Contacts of the helix formed by residues 146 - 159 (chain D) in PDB entry 6CNB
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 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ASP* 3.0 31.1 - - - +
143D ALA 5.1 1.1 - - - +
144D ARG 3.7 5.9 + - - +
145D PHE* 1.3 72.5 - - - +
147D GLU* 1.3 74.0 + - + +
148D LYS* 3.7 0.4 - - - +
149D THR* 2.6 17.4 + - - +
150D ILE* 2.7 46.9 + - - +
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Residues in contact with GLU 147 (chain D).
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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146D ASP* 1.3 91.7 - - + +
148D LYS* 1.3 63.3 + - + +
150D ILE* 3.4 5.2 - - - +
151D GLU* 2.9 33.5 + - - +
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Residues in contact with LYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PHE* 6.1 0.9 - - + -
145D PHE* 6.2 0.8 - - - +
146D ASP 6.2 0.2 - - - +
147D GLU* 1.3 79.5 - - + +
149D THR* 1.3 71.4 + - + +
151D GLU* 3.9 6.7 - - - +
152D GLU* 2.9 63.4 + - + +
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Residues in contact with THR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PHE* 4.2 27.9 - - + -
145D PHE* 2.9 56.2 + - + -
146D ASP 2.6 20.6 + - - +
148D LYS* 1.3 98.0 - - + +
150D ILE* 1.3 60.2 + - - +
153D MET* 3.3 31.7 + - - +
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D MET* 5.1 10.5 - - - +
134D LEU* 3.3 40.4 - - + +
135D TYR* 5.8 1.6 - - + -
141D CYS* 5.1 2.7 - - - +
142D ASP* 5.1 12.1 - - + +
145D PHE* 4.7 3.6 - - + +
146D ASP* 2.7 50.5 + - - +
147D GLU* 3.4 7.2 - - - +
149D THR* 1.3 78.0 - - - +
151D GLU* 1.3 63.7 + - + +
153D MET* 3.7 3.4 - - + +
154D LEU* 3.1 21.6 - - - +
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D GLU 2.9 21.4 + - - +
148D LYS* 4.2 3.9 - - - +
150D ILE* 1.3 77.5 - - + +
152D GLU* 1.3 80.3 + - - +
153D MET 3.1 2.0 - - - -
154D LEU* 2.8 44.5 + - + +
155D GLU* 3.5 24.0 + - - +
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Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LYS* 3.3 32.1 + - - -
113D PHE* 3.6 22.0 - - + -
148D LYS* 2.9 50.7 + - + +
151D GLU* 1.3 85.9 + - - +
153D MET* 1.3 55.8 + - - +
155D GLU* 3.1 26.2 - - + +
156D ILE* 2.9 43.3 + - + +
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Residues in contact with MET 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 5.9 4.9 - - + -
113D PHE* 4.0 26.2 - - + -
115D LEU* 3.9 31.9 - - + -
119D GLU* 6.2 0.4 - - - -
123D ILE* 5.3 11.0 - - + -
129D ALA* 3.7 12.1 - - + +
134D LEU* 3.5 41.1 - - + -
141D CYS* 5.7 2.9 - - - -
145D PHE* 5.4 6.1 - - + -
149D THR* 3.3 26.2 - - - +
150D ILE* 3.7 6.7 - - + +
151D GLU 3.0 0.6 + - - -
152D GLU* 1.3 78.1 - - - +
154D LEU* 1.3 56.8 + - - +
156D ILE* 4.1 4.9 - - - +
157D ILE* 2.8 32.9 + - - +
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Residues in contact with LEU 154 (chain D).
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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128D PRO 5.2 0.2 - - - +
129D ALA 3.1 26.5 - - - +
130D ASN* 3.5 25.6 - - + -
131D MET 4.1 7.2 - - - +
150D ILE 3.1 27.8 - - - +
151D GLU* 2.8 24.0 + - + +
153D MET* 1.3 68.5 - - - +
155D GLU* 1.3 60.1 + - - +
157D ILE* 3.1 7.5 - - + +
158D SER* 2.9 29.3 + - - -
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Residues in contact with GLU 155 (chain D).
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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109D LYS* 4.9 5.6 - - - +
151D GLU* 3.5 19.9 + - - +
152D GLU* 3.1 42.9 - - - +
154D LEU* 1.3 79.1 - - - +
156D ILE* 1.3 64.8 + - + +
158D SER* 2.4 23.7 + - - +
159D GLY* 3.3 6.4 + - - -
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Residues in contact with ILE 156 (chain D).
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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105D GLU 5.4 3.1 - - - +
106D LEU* 4.2 20.9 - - + +
108D THR* 5.6 2.2 - - - +
109D LYS* 3.7 36.8 - - + -
110D LEU* 3.6 36.1 - - + -
113D PHE* 5.5 1.8 - - + -
152D GLU* 2.9 28.4 + - + +
153D MET* 4.1 2.9 - - - +
155D GLU* 1.3 82.5 - - + +
157D ILE* 1.3 59.9 + - - +
158D SER 3.1 0.2 - - - -
159D GLY* 2.9 20.3 + - - -
160D TYR* 3.7 4.7 + - - +
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 5.6 10.5 - - + -
123D ILE* 3.8 23.1 - - + +
124D VAL* 5.0 7.4 - - - +
127D LEU 5.8 0.7 - - - +
128D PRO* 4.3 11.7 - - + +
129D ALA* 3.6 28.3 - - + +
153D MET 2.8 18.6 + - - +
154D LEU* 3.1 22.7 - - - +
156D ILE* 1.3 76.7 - - - +
158D SER* 1.3 54.9 + - - +
160D TYR* 3.3 8.6 + - + +
161D ALA* 2.7 55.2 + - + +
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Residues in contact with SER 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LEU 2.9 12.7 + - - -
155D GLU* 2.4 35.0 + - - +
157D ILE* 1.3 76.9 - - - +
159D GLY* 1.3 60.5 + - - +
160D TYR 4.1 0.3 - - - -
161D ALA 3.0 18.9 - - - +
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Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D SER* 5.4 4.6 - - - -
155D GLU 3.3 5.1 + - - -
156D ILE* 2.9 13.4 + - - -
158D SER* 1.3 80.8 + - - +
160D TYR* 1.3 56.3 + - - +
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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