Contacts of the helix formed by residues 53 - 59 (chain F) in PDB entry 6ASB
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 CYS 53 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F CYS* 3.2 10.5 - - - -
52F ASP* 1.3 80.0 - - - +
54F HIS* 1.3 60.9 + - - +
55F PHE 3.6 4.0 - - - -
56F CYS 3.3 15.3 + - - -
57F ARG* 3.0 28.6 + - - +
72F CYS* 4.8 0.2 - - - -
73F LEU* 3.1 41.7 - - + -
74F LEU* 5.2 3.6 - - + +
2002F ZN 2.3 32.8 - - - -
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Residues in contact with HIS 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E A 2.9 40.1 + - - -
53F CYS* 1.3 74.1 - - + +
55F PHE* 1.3 79.5 + + + +
57F ARG* 3.9 6.4 + - - +
58F ASP* 3.5 18.0 + - - +
68F MET* 3.5 23.4 - - + +
73F LEU* 5.8 3.6 - - + +
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Residues in contact with PHE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E A 5.0 1.3 - - - -
53F CYS* 3.2 2.6 - - - -
54F HIS* 1.3 89.6 - + + +
56F CYS* 1.3 66.9 + - - +
58F ASP* 3.1 15.8 + - - +
59F MET* 3.4 16.8 + - - +
68F MET* 3.6 31.1 - - + +
70F GLN* 3.6 33.6 - - + +
71F SER 3.3 26.5 - - - +
73F LEU* 3.6 43.7 - - + -
76F GLN* 4.1 8.1 - - - -
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Residues in contact with CYS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F GLU* 3.8 12.8 - - - -
51F GLY* 3.3 34.1 - - - -
53F CYS* 3.3 5.6 + - - +
55F PHE* 1.3 76.2 - - - +
57F ARG* 1.3 58.5 + - - +
59F MET* 2.8 37.7 + - - +
62F PHE* 3.3 16.2 - - + +
72F CYS* 3.4 19.5 - - - -
2002F ZN 2.4 34.3 - - - -
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F GLY 4.7 4.9 + - - +
52F ASP* 4.8 7.0 - - - +
53F CYS 3.0 17.2 + - - +
54F HIS* 4.2 6.3 - - - +
55F PHE 3.3 0.2 - - - -
56F CYS* 1.3 75.3 - - - +
58F ASP* 1.4 59.4 + - - +
59F MET 3.7 0.3 + - - +
62F PHE* 4.5 10.3 - - - +
63F GLY 4.7 0.2 - - - -
64F GLY* 3.4 17.8 + - - -
65F PRO* 4.7 0.5 - - - +
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Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E A 4.3 3.6 + - - -
54F HIS 3.5 6.3 + - - +
55F PHE 3.1 9.9 + - - +
56F CYS 3.1 1.2 - - - -
57F ARG* 1.4 75.4 - - - +
59F MET* 1.3 63.2 + - - +
64F GLY* 3.3 4.4 - - - -
65F PRO* 3.5 22.7 - - - +
66F GLY* 2.7 32.6 + - - -
67F ARG* 3.0 28.5 + - - +
68F MET* 3.2 46.3 + - + +
69F LYS 4.3 2.3 + - - -
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Residues in contact with MET 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D A 5.0 1.6 - - - +
49F GLU* 3.4 29.2 - - - +
55F PHE 3.4 7.6 + - - +
56F CYS* 2.8 31.8 + - - +
58F ASP* 1.3 79.3 - - - +
60F LYS* 1.4 60.1 + - - +
61F LYS* 3.8 26.5 - - + -
62F PHE* 2.9 29.7 + - + -
63F GLY 3.3 0.3 + - - -
64F GLY 2.9 12.7 + - - -
66F GLY* 4.6 2.5 - - - -
70F GLN 3.7 17.0 - - - +
71F SER* 4.1 1.1 - - - -
72F CYS* 3.6 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