Contacts of the helix formed by residues 59 - 64 (chain C) in PDB entry 3NBN
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 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.5 48.6 - - + -
97A GLU* 4.6 11.7 - - - +
98A MET* 4.7 6.7 - - + -
130A LYS* 4.0 18.4 - - + -
132A PHE* 4.0 15.7 - - + -
55C HIS* 3.2 40.3 + - + +
56C THR* 4.4 2.5 - - - -
57C PHE 2.5 5.5 + - - -
58C ALA* 1.3 75.1 - - - +
60C HIS* 1.3 60.2 + - - +
61C GLN 3.4 1.1 - - - -
62C ARG* 3.4 41.5 - - - +
63C CYS 3.5 0.3 + - - -
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Residues in contact with HIS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.8 28.0 - + + -
134A GLY* 2.8 28.1 + - - -
135A ASN 5.4 0.4 - - - -
136A SER* 3.5 21.9 + - - +
56C THR 3.3 19.4 + - - +
57C PHE* 2.5 17.3 + - - +
59C LEU* 1.3 69.4 - - - +
61C GLN* 1.3 69.7 + - - -
62C ARG 2.8 17.0 + - - -
63C CYS* 2.9 16.4 + - + +
64C ILE* 3.0 33.6 + - + +
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Residues in contact with GLN 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 3.3 46.9 + - - +
58C ALA* 4.6 11.0 - - - +
59C LEU 3.4 1.5 - - - -
60C HIS* 1.3 100.3 + - - +
62C ARG* 1.3 68.1 + - - +
64C ILE* 4.4 4.5 - - + +
65C GLN* 2.8 30.7 + - - +
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.4 28.3 - - + -
97A GLU* 4.3 20.4 + - - +
98A MET 3.1 28.5 + - - +
99A GLN* 4.3 0.2 - - - +
100A GLN* 3.0 28.8 + - - +
58C ALA 4.5 12.3 - - - +
59C LEU* 3.4 25.4 - - - +
60C HIS 2.8 1.8 + - - -
61C GLN* 1.3 78.6 - - - +
63C CYS* 1.3 65.6 + - - +
64C ILE 3.1 1.5 + - - -
65C GLN* 2.8 12.2 + - - -
66C ALA* 3.6 15.2 + - - +
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Residues in contact with CYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLN* 6.2 1.1 - - - -
86A CYS* 2.0 49.1 - - - -
88A PHE* 4.1 3.8 - - + -
100A GLN* 3.5 16.6 + - - +
132A PHE* 3.8 23.8 - - + -
134A GLY* 4.9 7.4 - - - -
59C LEU 3.5 2.4 + - - -
60C HIS* 2.9 15.9 + - - +
62C ARG* 1.3 80.2 - - - +
64C ILE* 1.3 63.2 + - - +
67C LYS* 3.7 19.6 + - - +
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLN* 5.2 15.7 - - + +
134A GLY* 5.0 5.8 - - - +
60C HIS* 3.0 37.9 + - + +
61C GLN* 4.4 5.6 - - + +
62C ARG 3.1 0.2 - - - -
63C CYS* 1.3 86.5 - - - +
65C GLN* 1.3 82.9 + - + +
66C ALA 3.4 1.1 - - - -
67C LYS* 3.5 15.5 - - + +
68C ALA* 3.3 19.2 + - - +
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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