Contacts of the helix formed by residues 112 - 124 (chain E) in PDB entry 5GOU
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 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E LYS* 2.8 55.0 + - + +
109E ASN* 4.4 0.4 - - - -
111E ASN* 1.3 96.8 + - - +
113E SER* 1.3 57.3 + - - +
114E LEU* 3.0 8.6 - - - +
115E LEU* 3.2 60.0 - - + +
116E GLU* 3.8 11.3 + - - +
133E ILE* 6.1 1.8 - - - +
137E TYR* 5.8 5.2 - - - +
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Residues in contact with SER 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLN* 2.9 27.6 + - - +
26E LEU* 3.3 12.6 - - - +
109E ASN 3.5 15.9 + - - -
110E VAL 3.0 14.0 + - - -
111E ASN 3.4 0.2 - - - -
112E GLN* 1.3 76.4 - - - +
114E LEU* 1.3 56.8 + - - +
115E LEU 3.4 0.9 - - - -
116E GLU* 3.4 26.2 - - - +
117E LEU* 2.9 22.5 + - - +
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Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLN* 3.7 26.2 - - + +
27E GLU* 4.6 1.1 - - - +
69E LEU* 5.4 1.8 - - + -
110E VAL* 4.5 1.1 - - + +
111E ASN* 3.1 24.0 - - - +
112E GLN* 3.0 4.9 - - - +
113E SER* 1.3 75.1 - - - +
115E LEU* 1.3 54.0 + - - +
116E GLU 3.2 0.2 - - - -
117E LEU* 3.2 29.1 - - + +
118E HIS* 2.4 38.2 + - - +
133E ILE* 4.1 18.4 - - + +
137E TYR* 3.4 58.8 - - + +
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Residues in contact with LEU 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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112E GLN* 3.2 52.6 + - + +
114E LEU* 1.3 76.9 - - - +
116E GLU* 1.3 52.2 + - + +
118E HIS* 3.3 11.2 - - + +
119E LYS* 2.4 38.0 + - - +
133E ILE* 6.4 1.1 - - + -
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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
----------------------------------------------------------
112E GLN 3.8 11.8 - - - +
113E SER* 3.4 25.6 + - - +
114E LEU 3.2 0.4 - - - -
115E LEU* 1.3 74.4 - - + +
117E LEU* 1.3 57.4 + - - +
119E LYS* 3.6 22.1 - - + +
120E LEU* 2.8 27.0 + - - +
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Residues in contact with LEU 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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16E SER 4.8 0.4 - - - +
19E ALA* 3.7 29.4 - - + +
20E ILE* 3.9 31.4 - - + +
23E GLN* 3.9 20.9 - - + +
69E LEU* 5.4 0.7 - - + -
113E SER 2.9 9.3 + - - +
114E LEU* 3.1 37.9 + - + +
116E GLU* 1.3 74.1 - - - +
118E HIS* 1.3 60.0 + - - +
120E LEU* 3.0 11.5 + - + +
121E ALA* 2.8 30.6 + - - +
129E LEU* 4.4 14.8 - - + -
133E ILE* 4.5 10.1 - - + -
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Residues in contact with HIS 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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114E LEU 2.4 31.0 + - - +
115E LEU* 3.6 15.5 - - + +
117E LEU* 1.3 67.5 - - - +
119E LYS* 1.3 51.2 + - - +
121E ALA* 3.9 4.6 - - - +
122E THR* 2.6 62.4 + - + +
130E CYS* 3.8 20.4 + - - +
133E ILE* 3.5 32.7 - - + +
134E GLU* 3.0 31.9 + - + +
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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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115E LEU 2.4 30.5 + - - +
116E GLU* 3.6 20.2 - - + +
118E HIS* 1.3 68.5 - - - +
120E LEU* 1.3 60.1 + - - +
122E THR* 2.9 18.1 + - - -
123E ASP* 3.0 41.5 + - - +
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Residues in contact with LEU 120 (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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13E HIS* 5.8 2.2 - - + +
15E ASP* 3.3 58.8 - - + +
16E SER* 3.7 16.6 - - - +
19E ALA* 3.8 15.3 - - + -
116E GLU 2.8 16.0 + - - +
117E LEU* 3.0 13.0 + - + +
119E LYS* 1.3 81.0 - - + +
121E ALA* 1.3 56.5 + - - +
123E ASP* 3.9 5.0 - - + +
124E LYS* 2.9 36.9 + - + +
129E LEU* 5.9 0.4 - - + -
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Residues in contact with ALA 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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117E LEU 2.8 18.5 + - - +
118E HIS* 4.1 3.6 - - - +
120E LEU* 1.3 73.8 - - - +
122E THR* 1.3 57.8 + - - +
124E LYS* 4.4 2.7 - - - -
125E ASN 2.9 4.5 + - - -
126E ASP* 2.6 36.7 + - + +
129E LEU* 3.8 36.8 - - + +
130E CYS* 3.6 23.8 - - - +
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Residues in contact with THR 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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118E HIS* 2.6 42.7 + - + +
119E LYS* 2.9 17.5 + - - -
121E ALA* 1.3 75.6 - - - +
123E ASP* 1.3 63.8 + - - +
124E LYS 3.3 0.2 - - - -
125E ASN* 2.8 27.6 + - - +
130E CYS* 3.6 19.3 - - - -
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Residues in contact with ASP 123 (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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119E LYS* 3.0 42.7 + - - +
120E LEU* 4.1 6.1 - - + +
122E THR* 1.3 81.6 + - - +
124E LYS* 1.3 59.0 + - - +
125E ASN* 3.6 6.1 + - - -
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Residues in contact with LYS 124 (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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11E ASN* 2.4 48.9 + - - +
12E TYR* 3.7 0.4 - - - +
13E HIS* 3.2 46.9 - - + +
16E SER* 3.2 21.5 - - - +
120E LEU* 2.9 22.6 + - + +
121E ALA* 4.1 1.3 - - - +
123E ASP* 1.3 76.4 - - - +
125E ASN* 1.3 68.7 + - - +
126E ASP* 3.3 35.3 + - + +
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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