Contacts of the helix formed by residues 1898 - 1904 (chain Q) in PDB entry 3ZWH
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 ARG1898 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A GLY* 5.4 1.4 - - - -
51A ASP* 4.6 7.5 + - - -
53A ALA* 4.0 13.9 + - - +
54A ALA* 3.8 37.8 - - + +
57A LYS* 3.9 18.2 - - - +
1096A ACT 4.7 11.8 + - - -
1896Q LEU 4.3 0.2 + - - -
1897Q GLN* 1.3 82.3 - - + +
1899Q GLU* 1.3 60.0 + - - +
1900Q LEU 3.3 2.7 - - - +
1901Q GLU* 2.6 54.3 + - + +
1902Q ASP* 2.9 34.2 + - - +
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Residues in contact with GLU1899 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 4.6 5.8 - - + -
85A MET* 3.1 30.4 - - + +
1894Q ARG* 2.8 58.4 + - + +
1895Q LYS 4.6 0.3 + - - -
1896Q LEU* 3.6 35.0 + - + +
1897Q GLN 3.1 11.6 + - - +
1898Q ARG* 1.3 76.6 - - - +
1900Q LEU* 1.3 58.2 + - - +
1902Q ASP* 3.2 12.1 + - - +
1903Q ALA* 2.9 24.1 + - - +
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Residues in contact with LEU1900 (chain Q).
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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38A LEU* 4.0 22.4 - - + -
45A TRP* 3.6 46.4 - - + +
58A LEU* 3.9 34.3 - - + -
78A PHE* 4.1 9.2 - - + -
82A ILE* 3.8 31.6 - - + -
1096A ACT 4.1 13.8 + - - +
1898Q ARG 3.3 0.4 - - - -
1899Q GLU* 1.3 77.1 - - - +
1901Q GLU* 1.3 60.5 + - - +
1903Q ALA* 3.3 7.6 + - + +
1904Q THR* 2.9 32.3 + - + +
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Residues in contact with GLU1901 (chain Q).
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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54A ALA 4.7 3.2 - - - +
57A LYS* 3.2 39.0 + - + +
58A LEU* 4.5 9.7 - - + +
61A ASN* 3.2 12.9 + - - +
1898Q ARG* 2.6 54.0 + - - +
1900Q LEU* 1.3 76.2 - - - +
1902Q ASP* 1.3 65.2 + - - +
1904Q THR* 3.0 16.5 + - - -
1905Q GLU* 2.6 29.7 - - - +
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Residues in contact with ASP1902 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A MET* 4.3 8.6 - - + +
1897Q GLN 5.0 1.4 - - - +
1898Q ARG* 2.9 24.6 + - - +
1899Q GLU* 3.4 17.7 - - - +
1901Q GLU* 1.3 79.9 - - - +
1903Q ALA* 1.3 62.4 + - - +
1904Q THR 3.3 0.9 + - - -
1905Q GLU* 3.6 20.7 + - - +
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Residues in contact with ALA1903 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 3.3 32.5 + - - +
82A ILE* 5.1 0.7 - - + +
84A MET* 5.9 2.6 - - - +
85A MET* 3.7 29.4 - - + +
1899Q GLU 2.9 15.6 + - - +
1900Q LEU* 3.5 12.6 - - + +
1901Q GLU 3.1 0.6 - - - -
1902Q ASP* 1.3 77.3 - - - +
1904Q THR* 1.3 59.4 + - + +
1905Q GLU 3.5 0.8 + - - -
1906Q THR* 5.0 5.2 + - - -
1910Q MET* 5.9 0.7 - - - +
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Residues in contact with THR1904 (chain Q).
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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58A LEU* 3.8 4.9 - - + +
61A ASN* 3.1 35.1 + - - +
62A LEU* 3.7 25.6 - - + -
77A VAL 5.8 0.2 - - - -
78A PHE* 4.2 11.0 - - + -
81A SER* 3.8 22.4 - - - +
82A ILE* 6.3 0.2 - - + -
1900Q LEU* 2.9 19.1 + - + +
1901Q GLU* 3.0 3.7 + - - -
1903Q ALA* 1.3 81.2 - - + +
1905Q GLU* 1.3 62.9 + - - +
1906Q THR 3.2 3.1 - - - -
1907Q ALA* 3.2 22.2 + - + +
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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