Contacts of the helix formed by residues 397 - 405 (chain G) 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 LEU 397 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393G THR 4.3 3.4 + - - -
394G LEU* 2.9 10.7 + - - +
396G ALA* 1.3 76.2 - - - +
398G ASP* 1.3 58.8 + - - +
400G GLY* 3.8 3.4 - - - +
401G GLN* 2.8 31.2 + - - -
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Residues in contact with ASP 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F ASP 4.3 18.3 - - - +
274F THR* 4.9 10.2 + - - +
394G LEU 3.8 6.7 + - - -
395G THR 4.9 1.5 - - - -
396G ALA* 3.3 0.8 - - - +
397G LEU* 1.3 77.5 - - - +
399G ARG* 1.3 59.0 + - - +
400G GLY 3.5 0.2 + - - -
402G GLN* 3.7 17.5 + - - +
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Residues in contact with ARG 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370G GLY* 4.7 9.1 - - - +
395G THR 5.1 1.6 + - - -
396G ALA* 3.5 12.1 + - - +
397G LEU 3.2 0.4 - - - -
398G ASP* 1.3 74.5 - - - +
400G GLY* 1.3 62.1 + - - +
402G GLN* 4.5 1.6 - - - +
403G GLN* 4.1 7.4 + - - -
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Residues in contact with GLY 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369G ALA* 6.0 2.2 - - - -
370G GLY 5.2 9.6 - - - -
374G ALA* 4.9 15.5 - - - -
396G ALA 3.0 11.8 + - - -
397G LEU* 2.9 11.8 + - - -
399G ARG* 1.3 77.2 - - - +
401G GLN* 1.3 57.6 + - - -
403G GLN* 2.9 18.9 + - - -
404G VAL 3.7 5.4 + - - -
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Residues in contact with GLN 401 (chain G).
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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397G LEU 2.8 15.1 + - - -
400G GLY* 1.3 71.9 - - - -
402G GLN* 1.3 52.8 + - - +
403G GLN 3.0 0.2 - - - -
404G VAL* 3.0 6.3 + - - +
405G PHE* 2.7 34.3 + - - -
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Residues in contact with GLN 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398G ASP 3.7 16.1 + - - -
399G ARG* 4.6 2.9 - - - -
400G GLY 3.2 1.4 - - - -
401G GLN* 1.3 74.8 - - - +
403G GLN* 1.3 57.3 + - - +
405G PHE* 4.6 1.3 - - - +
406G LYS* 3.8 15.7 + - - +
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Residues in contact with GLN 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374G ALA 5.6 3.4 - - - -
378G GLN* 6.0 0.9 - - - -
399G ARG 4.1 4.3 + - - -
400G GLY 2.9 11.0 + - - -
402G GLN* 1.3 75.4 - - - +
404G VAL* 1.3 56.1 + - - +
405G PHE 2.9 5.6 + - - -
407G GLY* 2.8 34.1 + - - +
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Residues in contact with VAL 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374G ALA 5.0 6.0 + - - -
377G ALA 5.9 0.7 - - - -
378G GLN* 4.7 20.4 - - - +
400G GLY 3.7 5.9 + - - -
401G GLN* 3.0 7.2 + - - +
403G GLN* 1.3 73.5 - - - +
405G PHE* 1.3 56.5 + - - +
407G GLY 5.6 0.9 - - - -
408G LEU* 4.4 10.0 + - - -
426G PHE* 5.8 4.3 - - - -
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Residues in contact with PHE 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401G GLN 2.7 18.5 + - - -
402G GLN* 5.0 0.7 - - - +
404G VAL* 1.3 74.9 - - - +
406G LYS* 1.3 57.6 + - - +
407G GLY 3.4 0.4 - - - -
408G LEU* 2.9 15.5 + - - +
409G ASN* 3.0 14.4 + - - -
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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