Contacts of the helix formed by residues 142 - 152 (chain A) in PDB entry 4JU5
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LEU 3.5 2.8 - - - -
141A PRO* 1.3 87.3 - - + +
143A GLY* 1.3 63.9 + - - +
144A ALA* 3.7 10.8 - - - +
145A ALA* 2.9 35.3 + - - +
146A ALA* 3.4 14.9 + - - +
189A ASN* 3.9 6.3 - - - +
192A VAL* 3.6 11.4 - - - +
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Residues in contact with GLY 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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142A ASP* 1.3 74.3 - - - +
144A ALA* 1.3 57.2 + - - +
146A ALA* 3.4 4.0 + - - +
147A GLU* 3.1 36.7 + - - +
189A ASN* 5.0 0.2 - - - +
191A ASP* 6.0 2.0 - - - +
192A VAL* 3.8 9.8 - - - +
195A LYS* 3.9 25.1 - - - -
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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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142A ASP* 3.2 13.1 - - + +
143A GLY* 1.3 75.2 - - - +
145A ALA* 1.3 64.6 + - - +
147A GLU* 3.5 8.2 + - - +
148A SER* 3.1 26.9 + - - -
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Residues in contact with ALA 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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139A THR 5.1 1.1 - - - +
140A LEU* 3.8 17.5 - - + +
141A PRO* 4.2 15.9 - - + -
142A ASP* 2.9 21.7 + - - +
144A ALA* 1.3 73.6 - - - +
146A ALA* 1.3 65.4 + - - +
148A SER* 3.4 8.1 + - - -
149A LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 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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140A LEU* 4.0 21.0 - - + +
142A ASP 3.4 10.2 + - - +
143A GLY 3.5 8.5 - - - +
144A ALA 3.3 0.8 - - - -
145A ALA* 1.3 78.0 - - - +
147A GLU* 1.3 63.2 + - - +
149A LEU* 3.1 5.4 + - - +
150A VAL* 2.9 25.1 + - - +
158A ILE* 4.3 4.2 - - + +
192A VAL* 4.1 12.3 - - + -
196A TYR* 3.4 30.3 - - + +
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Residues in contact with GLU 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 GLY 3.1 17.9 + - - +
144A ALA* 4.0 6.5 - - - +
145A ALA 3.4 0.2 - - - -
146A ALA* 1.3 74.9 - - - +
148A SER* 1.3 57.8 + - - +
150A VAL* 3.2 5.6 + - - +
151A GLU* 2.8 39.4 + - + +
195A LYS* 3.2 33.1 + - - +
196A TYR* 3.7 7.2 - - - +
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Residues in contact with SER 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 3.1 15.9 + - - -
145A ALA* 3.5 12.5 - - - -
147A GLU* 1.3 76.0 - - - +
149A LEU* 1.3 57.1 + - - +
151A GLU* 3.4 5.6 + - - +
152A SER* 3.0 29.6 + - - -
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Residues in contact with LEU 149 (chain A).
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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138A THR* 4.7 10.3 - - + +
140A LEU* 4.2 17.3 - - + -
145A ALA 3.0 13.5 + - - +
146A ALA* 3.1 7.4 + - - +
148A SER* 1.3 74.8 - - - +
150A VAL* 1.3 66.5 + - - +
152A SER* 3.2 18.8 + - - -
153A SER 4.1 1.4 + - - -
156A ALA* 3.7 23.6 - - + +
157A VAL 4.2 8.5 - - - +
158A ILE* 4.0 24.9 - - + -
183A PRO* 3.8 29.9 - - + +
184A PHE 4.6 5.8 - - - +
185A GLY* 4.2 8.3 - - - +
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Residues in contact with VAL 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 ALA 2.9 17.7 + - - +
147A GLU* 3.2 8.9 + - - +
149A LEU* 1.3 75.7 - - + +
151A GLU* 1.3 68.8 + - + +
152A SER 3.4 0.9 + - - -
153A SER 3.4 16.1 + - - +
156A ALA* 3.9 11.8 + - - +
158A ILE* 3.9 15.5 - - + -
196A TYR* 4.1 11.0 - - + +
206A PHE* 3.8 50.4 - - + +
208A LYS* 4.2 4.3 - - + +
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Residues in contact with GLU 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 GLU* 2.8 22.5 + - + +
148A SER* 3.6 6.1 - - - +
150A VAL* 1.3 83.5 - - + +
152A SER* 1.3 57.9 + - - +
153A SER 3.3 0.7 - - - -
208A LYS* 2.7 44.2 + - - +
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Residues in contact with SER 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 SER 3.0 16.1 + - - -
149A LEU* 3.2 18.4 + - - -
151A GLU* 1.3 77.8 - - - +
153A SER* 1.3 60.0 + - - +
183A PRO* 5.2 4.1 - - - +
208A LYS* 4.7 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