Contacts of the helix formed by residues 132 - 143 (chain B) in PDB entry 2O52
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 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B ARG* 4.1 10.3 - - - +
130B GLU 5.8 1.1 - - - +
131B VAL* 1.3 76.6 - - - +
133B PHE* 1.3 65.1 + - - +
134B LEU* 3.7 9.0 + - - +
135B GLU* 3.0 41.8 + - - +
136B ALA* 3.3 19.8 + - - +
149B GLU* 4.6 0.4 - - - -
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 3.8 10.3 - - - +
132B THR* 1.3 72.2 - - - +
134B LEU* 1.3 57.8 + - - +
136B ALA 3.3 1.4 + - - -
137B SER* 2.7 51.7 + - - -
147B PHE* 3.3 42.8 - + - -
148B LEU* 5.3 0.4 - - - -
149B GLU* 3.7 37.0 - - + +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B THR* 3.9 9.4 - - - +
133B PHE* 1.3 84.7 - - - +
135B GLU* 1.3 58.0 + - - +
137B SER* 3.1 6.3 + - - -
138B ARG* 2.9 41.7 + - - +
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ARG* 2.7 45.5 + - - -
96B TYR* 3.1 17.6 + - - +
130B GLU 4.2 0.2 - - - +
131B VAL* 3.5 8.6 - - + -
132B THR* 3.0 44.9 + - - +
134B LEU* 1.3 78.6 - - - +
136B ALA* 1.3 65.9 + - - +
138B ARG* 3.5 13.7 + - - +
139B PHE* 3.1 17.5 + - - +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 3.0 30.1 - - + +
96B TYR* 3.5 21.8 - - + -
118B LEU* 3.8 5.3 - - + +
131B VAL* 4.4 0.4 - - + -
132B THR 3.3 12.1 + - - +
135B GLU* 1.3 82.6 - - - +
137B SER* 1.3 57.6 + - - +
139B PHE* 3.3 2.8 + - - +
140B ALA* 2.9 28.4 + - - +
147B PHE* 3.4 17.7 - - + -
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE* 2.7 36.4 + - - -
134B LEU* 3.1 8.0 + - - -
136B ALA* 1.3 72.2 - - - +
138B ARG* 1.3 59.1 + - - +
140B ALA* 3.3 3.4 + - - +
141B GLN* 2.9 48.5 + - - +
147B PHE* 3.6 21.5 - - - +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 2.9 28.0 + - - +
135B GLU* 3.6 12.4 - - - +
137B SER* 1.3 76.3 - - - +
139B PHE* 1.3 51.1 + - - +
141B GLN* 3.2 11.7 + - - +
142B GLU* 2.7 36.9 + - - +
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Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 5.0 2.5 - - + -
96B TYR* 3.5 26.2 - + - +
99B LEU* 4.0 36.6 - - + -
100B ALA* 4.3 22.2 - - + -
103B LEU* 4.7 4.5 - - + -
118B LEU* 4.0 20.9 - - + -
135B GLU 3.1 4.5 + - - +
136B ALA 3.3 4.2 + - - +
138B ARG* 1.3 80.1 - - - +
140B ALA* 1.3 65.1 + - - +
142B GLU* 3.4 5.8 + - + +
143B ASN* 3.1 57.0 + - - -
145B LEU* 4.9 9.2 - - + -
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 4.1 8.3 - - + -
136B ALA 2.9 10.8 + - - +
137B SER 3.5 6.7 - - - +
138B ARG 3.3 0.2 - - - -
139B PHE* 1.3 80.8 - - - +
141B GLN* 1.3 56.8 + - + +
143B ASN 3.1 4.0 + - - -
144B GLU 2.9 9.7 + - - -
145B LEU* 2.9 47.1 + - + +
147B PHE* 3.5 32.5 - - + -
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B SER* 2.9 40.8 + - - +
138B ARG* 3.7 9.7 - - - +
140B ALA* 1.3 76.4 - - + +
142B GLU* 1.3 64.4 + - - +
144B GLU* 2.9 20.6 + - - +
145B LEU 4.6 5.2 - - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ARG 2.7 21.5 + - - +
139B PHE* 3.6 9.6 - - + +
141B GLN* 1.3 71.9 - - - +
143B ASN* 1.3 66.5 + - - +
144B GLU* 4.7 4.3 - - - +
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Residues in contact with ASN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.8 21.0 - - + +
107B ARG* 3.7 19.3 + - - +
139B PHE* 3.1 49.1 + - - +
140B ALA 3.1 5.1 + - - +
142B GLU* 1.3 82.0 - - - +
144B GLU* 1.3 71.0 + - - +
145B LEU* 3.4 25.3 - - + +
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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