Contacts of the helix formed by residues 85 - 93 (chain C) in PDB entry 3PLA
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 SER 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ALA* 4.4 2.5 - - - -
59C ASP* 3.5 7.4 + - - -
83C VAL* 3.8 6.5 - - - +
84C SER* 1.3 84.1 + - - +
86C LYS* 1.3 62.8 + - - +
87C LYS* 3.2 10.9 + - - +
88C ALA* 3.2 31.2 + - - +
89C LEU* 3.3 21.1 + - - +
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ALA* 3.8 10.5 - - + -
59C ASP* 3.0 43.3 + - - +
60C VAL* 4.7 6.7 - - + -
61C GLN* 5.4 8.4 - - - +
85C SER* 1.3 71.9 + - - +
87C LYS* 1.3 73.2 + - + +
88C ALA 3.2 0.2 - - - -
89C LEU* 3.3 1.0 + - - +
90C GLY 3.0 24.3 + - - -
98C ALA* 3.8 20.4 - - + -
99C THR 3.1 35.7 + - - +
100C ALA* 4.6 5.6 - - + +
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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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85C SER* 3.2 7.6 + - - +
86C LYS* 1.3 92.7 - - + +
88C ALA* 1.3 55.9 + - - +
90C GLY* 4.0 0.3 - - - -
91C GLU* 3.0 60.0 + - - +
96C GLN 6.1 0.4 - - - +
97C VAL* 4.8 1.2 - - - +
98C ALA* 4.1 23.2 - - + +
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Residues in contact with ALA 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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23C LEU* 3.7 21.1 - - + +
85C SER* 3.2 27.9 + - - +
87C LYS* 1.3 78.7 - - - +
89C LEU* 1.3 55.5 + - - +
91C GLU* 3.8 3.8 - - - +
92C ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.7 17.0 - - + +
26C VAL* 4.4 16.2 - - + -
55C ILE* 3.8 48.9 - - + +
57C ALA* 4.5 5.6 - - + +
83C VAL* 3.9 13.7 - - + -
85C SER 3.3 14.1 + - - +
86C LYS 3.3 4.0 + - - +
88C ALA* 1.3 75.0 - - - +
90C GLY* 1.3 61.2 + - - +
92C ALA* 3.3 3.5 + - + +
93C CYS* 2.9 40.5 + - - -
99C THR* 3.7 24.9 - - + +
101C SER* 4.3 3.4 - - - -
102C ALA* 4.3 9.0 - - + +
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C LYS 3.0 11.2 + - - -
87C LYS 4.1 0.2 - - - -
89C LEU* 1.3 75.9 - - - +
91C GLU* 1.3 57.1 + - - +
93C CYS* 2.9 20.5 + - - +
95C LEU* 3.1 21.0 + - - +
97C VAL 3.5 20.9 - - - -
99C THR* 3.4 23.2 - - - +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C ARG* 5.8 0.2 - - - -
87C LYS* 3.0 45.8 + - + +
88C ALA* 3.8 4.7 - - - +
90C GLY* 1.3 72.9 - - - +
92C ALA* 1.3 65.3 + - - +
94C GLY* 3.9 5.2 + - - -
95C LEU 3.2 18.2 - - - +
96C GLN* 4.5 19.4 - - + +
97C VAL 4.7 1.1 - - - +
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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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23C LEU* 4.0 20.9 - - + +
26C VAL* 5.0 2.7 - - + -
27C ARG* 3.9 25.1 - - + +
30C LYS* 2.6 31.4 + - - +
88C ALA 2.9 16.4 + - - +
89C LEU* 3.3 10.1 - - + +
91C GLU* 1.3 78.9 - - - +
93C CYS* 1.3 50.4 + - - +
94C GLY* 2.7 14.0 + - - -
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Residues in contact with CYS 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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26C VAL* 4.3 15.0 - - - -
30C LYS* 3.1 25.9 - - - +
35C ILE* 4.2 3.9 - - + +
37C LYS* 4.1 29.9 - - + +
89C LEU* 2.9 24.9 + - - +
90C GLY* 2.9 14.5 + - - +
92C ALA* 1.3 73.8 - - - +
94C GLY* 1.3 57.9 + - - +
95C LEU* 4.3 9.6 - - + -
99C THR* 4.2 6.5 - - - -
102C ALA* 4.0 26.9 - - - -
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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