Contacts of the helix formed by residues 143 - 155 (chain A) in PDB entry 2EQB
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 THR 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TYR* 5.3 1.1 + - - -
140A ARG* 4.5 5.6 - - - +
141A VAL 5.7 0.2 - - - -
142A VAL* 1.3 82.5 - - - +
144A ALA* 1.3 65.2 + - - +
145A ASP* 3.4 11.3 + - - +
146A GLN* 2.7 58.8 + - + +
147A GLY* 3.3 4.7 + - - -
160A GLU* 4.6 1.8 - - - -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 4.6 3.9 - - - +
143A THR* 1.3 72.3 - - - +
145A ASP* 1.3 62.5 + - - +
147A GLY 3.6 0.9 + - - -
148A GLU* 2.9 39.2 + - - +
158A PHE* 3.8 6.2 - - + -
160A GLU* 3.5 35.7 + - - +
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Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 3.0 9.9 + - - +
144A ALA* 1.3 75.9 - - - +
146A GLN* 1.3 66.9 + - + +
148A GLU* 3.1 24.0 + - - +
149A ALA* 3.2 11.6 + - - +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.9 13.4 - - + -
141A VAL 4.1 4.3 + - - +
142A VAL* 3.1 25.8 - - + +
143A THR* 2.7 53.7 + - + +
145A ASP* 1.3 76.7 - - + +
147A GLY* 1.3 57.5 + - - +
149A ALA* 2.9 28.2 - - - +
150A LEU* 3.6 9.2 + - - +
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 3.5 24.0 + - - -
108A PHE* 4.0 10.4 - - - -
130A LEU* 4.2 1.2 - - - +
143A THR 3.3 6.5 + - - -
144A ALA 3.6 1.5 + - - -
145A ASP 3.3 0.4 - - - -
146A GLN* 1.3 74.9 - - - +
148A GLU* 1.3 58.1 + - - +
149A ALA 3.0 9.8 + - - -
150A LEU* 3.5 8.1 + - - +
151A ALA* 3.2 22.5 + - - +
158A PHE* 3.9 11.1 - - - -
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA* 2.9 35.8 - - - +
145A ASP* 3.1 15.3 + - - +
147A GLY* 1.3 75.0 - - - +
149A ALA* 1.3 56.5 + - - +
151A ALA* 4.0 8.3 - - - +
152A LYS* 3.2 26.6 + - - +
158A PHE* 3.3 27.5 - - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ASP 3.2 8.3 + - - +
146A GLN* 2.9 17.0 + - - +
147A GLY 3.0 0.4 - - - -
148A GLU* 1.3 76.1 - - - +
150A LEU* 1.3 58.2 + - + +
152A LYS* 2.9 8.4 + - - +
153A GLU* 2.7 45.7 + - + +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 2.9 54.1 - - + -
111A ILE* 4.3 20.2 - - + -
112A LYS* 5.1 17.3 - - + -
130A LEU* 4.6 7.4 - - + -
146A GLN 3.7 4.7 - - - +
147A GLY* 4.0 10.1 - - - +
149A ALA* 1.3 74.4 - - + +
151A ALA* 1.3 52.7 + - - +
153A GLU* 2.9 20.9 + - - +
154A LEU* 2.6 54.5 + - + +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.9 11.4 - - + +
147A GLY 3.2 15.2 + - - +
148A GLU* 4.0 6.1 - - - +
149A ALA 3.1 0.2 - - - -
150A LEU* 1.3 78.7 - - - +
152A LYS* 1.3 57.1 + - - +
154A LEU* 3.3 0.7 + - - +
155A GLY 2.8 23.2 + - - -
156A ILE* 3.0 37.5 + - - +
157A PRO 3.9 3.6 - - - +
158A PHE* 3.7 22.7 - - + -
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU 3.2 17.0 + - - +
149A ALA* 2.9 7.8 + - - +
151A ALA* 1.3 75.7 - - - +
153A GLU* 1.3 63.7 + - - +
155A GLY* 3.4 11.3 + - - +
156A ILE 4.9 0.4 - - - -
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LYS* 3.9 24.6 + - - -
149A ALA* 2.7 24.9 + - + +
150A LEU* 2.9 31.6 + - - +
152A LYS* 1.3 73.3 - - - +
154A LEU* 1.3 65.4 + - + +
155A GLY 3.4 0.2 - - - -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.9 7.9 - - + +
112A LYS* 5.3 13.9 - - + -
115A PHE* 3.3 58.6 - - + -
130A LEU* 3.6 24.2 - - + -
150A LEU* 2.6 44.2 + - + +
151A ALA 3.7 3.4 - - - +
153A GLU* 1.3 79.6 - - + +
155A GLY* 1.3 60.5 + - - +
156A ILE* 3.9 14.6 - - + +
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA 2.8 5.7 + - - -
152A LYS* 3.4 8.6 + - - -
153A GLU 3.4 3.6 - - - -
154A LEU* 1.3 79.0 - - - +
156A ILE* 1.3 63.8 + - - +
157A PRO* 4.9 0.5 - - - +
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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