Contacts of the helix formed by residues 85 - 99 (chain C) in PDB entry 1PZY
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 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.1 17.7 - - + -
8C VAL* 5.9 0.4 - - - -
11C ALA* 4.0 27.1 - - + +
12C ILE* 4.8 2.9 - - + -
38C THR* 4.0 19.7 - - + -
52C LEU* 3.8 31.2 - - + -
53C PHE* 5.3 0.2 - - + -
82C ASP 4.6 7.6 - - - +
83C ASP 3.6 9.5 + - - +
84C GLU* 1.3 73.8 - - - +
86C ASP* 1.3 56.3 + - - +
87C ASP 3.3 2.0 - - - -
88C ASP* 3.6 24.7 - - + +
89C ILE* 2.7 50.7 + - + +
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Residues in contact with ASP 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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84C GLU* 3.2 29.0 - - + +
85C LEU* 1.3 79.8 + - - +
87C ASP* 1.3 58.4 + - + +
89C ILE* 3.6 10.0 + - - +
90C ALA* 3.1 24.9 + - - +
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Residues in contact with ASP 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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75C ILE* 4.5 24.2 - - + +
79C LYS* 3.3 31.7 - - - +
80C LEU* 4.2 6.0 - - - +
82C ASP* 4.9 1.1 - - - +
84C GLU* 2.9 5.6 - - - +
86C ASP* 1.3 74.3 - - + +
88C ASP* 1.3 70.5 + - - +
90C ALA* 3.7 9.5 - - - +
91C CYS* 3.1 25.8 + - - +
404C CA 2.5 23.5 - - - -
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Residues in contact with ASP 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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38C THR 5.5 0.2 - - - +
50C TYR 5.4 0.5 - - - +
51C GLY* 4.9 0.5 - - - -
52C LEU 4.8 5.9 + - - -
53C PHE* 3.8 24.6 + - + +
55C ILE* 3.9 4.2 - - + +
80C LEU* 3.2 43.4 - - + +
82C ASP 5.5 0.3 - - - +
84C GLU 3.1 2.6 - - - +
85C LEU* 3.1 25.0 + - + +
87C ASP* 1.3 101.1 - - - +
89C ILE* 1.3 61.8 + - - +
91C CYS* 3.3 2.3 + - - +
92C ALA* 2.8 31.0 + - - +
404C CA 2.6 12.8 - - - -
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Residues in contact with ILE 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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11C ALA 3.1 27.8 - - - +
12C ILE* 3.5 27.8 - - + -
14C ASP* 4.7 12.3 - - + +
15C ILE* 4.0 19.7 - - + -
53C PHE* 4.2 9.6 - - + -
85C LEU* 2.7 30.9 + - + +
86C ASP* 3.7 8.3 - - - +
88C ASP* 1.3 77.8 - - - +
90C ALA* 1.3 57.1 + - - +
92C ALA* 3.4 7.5 + - - +
93C LYS* 2.9 56.7 + - - +
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Residues in contact with ALA 90 (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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86C ASP 3.1 16.4 + - - +
87C ASP* 3.8 10.1 - - - +
88C ASP 3.1 0.2 - - - -
89C ILE* 1.3 75.4 - - - +
91C CYS* 1.3 65.6 + - - +
93C LYS* 3.1 26.4 + - + +
94C LYS* 3.1 16.0 + - - +
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Residues in contact with CYS 91 (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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55C ILE* 3.6 41.5 - - + -
60C TRP* 4.1 2.5 - - - -
73C CYS* 2.0 52.9 - - + -
75C ILE* 5.6 3.4 - - + -
80C LEU* 5.0 4.7 - - + -
87C ASP 3.1 15.4 + - - +
90C ALA* 1.3 76.2 - - - +
92C ALA* 1.3 67.2 + - - +
94C LYS* 3.0 7.5 + - - +
95C ILE* 3.0 22.1 + - - +
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Residues in contact with ALA 92 (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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15C ILE* 4.3 7.4 - - + -
26C TRP* 4.9 0.9 - - + -
53C PHE* 3.8 34.3 - - + -
55C ILE* 4.4 1.9 - - - +
88C ASP 2.8 17.2 + - - +
89C ILE* 3.5 7.4 - - - +
91C CYS* 1.3 77.1 - - - +
93C LYS* 1.3 57.6 + - - +
95C ILE* 3.1 7.5 + - - +
96C LEU* 2.8 33.4 + - - +
104C TRP* 3.8 16.0 - - + -
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Residues in contact with LYS 93 (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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14C ASP* 3.3 33.5 + - - -
15C ILE* 4.3 10.8 - - + +
18C TYR* 3.6 35.7 - - + -
89C ILE* 2.9 44.8 + - - +
90C ALA* 3.1 14.6 + - - +
92C ALA* 1.3 75.9 - - - +
94C LYS* 1.3 63.0 + - + +
96C LEU* 3.0 8.9 + - - +
97C ALA* 2.9 20.7 + - - +
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Residues in contact with LYS 94 (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 TRP* 4.4 2.9 - - + -
72C ILE* 3.5 30.5 + - + +
73C CYS* 4.1 26.4 + - - +
90C ALA 3.1 10.8 + - - +
91C CYS* 3.0 10.1 + - - +
93C LYS* 1.3 79.1 - - + +
95C ILE* 1.3 52.8 + - - +
97C ALA* 3.1 6.2 + - - -
98C ILE* 2.8 50.0 + - + +
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Residues in contact with ILE 95 (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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55C ILE* 4.1 25.8 - - + -
60C TRP* 3.4 55.6 - - + -
91C CYS* 3.0 17.8 + - - +
92C ALA* 3.4 7.6 - - - +
94C LYS* 1.3 74.8 - - - +
96C LEU* 1.3 57.9 + - - +
99C LYS* 2.8 26.8 + - + -
100C GLY 2.8 7.4 + - - -
103C TYR* 3.6 46.9 - - + -
104C TRP* 3.6 15.3 - - + -
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Residues in contact with LEU 96 (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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15C ILE* 4.1 13.7 - - + -
18C TYR* 3.8 37.7 - - + +
19C GLN* 3.6 24.1 + - + +
21C ILE* 4.7 2.2 - - + -
26C TRP* 3.8 25.8 - - + +
92C ALA 2.8 16.7 + - - +
93C LYS* 3.0 9.4 + - - +
95C ILE* 1.3 78.0 - - - +
97C ALA* 1.3 59.2 + - - +
100C GLY* 3.2 22.5 + - - +
101C ILE* 3.9 25.4 - - + +
104C TRP* 3.6 22.4 - - + -
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Residues in contact with ALA 97 (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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18C TYR* 3.6 22.4 - - - +
19C GLN* 4.1 10.4 + - - +
93C LYS 2.9 10.5 + - - +
94C LYS* 3.7 6.1 - - - +
96C LEU* 1.3 77.2 - - - +
98C ILE* 1.3 66.9 + - + +
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Residues in contact with ILE 98 (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 TRP* 3.9 18.6 - - + -
72C ILE* 3.9 32.1 - - + -
94C LYS* 2.8 30.0 + - + +
97C ALA* 1.3 82.1 - - + +
99C LYS* 1.3 61.5 + - + +
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Residues in contact with LYS 99 (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 TRP* 4.3 20.2 - - + +
95C ILE* 2.8 16.7 + - + +
98C ILE* 1.3 77.7 - - + +
100C GLY* 1.3 61.7 + - - +
102C ASP* 5.0 10.3 + - + +
103C TYR* 4.0 40.3 - - + +
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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