Contacts of the helix formed by residues 133 - 147 (chain E) in PDB entry 2ZNZ
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 ASN 133 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E SER* 4.5 2.2 - - - +
87E MET* 4.1 10.1 - - - -
131E THR* 3.0 19.8 + - - -
132E LYS* 1.3 85.3 - - - +
134E SER* 1.3 62.6 + - - +
135E GLU* 3.2 17.4 + - - +
136E GLU* 2.9 41.6 + - - +
137E LEU 3.2 7.8 + - - -
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Residues in contact with SER 134 (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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87E MET* 3.7 25.1 - - - +
133E ASN* 1.3 72.6 - - - +
135E GLU* 1.3 60.9 + - - +
136E GLU 3.4 0.2 - - - -
137E LEU* 3.6 8.5 - - - +
138E ASN* 2.9 28.1 + - - +
157E ILE* 6.2 0.2 - - - -
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Residues in contact with GLU 135 (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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133E ASN* 3.2 16.2 + - - +
134E SER* 1.3 78.2 + - - +
136E GLU* 1.3 72.8 + - - +
138E ASN* 3.2 8.8 + - + +
139E ASN* 3.0 37.7 + - - +
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Residues in contact with GLU 136 (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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131E THR* 4.2 11.7 - - + -
132E LYS* 4.4 17.5 - - + +
133E ASN* 2.9 30.6 + - - +
135E GLU* 1.3 83.0 - - - +
137E LEU* 1.3 59.2 + - - +
139E ASN* 3.1 24.1 + - - +
140E PHE* 3.0 44.6 + - + -
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Residues in contact with LEU 137 (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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87E MET* 4.1 14.4 - - + -
89E ALA* 4.2 6.3 - - + -
91E ILE* 4.5 5.2 - - + -
129E ILE* 3.7 32.8 - - + -
131E THR* 3.6 25.0 + - + +
133E ASN 3.2 8.7 + - - +
134E SER* 3.6 11.9 - - - +
136E GLU* 1.3 76.7 - - - +
138E ASN* 1.3 57.4 + - - +
140E PHE* 3.1 4.1 + - - +
141E LEU* 2.9 49.8 + - + +
155E THR* 4.2 9.0 - - + -
157E ILE* 3.4 33.0 - - + -
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Residues in contact with ASN 138 (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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134E SER 2.9 15.7 + - - +
135E GLU* 3.2 12.9 + - + +
137E LEU* 1.3 76.1 - - - +
139E ASN* 1.3 65.2 + - - +
141E LEU* 3.4 8.8 + - - +
142E ASP* 3.1 30.7 + - - +
172E LYS* 2.9 33.0 + - - +
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Residues in contact with ASN 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E GLU* 3.0 26.5 + - - +
136E GLU* 3.1 32.9 + - - +
138E ASN* 1.3 81.3 - - - +
140E PHE* 1.3 63.1 + - + +
142E ASP* 3.4 16.2 + - - +
143E LEU* 3.1 28.4 + - + +
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Residues in contact with PHE 140 (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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110E TYR* 4.3 24.7 - + + -
112E GLU* 3.2 46.0 - - + -
113E ILE* 6.0 0.4 - - + -
129E ILE* 3.8 24.9 - - + -
131E THR* 3.8 18.8 - - + -
136E GLU* 3.0 34.2 + - + -
137E LEU* 3.6 5.8 - - + +
139E ASN* 1.3 74.6 - - + +
141E LEU* 1.3 60.3 + - + +
143E LEU* 3.3 22.4 + - + +
144E ILE* 2.8 40.0 + - + +
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Residues in contact with LEU 141 (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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91E ILE* 3.7 28.5 - - + -
137E LEU* 2.9 40.5 + - + +
138E ASN* 3.7 7.6 - - - +
139E ASN 3.3 0.2 - - - -
140E PHE* 1.3 73.0 - - - +
142E ASP* 1.3 58.7 + - - +
144E ILE* 3.9 4.4 - - + +
145E GLY* 2.9 25.6 + - - -
153E THR* 3.9 14.7 + - + +
155E THR* 3.3 30.3 - - + +
172E LYS* 3.7 42.1 - - + +
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Residues in contact with ASP 142 (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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138E ASN* 3.1 23.1 + - - +
139E ASN* 3.5 16.6 + - - +
141E LEU* 1.3 75.7 - - - +
143E LEU* 1.3 61.4 + - + +
145E GLY* 3.4 2.3 + - - -
146E SER* 3.1 26.1 + - - -
172E LYS* 2.6 29.6 + - - -
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Residues in contact with LEU 143 (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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110E TYR* 3.8 31.1 + - + +
139E ASN* 3.1 20.9 + - + +
140E PHE* 3.3 29.6 + - + +
142E ASP* 1.3 72.1 - - + +
144E ILE* 1.3 66.1 + - - +
146E SER* 3.0 18.6 + - - -
147E ILE* 3.4 13.2 + - - +
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Residues in contact with ILE 144 (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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91E ILE* 3.8 29.4 - - + -
93E VAL* 4.8 6.5 - - + -
107E LEU* 3.7 32.8 - - + -
110E TYR* 4.9 6.7 - - + -
113E ILE* 4.1 13.9 - - + -
127E VAL* 5.4 1.1 - - + -
129E ILE* 4.7 1.1 - - + -
140E PHE* 2.8 33.6 + - + +
141E LEU* 3.9 6.5 - - + +
143E LEU* 1.3 70.9 - - - +
145E GLY* 1.3 63.4 + - - +
147E ILE* 3.2 26.7 + - + +
150E VAL* 3.4 15.3 - - + +
153E THR* 3.7 25.1 - - + -
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Residues in contact with GLY 145 (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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141E LEU 2.9 18.8 + - - -
142E ASP* 3.4 3.6 + - - -
143E LEU 3.3 0.4 - - - -
144E ILE* 1.3 75.8 - - - +
146E SER* 1.3 59.1 + - - +
147E ILE 3.7 6.2 + - - +
150E VAL* 4.1 19.3 - - - +
152E GLY* 6.4 0.4 - - - -
153E THR* 5.5 2.5 - - - -
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Residues in contact with SER 146 (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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142E ASP 3.1 12.2 + - - -
143E LEU* 3.0 15.2 + - - -
145E GLY* 1.3 74.9 - - - +
147E ILE* 1.3 65.4 + - - +
148E PRO* 3.3 9.5 - - - +
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Residues in contact with ILE 147 (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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102E GLU 5.2 0.4 - - - +
103E VAL* 4.3 10.1 - - + -
106E ASN* 3.4 48.0 - - + +
107E LEU* 3.8 25.8 - - + +
110E TYR* 4.8 7.4 - - + +
143E LEU 3.4 7.1 + - - +
144E ILE* 3.2 29.9 + - + +
145E GLY 4.0 3.1 - - - +
146E SER* 1.3 76.8 - - - +
148E PRO* 1.4 82.6 - - + +
149E GLY 3.3 0.2 + - - -
150E VAL* 3.1 31.9 + - + +
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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