Contacts of the helix formed by residues 116 - 128 (chain E) in PDB entry 4CQM
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 SER 116 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E HIS 3.3 6.4 + - - -
115E MET* 1.3 90.4 - - - +
117E GLU* 1.3 63.6 + - - +
118E ASP* 3.8 6.2 + - - +
119E ASP* 2.9 34.8 + - - +
120E TRP* 3.4 9.9 + - - +
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Residues in contact with GLU 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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116E SER* 1.3 74.0 - - - +
118E ASP* 1.3 64.5 + - - +
120E TRP* 3.2 8.8 + - + +
121E ASP* 2.8 55.6 + - - +
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Residues in contact with ASP 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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226A HIS* 5.9 1.2 + - - -
170B LYS* 3.9 37.6 - - + +
116E SER* 3.4 7.0 + - - +
117E GLU* 1.3 79.1 - - - +
119E ASP* 1.3 68.1 + - - +
121E ASP* 4.0 10.1 - - - +
122E LYS* 3.2 34.9 + - + +
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Residues in contact with ASP 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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3B LYS* 4.6 10.4 + - - -
108E GLN* 3.8 29.9 - - + +
109E ASP 5.2 0.2 - - - +
110E GLU* 4.2 18.4 - - + +
115E MET* 4.1 11.7 - - + -
116E SER* 2.9 29.6 + - - +
117E GLU 3.3 0.6 - - - -
118E ASP* 1.3 80.4 - - - +
120E TRP* 1.3 56.4 + - - +
122E LYS* 4.2 5.0 + - - +
123E VAL* 3.2 17.3 + - - +
168E ASN* 2.8 26.7 + - - +
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Residues in contact with TRP 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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115E MET* 4.3 12.1 - - + +
116E SER 3.4 9.9 + - - +
117E GLU* 3.2 11.6 + - + +
118E ASP 3.2 0.6 - - - -
119E ASP* 1.3 80.0 - - - +
121E ASP* 1.3 82.5 + - - +
123E VAL* 3.6 1.9 + - - +
124E ILE* 3.2 45.1 + - + +
167E THR* 3.9 18.2 - - + -
168E ASN* 3.6 41.7 - - + +
171E ALA* 3.6 20.0 - - + -
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Residues in contact with ASP 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 GLU* 2.8 48.8 + - - +
118E ASP* 3.3 11.3 + - - +
120E TRP* 1.3 89.8 + - - +
122E LYS* 1.3 57.9 + - - +
124E ILE* 3.8 3.3 + - - +
125E ALA* 3.1 27.5 + - - +
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Residues in contact with LYS 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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78B ASN* 5.9 1.0 - - - +
125B GLN* 3.2 27.9 + - - +
126B GLN* 3.6 33.9 + - + +
127B GLY* 4.6 7.5 + - - -
106E ILE* 3.9 11.7 - - + +
108E GLN* 3.1 44.2 + - - +
118E ASP* 3.2 22.2 + - + +
119E ASP* 4.2 7.2 + - - +
121E ASP* 1.3 77.7 - - + +
123E VAL* 1.3 64.8 + - + +
124E ILE 3.3 0.4 - - - -
125E ALA* 3.7 5.8 - - - -
126E VAL* 3.0 34.0 + - - +
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Residues in contact with VAL 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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106E ILE* 4.3 13.7 - - + +
107E THR 4.5 2.2 - - - -
108E GLN* 3.7 27.6 - - + +
119E ASP 3.2 20.6 + - - +
120E TRP 3.6 0.6 + - - +
121E ASP 3.5 0.4 - - - -
122E LYS* 1.3 78.8 - - + +
124E ILE* 1.3 58.2 + - - +
127E ASN* 3.0 48.6 + - - +
168E ASN* 3.4 44.4 - - + +
169E TYR* 3.8 7.2 - - + +
172E SER* 3.9 1.1 - - - +
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Residues in contact with ILE 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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120E TRP* 3.2 56.3 + - + +
121E ASP* 4.0 3.4 - - - +
123E VAL* 1.3 76.6 - - - +
125E ALA* 1.3 60.0 + - - +
128E LEU* 2.9 30.3 + - + -
129E LYS* 2.9 28.6 + - + +
168E ASN 3.6 21.5 - - - +
171E ALA* 4.3 2.7 - - + -
172E SER* 3.7 19.7 - - - +
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Residues in contact with ALA 125 (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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126B GLN* 5.2 3.4 - - - +
77E SER* 3.5 20.7 - - - +
121E ASP 3.1 19.8 + - - +
122E LYS* 3.9 7.9 - - - +
123E VAL 3.4 0.4 - - - -
124E ILE* 1.3 79.1 - - - +
126E VAL* 1.3 53.1 + - + +
129E LYS* 3.3 19.7 - - + +
130E GLY* 2.7 29.6 + - - -
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Residues in contact with VAL 126 (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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126B GLN* 4.1 24.0 - - - +
43E LEU* 6.4 0.7 - - + -
75E ASP* 5.0 3.1 - - - +
76E VAL* 3.9 13.5 - - + +
77E SER* 4.3 10.3 - - - -
104E ALA* 4.0 9.0 - - + +
105E GLY* 3.8 18.8 - - - +
106E ILE* 3.8 25.1 - - + +
122E LYS 3.0 18.1 + - - +
125E ALA* 1.3 76.8 - - - +
127E ASN* 1.3 78.5 + - - +
130E GLY* 3.3 18.5 - - - -
131E THR 3.8 1.9 + - - -
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Residues in contact with ASN 127 (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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104E ALA 4.5 4.3 - - - -
105E GLY* 3.3 8.4 - - - -
106E ILE* 3.1 42.8 + - - +
123E VAL* 3.0 19.6 + - - +
126E VAL* 1.3 80.1 - - - +
128E LEU* 1.3 58.0 + - - +
131E THR* 2.6 27.9 + - - -
169E TYR* 3.7 16.2 - - - -
172E SER* 3.5 23.5 + - - +
173E LYS* 3.7 19.6 + - - +
176E VAL* 3.4 10.8 - - - +
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Residues in contact with LEU 128 (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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124E ILE* 2.9 32.1 + - + +
127E ASN* 1.3 77.9 - - - +
129E LYS* 1.3 65.8 + - - +
130E GLY 3.2 0.7 - - - -
131E THR* 3.3 4.3 + - - -
132E PHE* 3.0 21.8 + - - +
171E ALA 4.6 2.0 - - - +
172E SER* 4.1 18.6 - - - -
175E GLY* 3.4 42.8 - - - +
176E VAL* 3.7 4.9 - - - +
179E LEU* 3.9 13.5 - - + +
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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