Contacts of the helix formed by residues 67 - 79 (chain C) in PDB entry 5FNA
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 ALA 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C LEU* 5.0 0.5 - - - +
33C VAL* 4.0 35.8 - - + +
64C GLY* 3.0 17.2 + - - +
66C GLN* 1.3 77.8 - - + +
68C CYS* 1.3 57.2 + - - +
69C GLN 3.0 5.8 - - - -
70C ILE* 3.0 35.3 + - + +
71C CYS* 3.6 4.7 + - - -
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Residues in contact with CYS 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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2C ASP* 5.4 7.9 - - - -
59C SER 4.5 5.2 - - - -
60C VAL* 3.7 45.3 - - + -
64C GLY 4.9 1.6 - - - -
65C ALA* 2.9 18.4 + - - +
67C ALA* 1.3 76.1 - - - +
69C GLN* 1.3 60.4 + - - +
70C ILE 3.1 1.1 - - - -
71C CYS* 3.1 23.3 + - + +
72C ILE* 2.8 33.0 + - + +
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Residues in contact with GLN 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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1C ALA 5.6 3.2 - - - +
2C ASP* 3.0 31.2 + - - +
65C ALA 4.1 0.2 + - - -
66C GLN* 3.3 23.2 - - - +
67C ALA 3.0 0.4 - - - -
68C CYS* 1.3 75.3 - - - +
70C ILE* 1.3 66.9 + - + +
72C ILE* 3.2 18.8 + - + +
73C THR* 3.0 28.5 + - + +
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Residues in contact with ILE 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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24C LEU* 6.2 0.7 - - + -
27C GLU* 4.2 17.3 - - + +
28C LEU* 5.1 5.6 - - + -
31C THR* 3.9 43.5 - - + +
33C VAL* 4.0 11.7 - - + -
66C GLN 5.3 0.9 - - - +
67C ALA* 3.0 20.7 + - + +
69C GLN* 1.3 78.8 - - + +
71C CYS* 1.3 63.3 + - - +
73C THR* 2.7 27.6 + - - +
74C TYR* 2.9 8.5 + - + +
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Residues in contact with CYS 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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24C LEU* 3.8 30.0 - - + +
28C LEU* 3.7 31.2 - - - -
67C ALA 4.4 0.9 - - - -
68C CYS* 3.1 31.8 + - + +
70C ILE* 1.3 79.5 - - - +
72C ILE* 1.3 55.2 - - + +
74C TYR* 3.0 4.7 + - - +
75C ILE* 2.8 38.4 + - + +
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Residues in contact with ILE 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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1C ALA* 5.6 2.5 - - + +
2C ASP* 5.2 8.1 - - - +
5C LEU* 3.9 28.0 - - + -
68C CYS* 2.8 23.8 + - + +
69C GLN* 3.5 20.9 - - + +
70C ILE 3.2 0.6 - - - -
71C CYS* 1.3 72.1 - - + +
73C THR* 1.3 66.9 + - + +
75C ILE* 3.0 18.5 + - + +
76C CYS* 2.9 33.5 + - - -
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Residues in contact with THR 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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69C GLN* 3.0 13.1 + - + +
70C ILE* 2.7 26.0 + - - +
72C ILE* 1.3 78.4 - - + +
74C TYR* 1.3 64.2 + - - +
76C CYS* 3.3 23.8 - - - +
77C GLU* 3.5 10.4 + - - +
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Residues in contact with TYR 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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20C THR* 2.7 32.6 + - - +
23C GLY* 3.3 21.3 - - - -
24C LEU* 3.3 38.8 + - + -
27C GLU* 4.6 16.4 - - + -
70C ILE* 2.9 11.8 + - + +
71C CYS 3.3 8.3 - - - +
73C THR* 1.3 78.4 + - - +
75C ILE* 1.3 50.5 + - - +
77C GLU* 3.1 6.2 + - + +
78C GLU* 2.7 68.0 + - + +
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Residues in contact with ILE 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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8C LYS* 6.2 4.5 - - - -
16C MET* 6.3 3.8 - - + -
24C LEU* 6.0 2.9 - - + -
71C CYS* 2.8 29.4 + - + +
72C ILE* 3.0 21.3 + - + +
74C TYR* 1.3 73.6 - - + +
76C CYS* 1.3 63.9 + - - +
78C GLU* 3.1 27.9 + - - +
79C ASP 3.2 15.2 + - - +
82C LEU* 4.0 18.2 - - + -
85C THR* 3.8 28.3 - - + +
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Residues in contact with CYS 76 (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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72C ILE* 2.9 34.9 + - - -
73C THR* 3.3 17.7 - - - +
75C ILE* 1.3 79.2 - - - +
77C GLU* 1.3 68.4 + - + +
79C ASP 4.5 2.4 + - - -
80C SER* 4.7 10.7 + - - -
85C THR* 5.0 11.9 - - - -
32G ARG* 4.8 1.4 + - - -
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Residues in contact with GLU 77 (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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73C THR 3.5 8.9 + - - +
74C TYR* 3.1 7.1 + - + +
76C CYS* 1.3 83.8 - - + +
78C GLU* 1.3 65.8 + - - +
79C ASP 3.5 0.4 - - - -
80C SER 5.3 0.4 + - - -
32G ARG* 2.7 57.0 + - - +
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Residues in contact with GLU 78 (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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16C MET* 4.8 15.6 - - - +
20C THR* 2.6 46.7 + - + +
21C ILE* 4.8 0.5 + - - -
24C LEU* 5.6 2.4 - - - +
74C TYR* 2.7 51.7 + - + +
75C ILE* 3.3 26.3 - - - +
77C GLU* 1.3 75.9 - - - +
79C ASP* 1.3 68.5 + - + +
82C LEU* 5.2 7.1 - - - +
32G ARG* 5.8 0.3 + - - -
33G VAL 5.7 0.7 - - - +
35G ASN* 5.7 5.0 + - - +
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Residues in contact with ASP 79 (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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20C THR* 5.7 2.7 - - + -
75C ILE 3.2 8.2 + - - +
76C CYS 4.8 1.3 - - - -
77C GLU 3.5 0.6 - - - -
78C GLU* 1.3 93.1 - - + +
80C SER* 1.3 59.0 + - - +
81C TYR* 2.7 38.7 + - - +
82C LEU* 3.1 46.6 + - + +
85C THR* 4.0 9.9 - - - +
32G ARG 5.4 1.5 - - - +
33G VAL 4.6 10.6 - - - +
61G ILE* 4.8 16.3 - - - +
64G GLY* 5.6 0.7 - - - -
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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