Contacts of the helix formed by residues 143 - 154 (chain E) in PDB entry 3JAX
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 LYS 143 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E LYS* 4.3 0.6 - - - +
142E CYS* 1.3 69.3 - - - +
144E GLU* 1.3 58.3 + - - +
145E GLU* 2.6 48.1 + - + +
146E THR* 2.8 40.5 + - - +
147E LEU* 3.4 5.9 + - - +
175E ASN* 3.7 20.6 - - + +
176E GLY* 4.6 0.7 - - - -
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Residues in contact with GLU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E CYS 3.1 5.3 + - - -
143E LYS* 1.3 69.4 - - + +
145E GLU* 1.3 68.1 + - - +
147E LEU* 3.0 19.5 + - - +
148E LYS* 2.7 53.4 + - + +
172E ILE* 3.3 39.3 - - + +
175E ASN* 3.1 34.5 + - + +
176E GLY* 4.3 2.2 - - - +
177E LEU* 4.7 7.9 - - + +
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Residues in contact with GLU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LYS* 2.6 45.8 + - + +
144E GLU* 1.3 78.3 - - - +
146E THR* 1.3 58.3 + - - +
148E LYS* 3.9 10.6 - - - +
149E ARG* 2.9 34.0 + - + +
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Residues in contact with THR 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PHE* 5.4 1.1 - - + -
135E PHE* 3.9 32.3 - - + -
143E LYS* 2.8 27.3 + - - +
145E GLU* 1.3 76.9 - - - +
147E LEU* 1.3 62.9 + - + +
149E ARG* 4.5 15.4 + - - +
150E SER* 3.1 30.9 + - - +
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PHE* 3.5 47.3 - - + -
135E PHE* 6.1 0.4 - - + -
142E CYS* 3.5 26.7 - - + +
143E LYS 3.6 15.3 - - - +
144E GLU* 3.0 8.0 + - - +
146E THR* 1.3 84.3 - - + +
148E LYS* 1.3 65.5 + - + +
150E SER* 4.2 0.6 - - - -
151E LEU* 3.1 37.3 + - + +
177E LEU* 3.7 50.5 - - + +
179E ASP* 5.4 0.4 - - + -
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Residues in contact with LYS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLU* 2.7 54.7 + - + +
145E GLU* 3.9 10.3 - - - +
147E LEU* 1.3 76.3 - - + +
149E ARG* 1.3 65.9 + - - +
151E LEU* 3.5 5.3 + - - +
152E THR* 3.0 23.4 + - - -
163E VAL* 5.2 8.2 - - + +
167E LEU* 3.8 43.3 - - + +
172E ILE* 4.1 7.4 - - - +
177E LEU* 6.5 0.9 - - + -
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Residues in contact with ARG 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E PHE* 5.2 5.9 - - - -
145E GLU* 2.9 23.8 + - + +
146E THR* 4.3 18.1 + - - +
148E LYS* 1.3 73.4 - - - +
150E SER* 1.3 80.0 + - - +
152E THR* 4.1 1.4 - - - -
153E THR* 2.9 49.7 + - + +
154E TRP* 4.4 26.7 - - - -
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Residues in contact with SER 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A MET* 4.2 23.4 - - - +
132E PHE* 5.4 4.3 - - - -
135E PHE* 4.6 13.0 - - - -
146E THR 3.1 19.3 + - - -
147E LEU* 4.2 3.6 - - - -
149E ARG* 1.3 97.8 + - - +
151E LEU* 1.3 61.3 + - - +
152E THR 3.0 0.2 + - - -
154E TRP* 2.8 43.4 + - - +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A MET* 5.5 6.7 - - + -
825A ILE* 3.8 29.6 - - + +
826A GLN* 5.5 3.4 - - + +
829A CYS* 4.8 5.2 - - + -
132E PHE* 5.4 5.8 - - + -
147E LEU* 3.1 28.7 + - + +
148E LYS* 3.5 3.7 + - - +
150E SER* 1.3 76.3 - - - +
152E THR* 1.3 58.8 + - - +
156E GLU 4.0 4.4 - - - +
157E LYS* 3.8 4.3 - - - -
158E PHE* 3.1 64.7 + - + +
163E VAL* 4.5 18.8 - - + -
166E ALA* 5.3 6.3 - - + -
167E LEU* 6.0 3.1 - - + -
177E LEU* 6.5 0.7 - - + -
182E LYS* 5.2 12.1 - - - +
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Residues in contact with THR 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E LYS 3.0 16.4 + - - -
149E ARG* 4.2 1.8 - - - -
150E SER 3.1 0.2 - - - -
151E LEU* 1.3 79.0 - - - +
153E THR* 1.3 65.4 + - - +
157E LYS* 3.3 27.0 - - - +
158E PHE* 4.3 16.1 - - - +
159E SER 5.4 3.8 - - - +
160E GLN* 5.6 1.8 - - - +
163E VAL* 3.7 19.7 - - + +
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Residues in contact with THR 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ARG* 2.9 40.0 + - + +
152E THR* 1.3 75.3 - - - +
154E TRP* 1.3 65.6 + - + +
157E LYS* 2.6 30.3 + - - -
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Residues in contact with TRP 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A LEU* 5.4 8.5 - - + +
822A MET* 3.9 28.5 - - + +
826A GLN* 3.7 8.2 + - - -
20C ARG* 3.9 52.0 + - + -
21C THR* 5.2 7.8 - - + +
149E ARG* 4.4 25.8 - - - -
150E SER* 2.8 35.3 + - - +
152E THR 3.6 0.6 - - - -
153E THR* 1.3 79.8 - - + +
155E GLY* 1.3 65.5 + - - +
156E GLU 3.0 19.4 + - - +
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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