3 0.2 - - - -
393A GLU* 1.3 77.6 - - + +
395A LEU* 1.3 64.3 + - - +
396A ASP* 3.6 2.6 + - - +
437A GLU* 4.9 1.2 - - - +
441A LYS* 6.1 4.0 - - - +
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Residues in contact with LEU 395 (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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391A VAL 3.3 12.1 + - - +
392A VAL 3.8 9.8 - - - +
393A GLU 3.4 8.0 - - - +
394A GLU* 1.3 78.2 - - - +
396A ASP* 1.3 63.0 + - - +
397A TRP* 3.5 50.5 + - + +
399A ARG* 4.2 2.7 - - - +
400A TYR* 3.8 25.4 - - + -
441A LYS* 4.8 10.3 - - + +
444A LEU* 3.9 19.3 - - + +
445A MSE 3.6 41.5 - - + -
448A ALA* 4.2 4.9 - - + -
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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