Contacts of the helix formed by residues 405 - 414 (chain E) in PDB entry 5ZRV
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 PHE 405 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401E GLN 2.7 18.7 + - - -
402E GLN* 5.1 0.7 - - - +
404E VAL* 1.3 74.6 - - - +
406E LYS* 1.3 57.0 + - - +
407E GLY 3.4 0.2 - - - -
408E LEU* 2.9 15.1 + - - -
409E ASN* 3.0 14.6 + - - -
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Residues in contact with LYS 406 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402E GLN* 3.8 15.1 + - - +
403E GLN 3.0 5.4 + - - -
405E PHE* 1.3 75.1 - - - +
407E GLY* 1.3 58.1 + - - +
408E LEU 3.2 4.2 + - - -
409E ASN 3.9 0.2 + - - -
410E ASP* 3.8 14.6 + - - -
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Residues in contact with GLY 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E GLN* 2.8 18.6 + - - +
404E VAL* 5.1 1.8 - - - -
406E LYS* 1.3 70.5 - - - +
408E LEU* 1.3 56.0 + - - +
410E ASP* 4.9 1.1 - - - -
411E LYS 5.1 3.2 + - - -
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Residues in contact with LEU 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E GLN 4.3 0.2 + - - -
404E VAL 4.4 7.5 + - - -
405E PHE* 2.9 10.3 + - - +
407E GLY* 1.3 78.4 - - - +
409E ASN* 1.3 61.1 + - - +
410E ASP 3.2 2.0 - - - -
411E LYS* 2.9 23.2 + - - +
412E VAL 3.5 2.6 + - - -
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Residues in contact with ASN 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E PHE 3.0 13.3 + - - -
406E LYS 3.9 0.8 + - - -
408E LEU* 1.3 71.5 - - - +
410E ASP* 1.3 55.0 + - - +
411E LYS 3.1 1.1 - - - -
412E VAL* 3.0 5.9 + - - +
413E LYS* 2.6 31.0 + - - -
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Residues in contact with ASP 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E LYS 3.8 12.5 + - - -
407E GLY 5.6 0.9 - - - -
408E LEU 3.2 1.0 - - - +
409E ASN* 1.3 76.6 - - - +
411E LYS* 1.3 54.8 + - - +
413E LYS* 3.0 3.8 + - - +
414E LYS* 2.8 27.0 + - - -
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Residues in contact with LYS 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407E GLY 5.1 2.6 + - - -
408E LEU* 2.9 13.6 + - - +
410E ASP* 1.3 77.8 - - - +
412E VAL* 1.3 56.9 + - - +
414E LYS* 3.7 1.8 + - - +
415E LYS 3.6 1.9 + - - -
416E ALA* 3.1 27.9 + - - -
417E LEU* 3.8 3.1 + - - -
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Residues in contact with VAL 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E LEU 3.5 3.8 + - - -
409E ASN* 3.0 12.5 + - - +
411E LYS* 1.3 74.7 - - - +
413E LYS* 1.3 62.4 + - - +
414E LYS 3.3 0.7 - - - -
415E LYS* 3.3 12.3 + - - +
417E LEU 4.5 16.3 - - - +
418E THR 5.5 3.4 - - - -
419E SER* 6.3 1.3 - - - +
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Residues in contact with LYS 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409E ASN 2.6 18.3 + - - -
410E ASP* 3.0 7.7 + - - +
412E VAL* 1.3 75.2 - - - +
414E LYS* 1.3 55.8 + - - +
415E LYS 3.3 1.4 + - - -
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Residues in contact with LYS 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E ASP 2.8 13.0 + - - -
411E LYS* 3.7 1.7 + - - +
412E VAL 3.3 0.2 - - - -
413E LYS* 1.3 75.8 - - - +
415E LYS* 1.3 61.7 + - - +
416E ALA* 3.1 5.6 + - - -
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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