Contacts of the helix formed by residues 397 - 405 (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 THR 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.4 2.4 + - - -
395A VAL 3.8 0.6 + - - -
396A PRO* 1.3 72.2 - - - +
398A LYS* 1.3 58.0 + - - +
400A LEU* 2.9 24.3 + - - +
401A CYS* 3.0 27.3 + - - -
408A THR* 4.3 8.7 - - + +
411A VAL* 3.9 11.0 - - + -
412A GLU* 3.3 37.6 + - + +
433A PHE* 3.3 16.2 + - - +
435A TYR* 3.4 24.7 - - + -
478A GLU* 3.4 7.2 + - - -
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Residues in contact with LYS 398 (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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396A PRO 3.1 0.2 + - - -
397A THR* 1.3 73.4 - - - +
399A VAL* 1.3 61.0 + - - +
401A CYS* 3.3 19.7 - - + +
402A ILE* 3.1 28.7 + - + +
408A THR* 6.1 0.4 - - - +
467A TYR* 4.0 27.3 - - - -
468A HIS* 5.0 6.1 - - - -
478A GLU* 2.6 33.9 + - + +
479A ASP* 3.3 31.0 - - + +
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 6.2 0.7 - - + -
395A VAL* 3.5 25.4 - - + -
396A PRO* 3.1 13.4 + - + -
398A LYS* 1.3 74.9 - - - +
400A LEU* 1.3 61.3 + - + +
402A ILE* 3.4 5.8 + - - +
403A LEU* 3.1 23.7 + - - +
460A ILE* 4.0 25.0 - - + +
479A ASP* 3.7 23.8 - - + -
482A TYR* 3.7 38.1 - - + +
483A TRP* 4.3 12.1 - - + -
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Residues in contact with LEU 400 (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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386A LEU* 3.7 28.3 - - + -
389A LEU* 4.9 11.2 - - + -
395A VAL* 4.5 13.9 - - + -
396A PRO 4.6 4.5 - - - +
397A THR 2.9 9.6 + - - +
399A VAL* 1.3 78.6 - - + +
401A CYS* 1.3 64.0 + - - +
402A ILE 3.2 1.1 - - - -
403A LEU* 4.1 19.3 - - + -
404A TRP* 2.9 39.4 + - + +
411A VAL* 3.9 13.2 - - + -
415A LEU* 3.5 31.0 - - + -
424A LEU* 6.1 0.2 - - + -
435A TYR* 4.1 19.1 - - + -
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Residues in contact with CYS 401 (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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397A THR* 3.0 21.2 + - - -
398A LYS* 3.3 26.7 - - + +
400A LEU* 1.3 75.8 - - - +
402A ILE* 1.3 53.5 + - - +
405A ASP* 2.7 30.0 + - - -
406A MET 3.0 30.2 + - - +
407A GLU* 4.6 0.2 - - - -
408A THR* 3.7 27.1 - - - -
411A VAL* 3.6 18.1 - - - +
467A TYR* 4.1 5.2 + - + -
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Residues in contact with ILE 402 (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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398A LYS* 3.1 19.0 + - + +
399A VAL* 3.5 9.2 - - - +
400A LEU 3.2 0.2 - - - -
401A CYS* 1.3 76.8 - - - +
403A LEU* 1.3 66.5 + - - +
404A TRP 3.2 0.7 + - - -
405A ASP* 3.3 5.2 + - - +
460A ILE* 4.8 1.1 - - + +
463A GLN* 3.2 52.1 + - + +
464A PHE* 3.7 8.3 - - + +
467A TYR* 3.6 30.6 - - + -
468A HIS* 3.6 23.6 - - + +
479A ASP* 3.5 24.7 - - - +
483A TRP* 4.1 18.8 - - + +
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Residues in contact with LEU 403 (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 ASP* 3.9 18.4 - - + +
386A LEU* 5.4 0.2 - - + -
388A ILE* 4.3 15.9 - - + -
399A VAL 3.1 15.6 + - - +
400A LEU* 3.4 24.0 + - + +
402A ILE* 1.3 78.6 - - - +
404A TRP* 1.3 78.0 + - + +
405A ASP* 4.8 0.2 - - - +
456A LEU 4.9 2.2 - - - +
459A LYS* 3.7 42.8 - - + -
460A ILE* 4.0 32.8 - - + +
463A GLN* 3.5 20.0 - - - +
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Residues in contact with TRP 404 (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* 3.3 59.5 + + + -
385A ASP* 2.7 32.8 + - + +
386A LEU* 3.9 20.0 - - + -
400A LEU* 2.9 32.1 + - + +
403A LEU* 1.3 91.7 - - + +
405A ASP* 1.3 73.3 + - - +
406A MET* 3.2 39.4 + - + +
411A VAL* 4.2 7.4 - - + -
414A ILE* 4.5 9.4 - - + -
415A LEU* 3.5 33.7 - - + -
418A PHE* 4.7 1.6 - + - -
459A LYS* 4.2 4.0 - - - +
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Residues in contact with ASP 405 (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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401A CYS 2.7 15.9 + - - -
402A ILE 3.3 2.2 + - - -
403A LEU 4.8 0.3 - - - +
404A TRP* 1.3 75.9 - - - +
406A MET* 1.3 58.3 + - - +
463A GLN* 2.7 38.2 + - - +
466A ARG* 5.2 3.9 - - - +
467A TYR* 3.4 29.4 + - - +
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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