Contacts of the helix formed by residues 133 - 144 (chain D) in PDB entry 2IK8
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 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C LYS* 4.6 8.2 - - - +
235C ALA* 3.6 25.1 - - + +
236C GLU* 4.3 2.7 - - - +
132D ILE* 1.3 78.4 - - - +
134D HIS* 1.3 63.3 + - - +
135D GLU* 3.0 18.1 + - - +
136D THR* 2.7 34.6 + - - -
137D ARG* 3.2 17.7 + - - +
158D LYS* 4.6 11.0 - - - +
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Residues in contact with HIS 134 (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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235C ALA 2.9 20.7 + - - +
236C GLU* 3.7 13.7 - - - +
237C ASP* 4.1 6.3 + - - +
238C GLU* 3.6 31.8 - - + +
239C GLU* 5.5 8.7 - - + +
133D ASP* 1.3 72.2 - - - +
135D GLU* 1.3 54.2 + - - +
137D ARG* 3.3 34.0 + - - +
138D GLU* 2.7 53.6 + - + +
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Residues in contact with GLU 135 (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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86C ARG* 5.3 6.4 + - - -
90C ARG* 3.0 39.8 + - - -
133D ASP* 3.0 16.1 + - - +
134D HIS* 1.3 78.9 - - - +
136D THR* 1.3 58.6 + - - +
138D GLU* 3.2 7.8 + - - +
139D LEU* 2.8 31.7 + - - +
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Residues in contact with THR 136 (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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132D ILE* 3.7 17.0 - - + -
133D ASP* 2.7 24.2 + - - -
135D GLU* 1.3 72.8 - - - +
137D ARG* 1.3 56.9 + - - +
139D LEU* 3.3 9.0 + - - +
140D THR* 3.0 32.4 + - - -
154D ALA* 3.9 8.6 + - + +
155D ALA* 3.4 40.6 - - + +
158D LYS* 3.6 26.8 - - + +
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Residues in contact with ARG 137 (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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236C GLU* 2.7 31.7 + - - +
237C ASP* 4.8 2.6 - - - +
118D PHE* 4.4 0.7 - - + -
122D ILE* 3.6 37.7 - - + -
123D CYS* 4.6 2.9 - - - +
124D SER* 4.7 9.4 - - - +
129D GLU* 5.0 6.4 + - - -
132D ILE* 3.7 20.7 + - + +
133D ASP 3.2 11.9 + - - +
134D HIS* 3.4 32.4 + - - +
136D THR* 1.3 74.8 - - - +
138D GLU* 1.3 67.4 + - - +
139D LEU 3.1 0.2 + - - -
140D THR* 3.2 4.3 + - - -
141D ARG* 3.0 53.4 + - - +
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Residues in contact with GLU 138 (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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134D HIS* 2.7 38.4 + - + +
135D GLU* 3.5 6.7 - - - +
137D ARG* 1.3 74.4 + - - +
139D LEU* 1.3 57.0 + - - +
141D ARG* 3.4 20.6 + - - +
142D MET* 3.1 60.7 + - + +
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Residues in contact with LEU 139 (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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135D GLU 2.8 17.3 + - - +
136D THR* 3.6 7.6 - - - +
138D GLU* 1.3 74.9 - - - +
140D THR* 1.3 60.8 + - - +
142D MET* 3.0 15.0 + - + +
143D ASN* 2.9 44.7 + - - +
154D ALA* 3.5 31.2 - - + -
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Residues in contact with THR 140 (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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118D PHE* 3.6 24.5 - - + -
122D ILE* 4.0 8.2 - - + +
136D THR 3.0 14.8 + - - -
137D ARG* 3.2 10.4 + - - -
139D LEU* 1.3 75.1 - - - +
141D ARG* 1.3 52.1 + - - +
143D ASN* 3.1 9.2 + - - +
144D LEU* 2.7 33.1 + - - +
151D CYS* 4.2 10.3 + - - +
152D PHE* 3.8 29.4 - - + -
154D ALA* 5.6 1.0 - - - +
155D ALA* 3.6 21.3 + - - +
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Residues in contact with ARG 141 (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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118D PHE* 3.6 39.9 - - + -
123D CYS* 4.8 7.7 - - - +
124D SER* 4.8 6.1 - - - +
137D ARG* 3.0 45.8 + - - +
138D GLU* 3.4 24.1 + - - +
139D LEU 3.2 0.2 - - - -
140D THR* 1.3 73.9 - - - +
142D MET* 1.3 72.6 + - + +
144D LEU* 3.6 12.8 + - + +
145D GLN* 3.7 13.3 + - - +
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Residues in contact with MET 142 (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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138D GLU* 3.1 38.5 + - + +
139D LEU* 3.0 15.9 + - + +
141D ARG* 1.3 83.6 - - + +
143D ASN* 1.3 65.8 + - - +
145D GLN* 3.2 47.8 - - + +
146D THR* 4.6 1.4 + - - -
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Residues in contact with ASN 143 (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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139D LEU* 2.9 36.2 + - - +
140D THR* 3.1 8.0 + - - +
142D MET* 1.3 74.9 - - - +
144D LEU* 1.3 61.6 + - - +
145D GLN 3.0 6.1 + - - -
146D THR* 3.2 25.4 + - - +
147D ALA* 3.7 2.8 + - - -
150D THR* 4.0 7.4 + - - -
151D CYS* 3.0 41.9 + - - +
153D ASP 5.5 0.2 - - - +
154D ALA* 5.6 4.2 - - - +
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Residues in contact with LEU 144 (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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114D ALA* 3.2 45.1 - - + +
115D HIS* 3.5 43.0 + - + +
118D PHE* 3.4 42.2 - - + -
119D GLU* 4.8 1.1 - - - +
140D THR* 2.7 20.2 + - + +
141D ARG* 3.9 10.8 - - + +
142D MET 3.4 0.6 - - - -
143D ASN* 1.3 71.2 - - - +
145D GLN* 1.3 65.6 + - - +
146D THR 3.3 0.4 + - - -
147D ALA 3.9 6.4 + - - +
151D CYS* 3.7 8.7 - - - -
152D PHE* 5.1 0.9 - - + -
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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