Contacts of the helix formed by residues 405 - 414 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A GLN 2.7 18.9 + - - -
402A GLN* 5.1 0.7 - - - +
404A VAL* 1.3 75.7 - - - +
406A LYS* 1.3 57.7 + - - +
407A GLY 3.4 0.2 - - - -
408A LEU* 2.9 15.6 + - - -
409A ASN* 3.0 14.4 + - - -
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Residues in contact with LYS 406 (chain A).
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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402A GLN* 3.8 14.9 + - - +
403A GLN 3.0 5.4 + - - -
405A PHE* 1.3 75.9 - - - +
407A GLY* 1.3 58.3 + - - +
408A LEU 3.2 3.8 + - - -
409A ASN 3.9 0.4 + - - +
410A ASP* 3.8 14.7 + - - -
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Residues in contact with GLY 407 (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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403A GLN* 2.8 19.1 + - - +
404A VAL* 5.1 1.8 - - - -
406A LYS* 1.3 69.7 - - - +
408A LEU* 1.3 57.0 + - - +
410A ASP* 4.9 1.1 - - - -
411A LYS 5.1 2.8 + - - -
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Residues in contact with LEU 408 (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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403A GLN 4.3 0.2 + - - -
404A VAL 4.4 8.0 + - - -
405A PHE* 2.9 9.8 + - - +
407A GLY* 1.3 78.8 - - - +
409A ASN* 1.3 62.4 + - - +
410A ASP 3.2 2.2 - - - -
411A LYS* 2.9 23.0 + - - -
412A VAL 3.5 2.6 + - - -
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Residues in contact with ASN 409 (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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405A PHE 3.0 12.9 + - - -
406A LYS 3.9 0.6 + - - -
408A LEU* 1.3 71.5 - - - +
410A ASP* 1.3 54.4 + - - +
411A LYS 3.1 1.3 - - - -
412A VAL* 3.0 6.2 + - - +
413A LYS* 2.6 31.2 + - - -
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Residues in contact with ASP 410 (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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406A LYS 3.8 13.1 + - - -
407A GLY 5.6 0.7 - - - -
408A LEU 3.2 0.8 - - - -
409A ASN* 1.3 76.6 - - - +
411A LYS* 1.3 54.8 + - - +
413A LYS* 3.0 4.0 + - - +
414A LYS* 2.8 27.0 + - - -
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Residues in contact with LYS 411 (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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407A GLY 5.1 2.6 + - - -
408A LEU* 2.9 14.4 + - - +
410A ASP* 1.3 76.6 - - - +
412A VAL* 1.3 56.8 + - - +
414A LYS* 3.7 2.4 + - - +
415A LYS 3.6 1.9 + - - -
416A ALA* 3.1 27.2 + - - -
417A LEU 3.8 3.5 + - - -
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Residues in contact with VAL 412 (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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408A LEU 3.5 4.0 + - - -
409A ASN* 3.0 12.1 + - - +
411A LYS* 1.3 74.1 - - - +
413A LYS* 1.3 62.3 + - - +
414A LYS 3.3 0.7 - - - -
415A LYS* 3.3 12.2 + - - +
417A LEU* 4.5 16.9 - - - +
418A THR 5.5 3.4 - - - -
419A SER* 6.3 1.1 - - - +
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Residues in contact with LYS 413 (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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409A ASN 2.6 18.2 + - - -
410A ASP* 3.0 8.1 + - - +
412A VAL* 1.3 76.2 - - - +
414A LYS* 1.3 56.4 + - - +
415A LYS 3.3 1.2 + - - -
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Residues in contact with LYS 414 (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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410A ASP 2.8 12.8 + - - -
411A LYS* 3.7 2.0 + - - +
412A VAL 3.3 0.2 - - - -
413A LYS* 1.3 76.4 - - - +
415A LYS* 1.3 61.9 + - - +
416A 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