Contacts of the helix formed by residues 113 - 125 (chain E) in PDB entry 1Z6Z
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 ASP 113 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ASP 4.7 0.6 + - - +
111E LEU* 3.5 2.4 - - - +
112E SER* 1.3 75.8 + - - +
114E SER* 1.3 57.4 + - - +
115E THR* 3.2 13.2 + - - +
116E GLN* 2.9 41.9 + - + +
117E VAL* 3.0 31.9 + - - +
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Residues in contact with SER 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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112E SER 3.3 5.8 + - - -
113E ASP* 1.3 69.9 + - - +
115E THR* 1.3 61.2 + - - +
117E VAL* 3.7 0.8 - - - -
118E ASN* 2.8 35.7 + - - -
70F GLU* 2.6 37.7 + - - -
73F LEU* 3.7 24.5 - - - -
74F GLN* 3.8 8.5 + - - +
77F LEU* 6.1 0.2 - - - -
126F THR* 3.7 10.9 - - - +
130F CYS* 3.9 12.6 - - - -
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Residues in contact with THR 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 ASP* 3.2 9.8 + - - +
114E SER* 1.3 73.2 + - - +
116E GLN* 1.3 64.0 + - - +
118E ASN* 3.8 6.8 - - - +
119E ASN* 2.9 42.5 + - - +
70F GLU* 3.9 28.3 - - + +
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Residues in contact with GLN 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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103E ASP* 4.7 24.4 + - - +
111E LEU* 4.6 15.4 - - - +
113E ASP* 2.9 35.9 + - - +
115E THR* 1.3 80.2 + - - +
117E VAL* 1.3 61.6 + - - +
119E ASN* 3.6 10.6 + - - +
120E TYR* 3.2 20.6 + - - +
166E LEU* 5.0 6.1 - - - +
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Residues in contact with VAL 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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111E LEU* 4.6 19.1 - - + +
113E ASP 3.0 23.5 + - - +
114E SER 3.8 3.6 - - - +
115E THR 3.2 0.2 - - - -
116E GLN* 1.3 77.8 - - - +
118E ASN* 1.3 63.1 + - - +
120E TYR* 3.0 18.0 + - - +
121E TRP* 3.2 39.3 + - + +
166E LEU* 4.1 16.6 - - + -
126F THR* 3.7 17.5 - - + +
129F LEU* 3.9 26.9 - - + -
130F CYS* 4.7 2.5 - - - -
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Residues in contact with ASN 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 SER 2.8 25.2 + - - +
115E THR* 3.4 7.4 + - - +
117E VAL* 1.3 71.5 - - - +
119E ASN* 1.3 60.6 + - - +
121E TRP* 3.3 9.9 + - - +
122E ALA* 3.0 27.3 + - - +
70F GLU* 3.5 19.8 + - - +
118F ASN* 4.8 4.9 - - - +
122F ALA* 3.5 24.9 + - - +
126F THR* 2.7 31.0 + - - +
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Residues in contact with ASN 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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68E GLY* 4.9 10.2 - - - +
115E THR* 2.9 33.1 + - - +
116E GLN* 3.7 9.4 - - - +
118E ASN* 1.3 76.4 - - - +
120E TYR* 1.3 65.2 + - - +
122E ALA* 3.4 8.2 + - - +
123E LEU* 3.2 23.4 + - - +
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Residues in contact with TYR 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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100E SER* 2.7 34.4 + - - -
101E LEU 3.8 1.2 + - - -
102E GLY* 3.7 24.2 - - - -
116E GLN 3.2 12.6 + - - +
117E VAL 3.0 11.2 + - - +
119E ASN* 1.3 78.5 - - - +
121E TRP* 1.3 73.8 + + - +
123E LEU* 5.0 1.3 - - - -
124E ASN* 3.0 65.5 + - + +
166E LEU* 3.3 46.9 - - + -
167E TYR* 3.3 23.4 + - - -
170E GLY* 4.8 3.2 - - - -
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Residues in contact with TRP 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 VAL* 3.2 24.2 + - + +
118E ASN* 3.3 8.5 + - - +
120E TYR* 1.3 85.5 - + - +
122E ALA* 1.3 61.4 + - - +
124E ASN* 5.8 0.2 - - + -
125E LEU* 2.7 47.2 + - + +
126E THR* 3.0 9.5 + - - -
166E LEU* 3.7 40.6 - - + -
169E ALA* 3.9 20.0 - - + -
170E GLY* 4.0 13.2 - - - -
118F ASN* 5.4 0.2 - - - +
121F TRP* 3.7 35.2 - - + -
125F LEU* 3.6 29.7 - - + +
126F THR* 3.1 28.8 + - - +
129F LEU* 4.5 7.6 - - + -
177F LEU* 4.8 6.1 - - + -
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Residues in contact with ALA 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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67E LEU 3.8 4.8 - - - +
68E GLY 3.7 19.1 - - - +
73E LEU* 6.0 0.3 - - - +
118E ASN 3.0 16.1 + - - +
119E ASN* 3.6 9.4 - - - +
120E TYR 3.3 0.2 - - - -
121E TRP* 1.3 76.9 - - - +
123E LEU* 1.3 58.4 + - - +
126E THR* 3.5 3.6 - - - -
127E SER* 3.1 30.1 + - - -
118F ASN* 3.4 32.0 + - - +
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Residues in contact with LEU 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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67E LEU* 4.0 17.5 - - + -
68E GLY* 4.0 8.9 - - - +
98E ALA* 5.1 11.8 - - + +
99E GLY* 5.0 3.1 - - - +
100E SER* 3.4 35.2 - - - +
119E ASN 3.2 13.1 + - - +
120E TYR* 5.0 0.7 - - - -
122E ALA* 1.3 80.7 - - - +
124E ASN* 1.3 68.8 + - - +
127E SER* 2.6 25.4 + - - +
128E MET* 4.5 0.3 + - - +
174E ARG* 5.1 1.4 + - - -
805E NAP 3.5 51.6 - - + +
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Residues in contact with ASN 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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98E ALA 4.7 1.3 - - - +
99E GLY* 3.3 9.7 - - - -
100E SER* 2.9 48.6 + - - +
120E TYR* 3.0 53.6 + - + +
123E LEU* 1.3 83.5 - - - +
125E LEU* 1.3 64.1 + - + +
128E MET* 3.6 2.1 - - - +
170E GLY* 5.3 3.8 - - - -
171E LYS* 5.5 3.1 + - - -
174E ARG* 2.9 42.9 + - - +
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Residues in contact with LEU 125 (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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121E TRP* 2.7 43.9 + - + +
124E ASN* 1.3 81.4 - - - +
126E THR* 1.3 64.9 + - - +
127E SER 3.4 1.8 - - - -
128E MET* 3.3 7.8 - - - +
129E LEU* 3.0 25.8 + - - +
170E GLY* 3.5 29.4 - - - +
173E ALA* 3.6 20.0 - - + -
174E ARG* 3.9 8.5 - - + +
177E LEU* 4.6 5.0 - - + +
121F TRP* 3.6 44.2 - - + +
125F LEU* 4.0 10.1 - - + -
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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