Contacts of the helix formed by residues 404 - 413 (chain B) in PDB entry 4ZG9
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 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B LYS 3.7 5.2 + - - +
403B TYR* 1.3 79.9 - - - +
405B PRO* 1.3 74.9 - - - +
406B LYS* 3.1 25.8 + - - +
407B ALA* 3.4 23.8 + - + +
408B ILE* 3.0 24.9 + - - +
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Residues in contact with PRO 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B TYR* 3.8 24.7 - - + +
404B ASP* 1.3 91.9 - - - +
406B LYS* 1.3 66.1 + - + +
408B ILE* 3.4 10.4 + - + +
409B ILE* 3.2 31.3 + - - +
425B LEU* 5.5 5.8 - - + -
443B ASP* 6.5 1.3 - - + -
444B ILE* 4.1 18.8 - - + +
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B ASP* 3.2 17.0 - - - +
405B PRO* 1.3 83.2 - - + +
407B ALA* 1.3 60.9 + - - +
409B ILE* 3.9 5.8 - - - +
410B ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ASN* 5.9 5.8 - - - +
404B ASP* 3.4 27.4 + - + +
406B LYS* 1.3 75.6 - - - +
408B ILE* 1.3 60.5 + - + +
410B ALA* 4.0 6.3 - - - +
411B ASN* 3.1 29.6 + - - +
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B LEU* 4.1 17.0 - - + -
379B ASN* 3.6 30.7 - - - +
383B ILE* 4.0 17.3 - - + -
393B ILE* 4.6 13.2 - - + -
403B TYR* 4.2 14.4 - - + -
404B ASP 3.0 21.8 - - - +
405B PRO* 3.5 10.1 - - + +
406B LYS 3.2 0.6 - - - -
407B ALA* 1.3 74.7 - - + +
409B ILE* 1.3 68.5 + - - +
411B ASN* 3.2 11.2 + - - +
412B LEU* 3.2 35.5 + - + +
444B ILE* 4.4 15.5 - - + -
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B PRO 3.2 14.3 + - - +
406B LYS* 3.9 8.1 - - - +
408B ILE* 1.3 77.3 - - - +
410B ALA* 1.3 52.2 + - - +
412B LEU* 2.7 27.1 + - + +
413B THR* 2.6 30.1 + - - +
423B PRO* 4.0 24.0 - - + +
424B TYR* 4.1 9.4 - - - -
425B LEU* 3.8 28.3 - - + +
444B ILE* 3.8 28.5 - - + -
803B GLU* 6.4 1.1 - - + -
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Residues in contact with ALA 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B LYS 2.9 20.2 + - - +
407B ALA* 4.0 7.6 - - - +
409B ILE* 1.3 75.9 - - - +
411B ASN* 1.3 61.6 + - - +
412B LEU 3.4 0.3 + - - -
413B THR* 3.5 17.3 + - - -
415B LYS* 3.5 15.6 + - - -
803B GLU* 6.4 1.3 - - - -
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Residues in contact with ASN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B TYR* 3.9 23.9 - - - +
377B LEU* 3.5 22.9 - - + -
407B ALA 3.1 20.8 + - - +
408B ILE 3.7 0.4 - - - +
409B ILE 3.0 0.6 + - - -
410B ALA* 1.3 75.2 - - - +
412B LEU* 1.3 58.2 + - - +
413B THR 3.4 0.4 - - - -
415B LYS* 3.5 22.3 - - - +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B LEU* 3.9 20.4 - - + -
376B TYR* 3.6 23.6 - - + -
377B LEU* 3.5 22.9 - - + -
393B ILE* 4.2 10.8 - - + -
408B ILE* 3.2 33.2 - - + +
409B ILE* 2.7 13.1 + - - +
411B ASN* 1.3 71.5 - - - +
413B THR* 1.3 55.8 + - - +
415B LYS* 4.5 1.6 - - - -
419B GLN* 2.5 33.2 + - - -
421B PHE* 4.0 8.7 - - + -
423B PRO* 3.7 19.1 - - + +
444B ILE* 5.5 1.6 - - + -
446B LEU* 4.1 23.1 - - + -
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Residues in contact with THR 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ILE* 2.6 37.1 + - + +
410B ALA* 3.7 9.9 - - - -
411B ASN 3.4 2.0 - - - -
412B LEU* 1.3 77.2 - - - +
414B CYS* 1.3 76.6 + - + +
415B LYS* 3.2 16.2 + - - +
423B PRO* 3.9 10.9 - - + +
803B GLU* 3.5 51.4 - - + +
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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