Contacts of the helix formed by residues 141 - 152 (chain A) in PDB entry 2O71
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 SER 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.9 3.8 - - - -
139A GLY 3.9 1.0 + - - -
140A LEU* 1.3 75.2 - - - +
142A GLN* 1.3 65.7 + - - +
143A THR* 3.4 10.7 + - - -
144A ASP* 2.9 43.8 + - - +
145A ILE* 3.1 14.0 + - - +
170A ARG* 5.2 1.8 - - - -
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Residues in contact with GLN 142 (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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132A GLU* 5.3 4.2 - - - +
136A LEU* 3.1 38.2 - - + +
141A SER* 1.3 73.9 - - - +
143A THR* 1.3 58.6 + - - +
145A ILE* 3.3 11.0 + - - +
146A TYR* 2.8 30.2 + - - +
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Residues in contact with THR 143 (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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141A SER* 3.1 9.2 + - - -
142A GLN* 1.3 78.2 - - - +
144A ASP* 1.3 66.5 + - - +
146A TYR* 3.2 8.6 + - + +
147A ARG* 2.9 58.1 + - + +
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Residues in contact with ASP 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 LEU* 3.5 18.3 - - + +
141A SER* 2.9 33.9 + - - +
143A THR* 1.3 76.6 - - - +
145A ILE* 1.3 62.8 + - - +
147A ARG* 3.3 22.9 + - - +
148A CYS* 3.0 28.3 + - - -
166A ARG* 5.8 6.2 - - + -
170A ARG* 2.6 45.7 + - - -
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Residues in contact with ILE 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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131A TRP* 3.9 21.3 - - + -
132A GLU* 3.7 27.8 - - + +
135A VAL* 3.6 28.3 - - + -
136A LEU* 3.4 41.3 - - + +
140A LEU* 4.7 7.2 - - + -
141A SER 3.1 7.9 + - - +
142A GLN* 3.5 13.0 - - - +
144A ASP* 1.3 77.5 - - - +
146A TYR* 1.3 62.9 + - - +
148A CYS* 3.2 10.2 + - - +
149A LYS* 3.2 29.4 + - - +
163A ALA* 5.8 0.2 - - + -
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Residues in contact with TYR 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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142A GLN 2.8 17.6 + - - +
143A THR* 3.2 11.4 + - + +
145A ILE* 1.3 77.5 - - - +
147A ARG* 1.3 59.5 + - + +
149A LYS* 3.3 12.2 + - + +
150A ALA* 2.9 33.1 + - + +
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Residues in contact with ARG 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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143A THR* 2.9 40.1 + - + +
144A ASP* 3.3 23.8 + - - +
146A TYR* 1.3 77.5 - - + +
148A CYS* 1.3 59.5 + - - +
150A ALA* 3.3 6.4 + - - +
151A ASN* 2.9 46.1 + - - +
162A GLU* 5.5 0.2 - - - +
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Residues in contact with CYS 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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131A TRP* 5.0 3.4 - - + -
140A LEU* 5.4 1.1 - - - -
144A ASP* 3.0 21.1 + - - -
145A ILE* 3.2 10.9 + - - +
147A ARG* 1.3 76.4 - - - +
149A LYS* 1.3 62.7 + - - +
151A ASN 3.4 0.2 + - - -
152A HIS* 3.4 24.8 + - - -
159A GLN* 3.6 22.8 - - + +
162A GLU* 3.7 23.3 - - + +
163A ALA* 3.5 38.6 - - + -
166A ARG* 4.6 7.9 - - - -
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Residues in contact with LYS 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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131A TRP* 4.1 11.4 - - + -
132A GLU* 3.0 41.5 + - - -
145A ILE* 3.2 21.8 + - + +
146A TYR* 3.6 12.7 - - + +
147A ARG 3.2 0.2 - - - -
148A CYS* 1.3 75.0 - - - +
150A ALA* 1.3 66.1 + - - +
152A HIS 3.1 22.7 + - - +
153A PRO* 3.5 4.5 - - - +
159A GLN* 3.5 31.2 - - - +
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Residues in contact with ALA 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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146A TYR* 2.9 28.0 + - + +
147A ARG* 3.7 8.3 - - - +
149A LYS* 1.3 75.9 - - - +
151A ASN* 1.3 65.2 + - - +
153A PRO* 3.4 18.5 - - - +
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Residues in contact with ASN 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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147A ARG* 2.9 25.5 + - - +
148A CYS 3.8 0.2 - - - +
149A LYS 3.1 0.4 - - - -
150A ALA* 1.3 81.3 - - - +
152A HIS* 1.3 76.8 + - + +
153A PRO* 3.5 6.1 - - - +
162A GLU* 2.6 32.0 + - - +
166A ARG* 5.5 2.2 - - - +
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Residues in contact with HIS 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 CYS 3.4 11.9 + - - -
149A LYS 3.1 6.6 + - - -
151A ASN* 1.3 90.1 + - + +
153A PRO* 1.3 64.2 - - - +
154A HIS 3.2 4.0 + - - -
155A ASN* 3.3 25.1 + - + +
158A SER* 3.4 37.9 + - - -
159A GLN* 2.9 24.5 - - + +
162A GLU* 2.7 35.1 + - + -
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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