Contacts of the helix formed by residues 85 - 99 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.3 16.4 - - + -
8A VAL* 5.8 0.2 - - - -
11A ALA* 3.9 28.3 - - + +
12A ILE* 4.8 2.7 - - + -
38A THR* 4.4 11.7 - - + -
52A LEU* 3.5 33.4 - - + -
53A PHE* 5.4 0.4 - - + -
82A ASP 4.4 9.0 - - - +
83A ASP 3.5 16.0 + - - +
84A GLU* 1.3 73.3 - - - +
86A ASP* 1.3 60.5 + - - +
87A ASP 3.2 2.7 - - - -
88A ASP* 3.0 20.8 + - + +
89A ILE* 2.7 46.4 + - + +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 5.2 2.6 - - - +
84A GLU* 3.3 8.0 - - + +
85A LEU* 1.3 78.7 + - - +
87A ASP* 1.3 58.4 + - - +
89A ILE* 3.5 12.9 + - - +
90A ALA* 3.1 26.2 + - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.5 31.7 - - + +
79A LYS* 3.4 13.5 - - - +
80A LEU* 4.2 3.1 - - - +
82A ASP* 4.6 1.7 - - - +
84A GLU* 3.0 6.8 + - - +
86A ASP* 1.3 74.0 - - - +
88A ASP* 1.3 77.7 + - - +
90A ALA* 3.9 7.0 - - - +
91A CYS* 3.2 23.4 + - - +
403A CA 2.4 30.5 - - - -
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR 5.4 0.3 - - - +
51A GLY* 5.0 0.2 - - - -
52A LEU* 4.7 8.0 + - - +
53A PHE* 3.8 22.0 + - + -
55A ILE* 3.7 6.1 - - + +
80A LEU* 3.3 44.3 - - + +
82A ASP 5.4 0.3 - - - +
84A GLU 3.0 5.0 - - - +
85A LEU* 3.0 22.4 + - + +
87A ASP* 1.3 86.5 - - - +
89A ILE* 1.3 60.2 + - - +
91A CYS* 3.3 3.1 + - - +
92A ALA* 2.8 28.4 + - - +
403A CA 2.5 29.1 - - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 3.6 24.5 - - - +
12A ILE* 3.7 20.0 - - + -
14A ASP* 5.0 8.5 - - + +
15A ILE* 4.1 27.3 - - + +
53A PHE* 4.0 17.5 - - + -
85A LEU* 2.7 29.2 + - + +
86A ASP* 3.7 12.8 - - - +
88A ASP* 1.3 74.9 - - - +
90A ALA* 1.3 65.4 - - - +
92A ALA* 3.0 9.0 + - - +
93A LYS* 2.9 36.8 + - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP 3.1 17.6 + - - +
87A ASP* 4.0 7.6 - - - +
88A ASP 3.4 0.2 - - - -
89A ILE* 1.3 77.2 - - - +
91A CYS* 1.3 62.6 + - - +
93A LYS* 3.3 13.4 + - - +
94A LYS* 3.2 26.7 + - + +
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 3.6 36.8 - - + -
60A TRP* 4.3 1.8 - - - -
73A CYS* 2.0 52.3 - - + -
75A ILE* 5.0 5.8 - - + -
80A LEU* 4.8 3.4 - - + -
87A ASP 3.2 15.8 + - - +
88A ASP* 3.6 4.7 - - - +
89A ILE 3.2 0.6 - - - -
90A ALA* 1.3 75.7 - - - +
92A ALA* 1.3 67.4 + - - +
94A LYS* 3.2 5.8 + - - +
95A ILE* 3.1 26.2 + - - +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.1 10.3 - - + -
53A PHE* 3.7 34.1 - - + -
55A ILE* 4.3 1.5 - - - +
88A ASP 2.8 14.5 + - - +
89A ILE 3.3 9.2 - - - +
91A CYS* 1.3 77.8 - - - +
93A LYS* 1.3 57.5 + - - +
95A ILE* 3.0 8.1 + - - +
96A LEU* 2.8 32.0 + - - +
104A TRP* 3.8 15.6 - - + -
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 2.7 45.1 + - - -
15A ILE* 4.2 15.0 - - + +
18A TYR* 3.8 49.1 - - + +
89A ILE* 2.9 23.2 + - - +
90A ALA* 3.4 14.6 - - - +
92A ALA* 1.3 77.3 - - - +
94A LYS* 1.3 57.8 - - + +
96A LEU* 2.9 7.6 + - - +
97A ALA* 2.8 30.4 + - - +
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TRP* 4.5 2.7 - - + -
72A ILE* 2.9 34.2 + - - +
73A CYS* 3.7 23.7 + - - +
90A ALA* 3.3 15.9 - - + +
91A CYS* 3.2 8.6 + - - +
93A LYS* 1.3 76.5 - - + +
95A ILE* 1.3 56.9 + - - +
97A ALA* 3.3 6.7 + - - +
98A ILE* 2.9 47.4 + - + +
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 4.1 25.6 - - + -
60A TRP* 3.4 50.0 - - + -
91A CYS 3.1 12.9 + - - +
92A ALA* 3.0 8.6 + - - +
94A LYS* 1.3 76.9 - - - +
96A LEU* 1.3 58.9 + - - +
99A LYS* 2.7 31.1 + - + -
100A GLY 2.8 6.6 + - - +
103A TYR* 3.5 44.2 - - + -
104A TRP* 3.7 17.0 - - + -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.0 14.8 - - + -
18A TYR* 3.8 26.7 - - + +
19A GLN* 3.8 34.7 + - + -
21A ILE* 4.6 1.6 - - + -
26A TRP* 3.7 20.0 - - + +
92A ALA 2.8 14.9 + - - +
93A LYS* 3.4 8.1 - - - +
95A ILE* 1.3 76.3 - - - +
97A ALA* 1.3 62.7 + - - +
100A GLY* 3.2 20.1 + - - +
101A ILE* 3.5 43.5 - - + +
104A TRP* 3.7 14.6 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 3.9 16.8 - - + +
19A GLN* 4.4 8.1 - - - -
93A LYS 2.8 14.5 + - - +
94A LYS* 3.3 8.3 + - - +
96A LEU* 1.3 79.5 - - - +
98A ILE* 1.3 63.4 + - + +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TRP* 4.0 20.2 - - + -
72A ILE* 3.9 31.4 - - + -
94A LYS* 2.9 28.9 + - + +
97A ALA* 1.3 84.5 - - + +
99A LYS* 1.3 61.5 + - + +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 5.5 9.3 - - - -
60A TRP* 4.5 16.7 - - + +
95A ILE* 2.7 21.1 + - + +
96A LEU 4.2 0.2 - - - -
98A ILE* 1.3 77.3 - - + +
100A GLY* 1.3 58.6 + - - +
102A ASP* 5.0 8.7 + - + +
103A TYR* 4.1 39.5 - - + +
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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