Contacts of the helix formed by residues 66 - 75 (chain C) in PDB entry 5IXG
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 SER 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C TRP* 4.1 8.5 - - - -
64C THR* 3.1 9.2 + - - -
65C GLY* 1.3 75.5 - - - +
67C ALA* 1.3 62.8 + - - +
68C LYS* 3.5 9.7 + - - +
69C LEU* 3.1 28.4 + - - +
70C ASP* 2.9 24.0 + - - -
14D SER* 4.8 8.6 - - - -
17D TYR* 3.6 13.9 + - - -
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Residues in contact with ALA 67 (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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65C GLY 4.0 2.8 + - - -
66C SER* 1.3 72.2 - - - +
68C LYS* 1.3 62.2 + - - +
70C ASP* 3.3 13.4 + - - +
71C GLU* 3.1 23.6 + - - +
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Residues in contact with LYS 68 (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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66C SER* 3.1 8.3 + - - +
67C ALA* 1.3 79.3 - - - +
69C LEU* 1.3 56.7 + - - +
71C GLU* 3.4 11.9 + - - +
72C HIS* 3.0 30.9 + - + +
201C OTP 4.9 12.1 - - - +
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Residues in contact with LEU 69 (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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31C TRP* 3.4 45.1 - - + -
64C THR* 3.8 15.7 - - + +
66C SER* 3.1 21.8 + - - +
68C LYS* 1.3 74.0 - - - +
70C ASP* 1.3 65.8 + - - +
72C HIS* 3.2 5.7 + - + -
73C LEU* 2.9 50.4 + - + +
201C OTP 3.6 52.5 - - + +
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Residues in contact with ASP 70 (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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62C ILE* 3.5 29.9 - - + +
63C HIS* 3.6 18.0 + - - -
64C THR* 2.7 41.4 + - - +
65C GLY 4.7 0.2 + - - -
66C SER 2.9 17.9 + - - +
67C ALA* 3.6 13.8 - - - +
68C LYS 3.3 0.2 - - - -
69C LEU* 1.3 77.7 - - - +
71C GLU* 1.3 61.9 + - - +
73C LEU* 3.5 6.7 + - - +
74C GLN* 3.3 26.7 + - - +
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Residues in contact with GLU 71 (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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67C ALA 3.1 12.9 + - - +
68C LYS* 3.7 11.2 - - - +
70C ASP* 1.3 77.3 - - - +
72C HIS* 1.3 66.2 + - - +
74C GLN* 3.2 23.3 + - - +
75C THR* 3.6 12.0 + - + +
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Residues in contact with HIS 72 (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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68C LYS* 3.0 20.5 + - + +
69C LEU* 3.6 6.7 - - + +
71C GLU* 1.3 77.7 - - - +
73C LEU* 1.3 76.9 + - + +
75C THR* 2.7 39.4 + - - +
77C GLU* 4.0 26.7 - - + +
78C PHE* 4.6 6.3 - - - +
153C TYR* 5.7 10.0 - + - -
201C OTP 3.9 32.9 + - - +
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Residues in contact with LEU 73 (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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62C ILE* 4.0 23.8 - - + -
64C THR* 4.0 9.6 - - + -
69C LEU* 2.9 48.7 + - + +
70C ASP* 3.9 6.3 - - - +
71C GLU 3.3 0.4 - - - -
72C HIS* 1.3 80.5 - - + +
74C GLN* 1.3 57.0 + - - +
75C THR 3.3 0.2 - - - -
78C PHE* 3.6 33.9 - - + -
79C PHE* 2.8 51.4 + - + +
201C OTP 4.0 26.5 - - + -
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Residues in contact with GLN 74 (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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59C ILE* 3.2 24.2 + - - +
60C ALA* 3.2 26.2 + - + +
62C ILE* 3.3 15.6 - - - +
70C ASP 3.3 23.5 + - - +
71C GLU* 3.4 12.6 - - + +
72C HIS 3.1 0.6 + - - -
73C LEU* 1.3 76.0 - - - +
75C THR* 1.3 65.6 - - + +
79C PHE* 4.7 1.1 - - - -
80C ASP* 3.4 0.5 - - - +
81C ALA* 2.9 54.2 + - + +
82C ALA* 4.4 1.7 + - - +
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Residues in contact with THR 75 (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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71C GLU* 3.6 18.6 - - + +
72C HIS* 2.7 27.7 + - - +
74C GLN* 1.3 80.8 - - + +
76C ALA* 1.3 65.9 + - - +
77C GLU* 3.0 20.5 + - - +
78C PHE 3.0 7.8 + - - -
79C PHE 3.7 0.2 + - - -
80C ASP* 3.0 16.1 + - - -
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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