Contacts of the helix formed by residues 85 - 91 (chain D) in PDB entry 4WLE
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D TYR* 4.7 0.2 - - - -
79D GLY 4.5 1.7 - - - +
80D TYR* 3.4 24.3 - - + +
81D LEU* 2.8 44.1 + - - +
82D GLY 2.9 9.5 + - - +
84D GLU* 1.3 83.7 + - + +
86D LEU* 1.3 63.7 + - - +
87D PRO* 3.4 2.5 - - - -
88D ASP* 3.4 15.4 + - - +
89D CYS* 3.2 20.3 + - - +
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.0 17.3 - - + -
56D TYR* 3.8 44.4 - - + +
82D GLY 3.5 2.6 + - - -
83D PRO* 3.2 19.2 + - + +
85D GLN* 1.3 77.6 - - - +
87D PRO* 1.4 64.5 - - + +
89D CYS* 3.2 3.2 + - + +
90D LEU* 3.2 28.2 + - + +
123D THR* 4.9 6.7 - - + +
124D LEU* 4.0 22.2 - - + -
127D ALA* 3.5 30.5 - - + -
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Residues in contact with PRO 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PRO 3.4 10.8 - - - +
84D GLU 3.6 9.9 - - - +
85D GLN 3.5 3.6 - - - -
86D LEU* 1.4 94.8 - - + +
88D ASP* 1.3 57.8 + - - +
90D LEU* 3.3 3.5 + - + +
91D LYS* 3.1 41.7 + - - +
127D ALA* 6.1 0.4 - - + -
131D HIS* 3.7 46.6 - - + +
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Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 5.6 1.6 + - - -
54D THR* 5.2 1.6 - - - +
80D TYR* 3.8 28.1 + - + +
84D GLU 4.8 3.2 - - - +
85D GLN* 3.4 19.7 + - - +
86D LEU 3.3 0.6 - - - -
87D PRO* 1.3 79.1 - - - +
89D CYS* 1.3 62.5 + - - +
90D LEU 3.5 0.2 + - - -
91D LYS* 3.6 31.5 + - - +
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Residues in contact with CYS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ALA* 4.1 2.0 - - - +
30D LEU* 4.3 10.8 - - - -
52D ARG* 4.3 0.9 + - - -
54D THR* 2.9 54.9 + - - +
56D TYR* 3.7 26.0 - - + -
80D TYR* 3.5 32.0 - - + -
85D GLN 3.2 6.0 + - - +
86D LEU* 3.2 13.8 + - + +
88D ASP* 1.3 80.9 - - - +
90D LEU* 1.3 56.8 + - - +
91D LYS 3.8 0.2 + - - -
93D CYS* 3.4 8.7 - - - -
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ALA* 4.2 4.9 - - + -
30D LEU* 4.0 22.0 - - + -
86D LEU* 3.2 25.6 + - + +
87D PRO 3.3 3.8 + - - +
89D CYS* 1.3 76.2 - - - +
91D LYS* 1.3 66.4 + - - +
92D GLY 3.1 3.5 + - - -
93D CYS* 3.1 20.1 + - - +
96D VAL* 4.1 10.1 - - + -
124D LEU 4.8 0.2 - - - +
127D ALA* 3.6 46.4 - - + +
128D CYS* 3.7 23.1 - - - +
131D HIS* 4.1 9.0 - - + -
132D CYS* 3.5 23.5 - - - +
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Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 3.1 29.4 + - - +
87D PRO* 3.1 28.1 + - - +
88D ASP* 3.7 28.2 + - - +
89D CYS 3.5 1.2 - - - -
90D LEU* 1.3 73.3 - - - +
92D GLY* 1.3 60.2 + - - +
131D HIS* 4.4 20.3 + - + +
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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