Contacts of the helix formed by residues 451 - 458 (chain N) in PDB entry 5G04
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 451 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398N THR* 6.0 5.8 - - + -
401N ILE* 6.1 4.5 - - + -
405N LYS* 4.4 19.8 + - - +
452N LEU* 1.3 67.2 + - - +
453N ALA* 3.3 4.7 - - - +
454N VAL* 3.3 13.4 + - - +
455N GLU* 3.2 21.8 + - - +
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Residues in contact with LEU 452 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N ILE* 4.8 20.7 - - + +
438N ILE 5.8 0.4 - - - +
441N GLY* 3.8 23.7 + - - +
442N LEU* 3.7 21.5 - - + +
451N ASP* 1.3 77.5 - - - +
453N ALA* 1.3 56.9 + - - +
455N GLU* 3.4 8.1 + - - +
456N LEU* 3.1 28.2 + - - +
501N ILE* 5.1 1.6 - - - +
504N LEU* 6.0 4.0 - - + -
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Residues in contact with ALA 453 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441N GLY 4.7 1.2 + - - +
442N LEU* 4.5 2.7 - - - +
443N THR* 3.5 44.0 - - - +
451N ASP 3.3 2.6 - - - +
452N LEU* 1.3 78.5 - - - +
454N VAL* 1.3 61.7 + - - +
456N LEU* 3.4 8.6 + - - +
457N SER* 3.2 22.0 + - - -
540N ARG* 5.6 0.7 + - - -
544N LEU* 5.1 2.1 - - - +
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Residues in contact with VAL 454 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451N ASP* 3.3 13.9 + - - +
453N ALA* 1.3 75.1 - - - +
455N GLU* 1.3 65.8 + - - +
457N SER* 3.5 18.9 + - - -
458N LYS* 3.7 8.1 + - - +
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Residues in contact with GLU 455 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N ILE* 5.8 4.3 - - + -
405N LYS* 5.2 15.0 - - - +
451N ASP 3.2 12.6 + - - +
452N LEU* 3.6 10.8 - - - +
454N VAL* 1.3 72.5 - - - +
456N LEU* 1.3 65.0 + - - +
457N SER 3.5 0.2 + - - -
458N LYS* 3.6 14.2 + - - +
500N ASP* 6.2 0.2 - - - +
501N ILE* 3.5 25.0 - - + +
504N LEU* 6.4 0.2 - - + -
548N ARG* 3.1 13.0 + - - -
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Residues in contact with LEU 456 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442N LEU* 4.2 16.2 - - + -
452N LEU 3.1 13.3 + - - +
453N ALA* 3.5 11.2 - - - +
455N GLU* 1.3 76.5 - - - +
457N SER* 1.3 60.6 + - - +
458N LYS 3.3 2.9 + - - +
501N ILE* 4.1 4.6 - - + +
541N ASN* 5.5 2.2 - - - +
544N LEU* 3.3 35.1 - - + +
548N ARG* 3.0 29.0 + - - +
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Residues in contact with SER 457 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453N ALA 3.2 11.0 + - - -
454N VAL* 3.6 13.7 - - - -
455N GLU 3.3 0.4 - - - -
456N LEU* 1.3 79.6 - - - +
458N LYS* 1.3 58.6 + - - +
540N ARG* 4.2 21.1 - - - -
544N LEU* 3.8 19.5 - - - +
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Residues in contact with LYS 458 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454N VAL 3.7 6.6 + - - +
455N GLU* 3.6 17.6 + - - +
456N LEU 3.3 5.8 - - - +
457N SER* 1.3 81.6 - - - +
547N LEU* 5.3 10.7 - - - +
548N ARG* 4.1 7.5 + - - -
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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