Contacts of the helix formed by residues 106 - 112 (chain A) in PDB entry 2WOE
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 ILE 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A MET* 4.2 8.3 - - + -
84A CYS 5.0 1.8 - - - +
87A PHE* 4.0 26.0 - - + +
88A ALA* 3.7 30.1 - - + +
90A TRP* 4.0 27.1 - - + -
91A LEU* 3.6 23.8 - - + -
102A CYS 3.0 27.1 + - - +
103A ARG 3.9 3.6 - - - +
105A GLY* 1.3 73.0 - - - +
107A ARG* 1.3 59.3 + - - +
109A TYR* 3.3 7.8 + - + +
110A MET* 2.9 30.7 + - - +
156A ILE* 5.2 2.7 - - + -
157A THR* 4.4 9.4 - - + +
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Residues in contact with ARG 107 (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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91A LEU* 4.3 14.1 - - + -
103A ARG* 2.9 41.3 + - + +
104A ARG* 3.7 6.2 - - - +
106A ILE* 1.3 74.5 - - - +
108A ARG* 1.3 65.0 + - - +
110A MET* 3.3 5.1 + - - -
111A HIS* 2.7 36.3 + - + +
52B ARG* 2.9 61.8 - - - +
94C ARG* 3.3 46.2 + - - +
95C PRO 3.0 26.9 + - - -
96C VAL* 4.7 4.8 + - - +
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Residues in contact with ARG 108 (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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104A ARG 3.0 16.0 + - - +
105A GLY* 3.4 32.6 + - - +
106A ILE 3.3 0.2 - - - -
107A ARG* 1.3 73.8 - - - +
109A TYR* 1.3 57.4 + - - +
112A GLU* 2.7 62.7 + - - +
114A THR* 2.9 38.7 + - - +
115A THR* 3.6 3.6 - - - +
116A THR 3.5 26.2 + - - +
117A ALA* 3.5 18.8 - - - +
118A PRO* 4.4 14.1 - - - +
156A ILE* 2.9 31.9 + - - +
94C ARG* 3.8 19.7 - - - +
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Residues in contact with TYR 109 (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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81A ALA* 3.6 10.9 + - + +
84A CYS* 3.5 47.1 - - + -
85A GLU* 2.5 41.3 + - - +
88A ALA* 4.7 3.6 - - + -
105A GLY 3.1 9.7 + - - +
106A ILE* 3.5 10.5 - - + +
108A ARG* 1.3 83.4 - - - +
110A MET* 1.3 69.6 + - + +
113A GLY* 2.7 48.8 + - - +
114A THR 3.5 24.5 - - - +
115A THR* 4.0 9.6 - - + -
156A ILE* 5.5 1.1 - - + -
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Residues in contact with MET 110 (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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88A ALA* 3.9 28.5 - - + +
91A LEU* 4.1 14.8 - - + -
92A LYS* 4.6 23.6 - - + +
106A ILE* 2.9 37.8 + - - +
107A ARG* 3.3 8.7 + - - +
109A TYR* 1.3 79.9 - - + +
111A HIS* 1.3 84.2 + - + +
113A GLY* 4.8 0.5 + - - -
50B TRP* 5.5 9.9 - - + +
52B ARG* 4.6 8.7 - - - +
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Residues in contact with HIS 111 (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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107A ARG* 2.7 33.8 + - + +
110A MET* 1.3 100.7 + - + +
112A GLU* 1.3 63.7 - - - +
113A GLY 3.7 0.4 - - - +
50B TRP* 5.2 10.8 - + - -
52B ARG* 3.0 40.6 + - - -
94C ARG* 3.8 20.2 - - - +
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Residues in contact with GLU 112 (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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108A ARG* 2.7 40.4 + - - +
111A HIS* 1.3 77.0 + - + +
113A GLY* 1.3 57.7 + - - +
114A THR* 3.2 24.7 + - + +
94C ARG* 3.5 25.4 + - - +
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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