Contacts of the helix formed by residues 78 - 89 (chain C) in PDB entry 5UQ9
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 GLY 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C LYS 3.4 1.6 + - - -
77C ALA* 1.3 74.0 - - - +
79C GLN* 1.3 66.0 + - - -
80C ALA 3.2 2.1 + - - -
81C VAL* 3.5 11.0 + - - +
82C ASP* 3.6 13.9 - - - +
104C SER* 5.4 0.8 + - - +
108C ASP* 5.4 4.9 - - - -
112C ARG* 3.7 15.6 + - - +
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Residues in contact with GLN 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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34A ARG* 5.2 4.2 - - - +
77C ALA 4.4 0.4 + - - -
78C GLY* 1.3 70.6 - - - -
80C ALA* 1.3 54.9 + - - +
82C ASP* 3.1 22.6 + - - +
83C ASP* 2.7 64.9 + - - +
86C GLU* 4.4 9.1 + - - -
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Residues in contact with ALA 80 (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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75C VAL* 4.0 10.7 - - + +
76C LYS* 3.3 37.9 - - + +
78C GLY 3.2 0.8 - - - -
79C GLN* 1.3 78.6 - - - +
81C VAL* 1.3 60.7 + - - +
83C ASP* 3.4 11.6 + - - +
84C PHE* 3.3 26.2 + - + +
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Residues in contact with VAL 81 (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 LEU* 4.2 13.8 - - + +
75C VAL* 3.9 16.8 - - + +
76C LYS 3.6 17.0 - - - +
77C ALA* 4.5 2.2 - - - -
78C GLY 3.5 7.8 + - - +
79C GLN 3.2 0.6 - - - -
80C ALA* 1.3 78.4 - - - +
82C ASP* 1.3 60.5 + - - +
83C ASP 3.3 0.2 + - - -
84C PHE* 3.4 3.0 + - - +
85C ILE* 3.1 39.4 + - + +
100C ASP* 4.2 21.3 - - - +
102C GLY* 6.3 1.1 - - - -
104C SER* 4.4 6.7 - - - +
112C ARG* 3.5 38.4 - - - +
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Residues in contact with ASP 82 (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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78C GLY 3.6 13.7 - - - +
79C GLN* 3.1 27.8 + - - +
81C VAL* 1.3 77.3 - - - +
83C ASP* 1.3 62.8 + - - +
85C ILE* 3.8 7.0 - - - +
86C GLU* 3.0 39.3 + - + +
108C ASP* 4.7 1.2 - - - +
111C ARG* 3.1 27.1 + - - -
112C ARG* 3.1 27.1 + - - +
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Residues in contact with ASP 83 (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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83A ASP* 4.9 16.2 - - - +
86A GLU* 6.1 0.4 - - - +
87A LYS* 5.3 1.0 - - - +
79C GLN* 2.7 56.7 + - - +
80C ALA* 3.6 10.7 - - - +
81C VAL 3.2 0.2 - - - -
82C ASP* 1.3 75.8 - - - +
84C PHE* 1.3 64.4 + - + +
86C GLU* 3.4 7.1 + - - +
87C LYS* 3.2 30.7 + - + +
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Residues in contact with PHE 84 (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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9C ILE* 3.5 38.1 - - + -
32C PHE* 4.5 12.3 - + - -
33C ASN* 4.8 0.9 - - - -
34C ARG* 3.8 37.5 - - + -
58C LEU* 5.5 4.3 - - + -
73C LEU* 4.3 19.1 - - + -
75C VAL* 3.6 30.1 - - + -
80C ALA* 3.3 16.2 + - + +
81C VAL 4.0 2.9 - - - +
83C ASP* 1.3 79.9 - - + +
85C ILE* 1.3 63.2 + - - +
87C LYS* 3.2 33.4 - - + +
88C LEU* 3.0 30.0 + - + +
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Residues in contact with ILE 85 (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 LEU* 3.8 15.0 - - + -
81C VAL* 3.1 24.6 + - + +
82C ASP* 3.8 7.6 - - - +
83C ASP 3.3 0.2 - - - -
84C PHE* 1.3 76.6 - - - +
86C GLU* 1.3 65.0 + - + +
88C LEU* 4.4 4.3 - - - -
89C VAL* 3.0 35.2 + - + +
98C ILE* 4.5 9.6 - - + -
112C ARG* 3.6 32.5 - - + -
116C LEU* 3.8 33.2 - - + -
119C LYS* 6.0 0.2 - - - +
123C PHE* 3.7 21.3 - - + -
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Residues in contact with GLU 86 (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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34A ARG* 2.8 41.1 + - - -
87A LYS* 3.6 34.7 + - + +
79C GLN* 4.4 6.5 + - - -
82C ASP* 3.0 33.1 + - + +
83C ASP* 3.9 6.1 - - - +
85C ILE* 1.3 78.8 - - + +
87C LYS* 1.3 58.2 + - - +
89C VAL* 4.6 2.8 - - - +
90C PRO* 3.3 24.3 - - - +
119C LYS* 5.9 4.5 - - - +
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Residues in contact with LYS 87 (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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86A GLU* 2.9 55.2 + - - +
87A LYS* 3.7 33.6 - - + +
90A PRO* 4.8 4.9 - - - +
34C ARG* 4.5 7.5 - - - +
58C LEU* 3.6 24.7 - - + +
83C ASP* 3.2 20.5 + - + +
84C PHE* 3.2 44.2 - - + +
86C GLU* 1.3 78.5 - - - +
88C LEU* 1.3 57.4 + - - +
89C VAL 3.7 0.2 - - - -
90C PRO* 4.1 5.7 - - - +
91C LEU* 4.1 8.3 - - - +
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Residues in contact with LEU 88 (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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9C ILE* 4.6 8.5 - - + -
58C LEU* 3.7 29.2 - - + -
61C MET* 4.1 0.9 - - + -
62C VAL* 3.8 2.0 - - + -
71C ILE* 3.6 41.5 - - + -
73C LEU* 5.0 5.8 - - + -
84C PHE* 3.0 20.1 + - + +
85C ILE* 3.2 3.1 + - - +
87C LYS* 1.3 78.3 - - - +
89C VAL* 1.3 65.4 + - - +
90C PRO* 3.5 1.1 - - - -
91C LEU* 3.1 41.5 - - + +
92C LEU* 3.2 11.2 - - + +
98C ILE* 4.0 25.1 - - + -
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Residues in contact with VAL 89 (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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85C ILE* 3.0 25.4 + - + +
86C GLU* 4.6 1.6 - - - +
88C LEU* 1.3 74.8 - - - +
90C PRO* 1.3 74.6 - - + +
92C LEU* 2.9 26.3 + - - +
98C ILE* 4.4 7.4 - - + -
116C LEU* 3.6 28.3 - - + -
119C LYS* 3.7 33.2 - - + +
121C ILE* 4.2 20.7 - - + +
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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