Contacts of the helix formed by residues 82 - 92 (chain C) in PDB entry 1L9B
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C GLN 3.7 3.9 + - - +
79C TYR 3.1 4.3 + - - -
81C GLN* 1.3 83.5 - - + +
83C PRO* 1.3 67.3 - - - +
84C THR* 3.1 10.9 + - - -
85C LYS* 2.8 53.9 + - + +
86C PHE* 3.1 23.7 + - - +
103C LYS* 3.2 29.5 + - - -
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Residues in contact with PRO 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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79C TYR* 3.3 39.5 - - + +
80C VAL 4.5 0.7 - - - +
81C GLN 4.3 0.4 - - - -
82C ASP* 1.3 85.4 - - - +
84C THR* 1.3 62.4 + - - +
86C PHE* 3.7 1.2 - - - +
87C LEU* 3.1 32.7 + - - +
98C GLY* 4.9 5.4 - - - -
100C MET* 3.8 39.7 - - + +
102C PHE 3.4 25.6 - - - +
103C LYS* 4.3 6.1 - - + -
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Residues in contact with THR 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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82C ASP* 3.1 7.2 + - - -
83C PRO* 1.3 76.8 - - - +
85C LYS* 1.3 66.6 + - - +
87C LEU* 3.2 3.2 + - - +
88C LYS* 3.0 45.5 + - + +
96C ALA 4.1 9.9 - - - +
97C LYS* 4.0 21.6 + - + +
98C GLY* 3.6 25.1 + - - +
100C MET 5.7 0.5 + - - -
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLN* 5.8 5.9 + - - -
81C GLN* 5.8 3.6 - - - +
82C ASP* 2.8 39.0 + - + +
84C THR* 1.3 73.3 - - - +
86C PHE* 1.3 66.1 + - - +
88C LYS* 3.1 28.1 + - - +
89C GLU* 3.1 40.4 + - + +
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Residues in contact with PHE 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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69C LEU* 3.8 24.7 - - + -
71C TRP* 4.1 9.6 - + - -
75C HIS* 3.4 51.8 - + + -
78C GLN* 3.4 29.2 - - + +
79C TYR* 3.5 27.4 - + - +
82C ASP 3.1 17.7 + - - +
83C PRO 3.7 2.5 - - - +
85C LYS* 1.3 82.5 - - - +
87C LEU* 1.3 73.7 + - + +
89C GLU* 3.6 9.7 + - - +
90C TYR* 3.2 31.0 + + + +
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Residues in contact with LEU 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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60C GLY 4.0 17.7 - - - +
61C MET* 4.1 32.5 - - + +
64C ALA* 4.2 14.8 - - + -
69C LEU* 5.1 0.4 - - + -
79C TYR* 4.3 13.9 - - + -
83C PRO 3.1 19.3 + - - +
84C THR* 3.9 3.6 - - - +
86C PHE* 1.3 94.1 - - + +
88C LYS* 1.3 54.4 + - - +
90C TYR* 4.7 2.0 - - + -
91C THR* 2.6 41.4 + - - +
96C ALA* 4.4 9.9 - - + +
97C LYS 4.4 2.5 - - - +
98C GLY* 3.8 26.5 - - - +
1009C HEM 4.5 5.4 - - - +
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Residues in contact with LYS 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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84C THR* 3.0 36.9 + - + +
85C LYS* 3.1 17.8 + - + +
87C LEU* 1.3 75.4 - - - +
89C GLU* 1.3 69.9 + - + +
91C THR* 3.3 3.2 - - - +
92C GLY 3.2 8.3 + - - -
93C ASP 2.7 25.4 - - - +
94C ALA* 3.4 27.6 - - - +
96C ALA* 3.3 20.6 - - - +
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Residues in contact with GLU 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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78C GLN* 5.5 2.6 - - - +
85C LYS* 3.1 42.4 + - + +
86C PHE* 3.9 9.6 - - - +
88C LYS* 1.3 76.7 - - + +
90C TYR* 1.3 57.2 + - - +
92C GLY* 2.7 27.7 + - - -
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Residues in contact with TYR 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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64C ALA* 3.6 28.3 - - + -
67C LYS* 4.0 20.3 + - + +
68C GLY 3.6 6.6 + - - -
69C LEU* 3.2 56.3 + - + +
75C HIS* 3.7 25.1 + + - -
86C PHE* 3.2 26.6 + + + +
87C LEU* 4.5 2.7 - - - +
89C GLU* 1.3 79.1 - - - +
91C THR* 1.3 65.4 + - - +
92C GLY* 3.2 1.4 + - - -
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Residues in contact with THR 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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60C GLY* 4.7 9.3 + - - -
63C GLU* 4.2 23.0 + - - +
64C ALA* 5.3 3.4 - - - -
67C LYS* 3.5 32.3 + - - +
87C LEU 2.6 25.2 + - - +
88C LYS 3.3 5.4 - - - +
90C TYR* 1.3 82.8 - - - +
92C GLY* 1.3 60.1 + - - +
93C ASP* 3.1 33.5 + - + +
96C ALA* 3.6 12.7 - - + +
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Residues in contact with GLY 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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88C LYS 3.6 0.7 - - - -
89C GLU* 2.7 17.3 + - - -
90C TYR 3.1 1.5 - - - -
91C THR* 1.3 76.5 - - - +
93C ASP* 1.3 66.9 + - - +
94C ALA* 5.2 0.7 - - - +
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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