Contacts of the helix formed by residues 85 - 91 (chain C) in PDB entry 4WLU
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 GLN 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C TYR* 4.7 1.6 - - - -
79C GLY 4.5 1.7 - - - +
80C TYR* 3.5 26.7 - - + +
81C LEU* 3.0 39.6 + - - +
82C GLY 2.9 9.0 + - - +
84C GLU* 1.3 83.5 + - + +
86C LEU* 1.3 63.7 + - - +
87C PRO* 3.4 2.0 - - - -
88C ASP* 3.4 15.9 + - - +
89C CYS* 3.2 20.4 + - - +
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Residues in contact with LEU 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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30C LEU* 4.1 14.1 - - + -
56C TYR* 3.7 45.3 - - + +
82C GLY 3.6 2.2 + - - -
83C PRO* 3.1 18.5 + - + +
85C GLN* 1.3 77.4 - - - +
87C PRO* 1.3 66.0 - - + +
89C CYS* 3.3 4.4 + - + +
90C LEU* 3.0 46.4 + - + +
123C THR* 5.1 5.2 - - + +
124C LEU* 3.9 23.6 - - + -
127C ALA* 3.5 24.0 - - + -
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Residues in contact with PRO 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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83C PRO 3.6 9.6 - - - +
84C GLU 3.7 9.9 - - - +
85C GLN 3.6 3.1 - - - -
86C LEU* 1.3 95.6 - - + +
88C ASP* 1.3 63.6 + - - +
90C LEU* 3.1 2.4 + - - +
91C LYS* 2.9 39.3 + - - +
127C ALA* 6.2 0.4 - - + -
131C HIS* 3.6 48.1 - - + +
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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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26C LYS* 4.2 6.8 + - - -
54C THR* 5.2 0.2 - - - +
80C TYR* 3.8 27.5 + - + +
84C GLU 5.1 2.5 - - - +
85C GLN* 3.4 17.6 + - - +
87C PRO* 1.3 81.5 - - - +
89C CYS* 1.3 62.9 + - - +
91C LYS* 3.7 30.8 + - - +
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Residues in contact with CYS 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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26C LYS* 3.8 1.7 + - - -
28C ALA* 4.3 9.2 - - - -
30C LEU* 4.4 4.7 - - - -
54C THR* 3.1 50.8 + - - +
56C TYR* 3.7 27.6 - - + -
80C TYR* 3.5 30.0 - - + -
85C GLN 3.2 8.4 + - - +
86C LEU* 3.5 13.0 - - + +
87C PRO 3.2 0.2 - - - -
88C ASP* 1.3 81.0 - - - +
90C LEU* 1.3 59.9 + - - +
93C CYS* 3.6 6.6 - - - -
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Residues in contact with LEU 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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28C ALA* 4.4 4.5 - - + -
30C LEU* 4.2 22.0 - - + -
86C LEU* 3.0 30.4 + - + +
87C PRO 3.1 2.9 + - - +
89C CYS* 1.3 75.8 - - - +
91C LYS* 1.3 65.3 + - - +
92C GLY 3.2 0.7 + - - -
93C CYS* 3.1 23.2 + - - +
96C VAL* 4.1 10.5 - - + -
124C LEU 4.8 0.4 - - - +
127C ALA* 3.4 47.1 - - + +
128C CYS* 3.7 23.1 - - - +
131C HIS* 4.0 10.5 - - + -
132C CYS* 3.4 20.3 - - - +
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Residues in contact with LYS 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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26C LYS* 2.4 34.4 + - - +
87C PRO* 2.9 25.6 + - - +
88C ASP* 3.8 29.8 - - - +
89C CYS 3.5 1.2 - - - -
90C LEU* 1.3 74.8 - - - +
92C GLY* 1.3 57.7 + - - +
131C HIS* 4.1 29.1 + - + +
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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