Contacts of the helix formed by residues 60 - 67 (chain C) in PDB entry 3EU9
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 ASP 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TRP* 1.3 81.7 - - - +
61C ILE* 1.3 62.3 + - + +
62C VAL* 2.7 13.4 + - - +
63C LYS* 2.5 56.1 + - - +
64C ALA* 3.0 15.9 + - - +
76C LEU* 4.0 2.0 - - - -
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Residues in contact with ILE 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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60C ASP* 1.3 74.6 - - + +
62C VAL* 1.3 63.7 + - + +
64C ALA* 3.4 3.1 + - - +
65C THR* 2.8 34.1 + - - -
73C CYS* 4.3 6.5 - - - +
76C LEU* 3.4 31.0 - - + +
77C VAL* 3.7 24.0 - - + -
81C TYR* 3.5 50.7 - - + +
93C LEU* 3.4 32.3 - - + -
109C TYR* 4.0 9.6 - - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASP* 2.7 17.3 + - - +
61C ILE* 1.3 79.2 - - + +
63C LYS* 1.3 65.9 + - - +
65C THR* 3.1 4.7 + - - -
66C GLN* 2.9 50.9 + - - +
81C TYR* 5.1 5.2 - - - +
87C ASP* 4.8 16.6 - - + +
93C LEU* 4.2 20.6 - - + -
96C TRP* 3.8 22.6 - - + +
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Residues in contact with LYS 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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59C TRP* 3.6 33.2 - - + -
60C ASP* 2.5 33.0 + - - +
62C VAL* 1.3 83.5 - - - +
64C ALA* 1.3 55.7 + - - +
66C GLN* 3.2 24.9 + - - +
67C TYR* 2.8 57.3 + - + +
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Residues in contact with ALA 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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59C TRP* 4.3 3.7 - - + +
60C ASP 3.0 18.1 + - - +
61C ILE* 3.7 4.9 - - - +
63C LYS* 1.3 75.8 - - - +
65C THR* 1.3 56.9 + - - +
68C GLY* 3.0 5.2 + - - -
69C ILE* 2.8 44.4 + - + +
72C ARG* 3.8 28.9 - - + -
73C CYS* 3.5 19.9 - - - +
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Residues in contact with THR 65 (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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61C ILE 2.8 18.4 + - - -
62C VAL* 3.1 10.5 + - - -
64C ALA* 1.3 74.9 - - - +
66C GLN* 1.3 67.1 + - - +
68C GLY* 3.0 10.7 + - - -
73C CYS* 3.8 5.8 - - - -
93C LEU* 3.6 20.1 - - - +
96C TRP* 3.7 7.2 - - + -
97C ALA* 3.5 35.9 - - + +
100C ASN* 4.8 0.2 - - - +
102C ARG* 3.5 15.8 - - - +
105C LEU* 4.0 4.0 - - + -
109C TYR* 2.7 28.0 + - + -
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Residues in contact with GLN 66 (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 VAL* 2.9 25.3 + - - +
63C LYS* 3.2 43.4 + - - +
65C THR* 1.3 77.8 - - - +
67C TYR* 1.3 62.7 + - + +
68C GLY 3.3 0.2 - - - -
96C TRP* 3.3 50.7 - - + -
100C ASN* 3.4 26.7 - - - +
102C ARG* 2.7 28.6 + - - -
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Residues in contact with TYR 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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59C TRP* 4.0 48.7 - + - -
63C LYS* 2.8 40.0 + - + +
66C GLN* 1.3 86.5 - - + +
68C GLY* 1.3 61.9 + - - +
69C ILE* 3.4 17.6 + - + +
102C ARG* 3.3 16.4 + - - +
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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