Contacts of the helix formed by residues 34 - 38 (chain G) in PDB entry 6ATU
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 LYS 34 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.7 26.0 - - + +
11G THR* 6.5 0.2 - - - -
33G LEU* 1.3 78.1 - - - +
35G ASP* 1.3 65.1 + - - +
36G THR* 3.4 20.4 - - - +
37G ASP* 3.1 27.8 + - - +
38G CYS 4.3 0.5 + - - -
44G CYS* 3.5 11.5 - - - +
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Residues in contact with ASP 35 (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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9G VAL 2.8 24.0 + - - +
10G SER* 3.4 2.2 - - - -
11G THR* 3.3 12.1 + - - +
12G LYS* 3.0 49.6 + - + -
34G LYS* 1.3 72.3 - - - +
36G THR* 1.3 61.3 + - - +
38G CYS* 3.2 10.2 + - - +
43G LYS* 2.8 41.7 + - - +
44G CYS* 2.7 39.8 + - - +
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Residues in contact with THR 36 (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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11G THR* 4.4 22.4 - - + +
12G LYS* 4.6 5.8 - - - +
34G LYS* 3.4 18.7 - - - +
35G ASP* 1.3 73.7 - - - +
37G ASP* 1.3 61.4 + - - +
38G CYS 3.1 13.0 + - - +
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Residues in contact with ASP 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ARG 5.1 2.8 - - - +
32G CYS* 3.8 16.8 - - + +
33G LEU* 3.0 26.2 + - - +
34G LYS* 3.1 22.1 + - - +
36G THR* 1.3 79.4 + - - +
38G CYS* 1.3 59.1 + - - +
39G PRO* 4.2 2.8 - - - +
53G CYS* 4.4 3.5 - - - -
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Residues in contact with CYS 38 (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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12G LYS* 3.0 19.8 + - - -
32G CYS* 3.8 15.5 - - - -
35G ASP 3.2 5.0 + - - +
36G THR 3.1 7.1 - - - +
37G ASP* 1.3 79.9 - - - +
39G PRO* 1.4 65.4 - - + +
40G GLY 4.0 0.2 + - - -
42G LYS* 3.5 21.1 - - + +
43G LYS 3.8 15.7 - - - -
44G CYS* 3.8 4.0 - - - -
53G CYS* 2.1 51.8 - - + -
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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