Contacts of the helix formed by residues 113 - 122 (chain E) in PDB entry 6WNX
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 THR 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ALA* 4.8 0.2 - - - -
112E LYS* 1.3 74.4 - - - +
114E PRO* 1.4 74.8 - - - +
115E GLU* 3.5 8.5 + - - +
116E GLU* 2.9 44.8 + - + +
117E ILE* 3.0 11.5 + - - +
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Residues in contact with PRO 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA* 3.5 36.5 - - + +
36D LEU* 3.6 30.5 - - + -
37D VAL* 4.2 8.2 - - + +
112E LYS 4.0 0.4 - - - -
113E THR* 1.4 86.1 - - - +
115E GLU* 1.3 62.6 + - - +
117E ILE* 3.1 6.8 + - + +
118E ARG* 2.9 45.4 + - - +
136E ARG* 6.0 0.7 - - - +
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Residues in contact with GLU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E THR* 3.2 8.4 + - - +
114E PRO* 1.3 77.7 - - - +
116E GLU* 1.3 61.8 + - + +
118E ARG* 2.9 40.7 + - - +
119E LYS* 3.1 46.8 + - - +
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Residues in contact with GLU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E GLY 4.8 1.4 - - - +
112E LYS* 3.9 30.9 - - + +
113E THR* 2.9 35.2 + - + +
115E GLU* 1.3 70.7 - - + +
117E ILE* 1.3 56.5 + - - +
119E LYS* 3.3 9.9 + - - +
120E THR* 2.8 31.4 + - - -
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Residues in contact with ILE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA* 5.4 3.8 - - + -
34D ALA 5.8 0.7 - - - +
37D VAL* 3.6 28.9 - - + -
41D TRP* 3.7 23.1 - - + -
108E MET 4.4 1.6 - - - +
109E ILE* 3.1 46.4 - - + +
112E LYS* 3.4 23.1 - - + +
113E THR 3.0 18.2 + - - +
114E PRO* 3.3 7.4 - - + +
116E GLU* 1.3 73.6 - - - +
118E ARG* 1.3 66.2 + - - +
120E THR* 3.1 21.6 + - - -
121E PHE* 3.2 16.7 + - + +
123E ILE* 4.8 0.2 - - + -
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Residues in contact with ARG 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.6 18.2 + - - +
37D VAL* 3.2 27.2 + - + +
114E PRO* 2.9 24.1 + - - +
115E GLU* 2.9 57.8 + - - +
117E ILE* 1.3 74.8 - - - +
119E LYS* 1.3 53.8 + - - +
121E PHE 3.7 0.2 - - - -
122E ASN* 2.7 32.6 + - - -
123E ILE* 3.0 42.3 + - + +
124E LYS 4.1 0.4 - - - -
125E ASN* 3.4 44.5 - - - +
132E GLU* 4.8 6.3 + - - -
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Residues in contact with LYS 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 5.3 0.7 + - - +
115E GLU* 3.1 35.3 + - - +
116E GLU* 3.7 11.0 - - - +
117E ILE 3.2 0.4 - - - -
118E ARG* 1.3 73.1 - - - +
120E THR* 1.3 65.5 + - - +
121E PHE 3.5 0.5 + - - -
122E ASN* 3.8 7.7 + - - +
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Residues in contact with THR 120 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D GLN* 3.5 14.0 - - - +
79E GLN* 4.1 8.1 + - - +
108E MET* 4.3 8.7 - - + +
112E LYS* 3.1 30.3 + - - +
116E GLU 2.8 17.5 + - - -
117E ILE* 3.1 9.9 + - - -
119E LYS* 1.3 78.1 - - - +
121E PHE* 1.3 82.2 + - + +
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Residues in contact with PHE 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 4.3 5.0 - - - +
4D ARG 3.7 22.0 + - - +
5D ASP* 4.2 8.1 - - - +
6D PHE* 4.1 17.9 - + + -
41D TRP* 4.4 7.4 - + - -
79E GLN* 3.3 25.1 - - - +
105E VAL* 4.5 9.9 - - + -
108E MET* 4.1 23.8 - - + -
109E ILE* 3.8 30.7 - - + -
117E ILE* 3.2 32.1 + - + -
120E THR* 1.3 96.9 - - + +
122E ASN* 1.3 73.3 + - - +
123E ILE* 3.7 22.7 - - + +
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Residues in contact with ASN 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 3.8 24.8 - - - +
118E ARG 2.7 10.0 + - - -
119E LYS* 3.8 6.3 + - - +
120E THR 3.6 2.4 - - - -
121E PHE* 1.3 82.6 - - - +
123E ILE* 1.3 56.0 + - - +
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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