Contacts of the helix formed by residues 85 - 91 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY 4.3 2.8 - - - +
80A TYR* 3.4 26.6 - - + +
81A LEU* 2.9 41.4 + - - +
82A GLY 2.9 8.4 + - - +
84A GLU* 1.3 85.9 + - + +
86A LEU* 1.3 65.4 + - - +
87A PRO* 3.4 2.7 - - - -
88A ASP* 3.2 23.0 + - - +
89A CYS 3.2 9.5 + - - -
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Residues in contact with LEU 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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30A LEU* 3.9 13.5 - - + -
56A TYR* 3.8 46.4 - - + +
82A GLY 3.4 3.2 + - - -
83A PRO* 3.3 12.7 + - + +
85A GLN* 1.3 76.5 - - - +
87A PRO* 1.4 70.5 - - + +
89A CYS* 3.1 10.9 + - + +
90A LEU* 3.3 24.0 + - + +
123A THR* 5.1 7.9 - - + +
124A LEU* 4.1 20.0 - - + -
127A ALA* 3.6 28.5 - - + -
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO 3.3 15.0 - - - +
84A GLU 3.5 9.4 - - - +
85A GLN 3.5 4.0 - - - -
86A LEU* 1.4 92.3 - - + +
88A ASP* 1.3 62.5 + - - +
90A LEU* 3.2 2.4 + - - +
91A LYS* 3.1 37.8 + - + +
131A HIS* 3.6 43.6 - - + +
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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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52A ARG* 5.6 2.1 + - - -
54A THR* 5.1 1.4 - - - +
80A TYR* 3.6 28.2 + - + -
84A GLU 4.3 5.4 - - - +
85A GLN* 3.2 22.9 + - - +
87A PRO* 1.3 80.5 - - - +
89A CYS* 1.3 62.1 + - - +
91A LYS* 3.9 20.8 + - - +
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Residues in contact with CYS 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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28A ALA* 4.0 9.1 - - - +
30A LEU* 4.3 5.2 - - - -
52A ARG* 4.4 1.0 + - - -
54A THR* 2.7 57.2 + - - +
55A LEU 3.8 3.8 - - - -
56A TYR* 3.7 26.9 - - + -
80A TYR* 3.6 26.8 - - + -
85A GLN 3.2 6.0 + - - +
86A LEU* 3.1 12.7 + - + +
88A ASP* 1.3 77.2 - - - +
90A LEU* 1.3 59.1 + - + +
93A CYS* 3.3 8.8 - - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 4.1 6.1 - - + -
30A LEU* 3.9 24.0 - - + -
86A LEU* 3.3 23.5 + - + +
87A PRO 3.2 7.0 + - - +
89A CYS* 1.3 78.6 - - - +
91A LYS* 1.3 66.5 + - - +
92A GLY 3.2 0.5 + - - -
93A CYS* 3.2 22.0 + - - +
96A VAL* 3.9 19.1 - - + -
127A ALA* 3.6 44.4 - - + +
128A CYS* 3.8 6.3 - - - +
131A HIS* 3.9 10.1 - - + -
132A CYS* 3.4 28.9 - - - +
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Residues in contact with LYS 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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52A ARG* 3.0 27.4 + - - -
87A PRO* 3.1 33.2 + - - +
88A ASP* 3.9 16.8 + - - +
89A CYS 3.6 1.0 - - - -
90A LEU* 1.3 74.7 - - - +
92A GLY* 1.3 58.1 + - - +
130A GLN 5.7 0.4 + - - -
131A HIS* 3.6 38.1 + - + +
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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