Contacts of the helix formed by residues 146 - 157 (chain A) in PDB entry 2JAJ
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 ASN 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASN 3.1 22.0 + - - -
123A ALA* 3.8 1.6 - - - -
124A THR* 3.0 35.6 + - - +
141A LEU* 3.5 9.1 - - - +
142A SER 5.7 0.4 - - - +
145A THR* 1.3 79.9 - - - +
147A GLN* 1.3 67.9 + - + +
148A ARG* 3.3 5.2 + - - +
149A GLY* 2.9 30.8 + - - -
150A ALA* 3.1 9.9 + - - +
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Residues in contact with GLN 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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141A LEU* 3.5 30.6 - - + +
146A ASN* 1.3 75.5 - - + +
148A ARG* 1.3 63.6 + - - +
150A ALA* 3.3 3.5 + - - +
151A GLU* 2.7 52.1 + - - +
164A THR* 4.6 6.5 + - - +
-2B LEU* 3.4 28.5 - - - +
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Residues in contact with ARG 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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120A ASP* 2.8 27.8 + - - +
122A ASN* 3.7 22.0 - - + +
123A ALA* 3.5 18.8 - - + -
146A ASN* 3.2 4.3 + - - +
147A GLN* 1.3 79.1 - - - +
149A GLY* 1.3 62.1 + - - +
151A GLU* 3.0 45.8 + - - +
152A ILE* 3.0 44.1 + - - +
155A ASP* 4.6 11.1 + - - -
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Residues in contact with GLY 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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118A MET* 3.6 27.4 - - - +
123A ALA* 3.9 4.0 - - - +
124A THR 3.5 20.6 - - - -
125A LEU* 3.7 10.1 - - - +
146A ASN* 2.9 11.1 + - - -
148A ARG* 1.3 75.0 - - - +
150A ALA* 1.3 57.0 + - - +
152A ILE* 3.2 2.1 + - - -
153A LEU 3.0 22.7 + - - -
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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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125A LEU* 4.0 9.7 - - - +
139A VAL* 3.9 18.6 - - + -
141A LEU* 4.1 3.8 - - + -
146A ASN 3.1 10.5 + - - +
147A GLN 3.5 8.1 - - - +
148A ARG 3.2 0.2 - - - -
149A GLY* 1.3 73.6 - - - +
151A GLU* 1.3 59.4 + - - +
153A LEU* 3.3 6.3 + - - +
154A ALA* 3.0 23.0 + - - +
162A VAL* 4.3 2.8 - - - +
164A THR* 3.8 18.2 - - + -
-2B LEU* 3.7 23.3 - - + +
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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 GLN* 2.7 51.7 + - - +
148A ARG* 3.0 39.2 + - - +
150A ALA* 1.3 76.2 - - - +
152A ILE* 1.3 58.0 + - - +
154A ALA* 3.1 5.6 + - - +
155A ASP* 2.9 36.2 + - - +
-2B LEU* 3.8 16.5 - - + +
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Residues in contact with ILE 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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88A LEU* 4.3 8.3 - - + -
116A VAL* 5.3 4.7 - - + -
117A GLU 5.5 0.7 - - - +
118A MET* 4.1 27.6 - - + -
119A LYS 5.6 0.2 - - - +
120A ASP* 3.6 20.2 - - + +
123A ALA* 3.6 31.6 - - + -
148A ARG* 3.0 36.7 + - - +
149A GLY 3.2 6.2 + - - +
151A GLU* 1.3 76.2 - - - +
153A LEU* 1.3 57.5 + - - +
155A ASP* 3.4 10.5 + - + +
156A THR* 2.6 41.7 + - - +
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Residues in contact with LEU 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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81A VAL* 4.4 5.8 - - + -
88A LEU* 3.8 27.5 - - + +
125A LEU* 4.1 10.3 - - + -
130A VAL* 3.7 35.4 - - + -
137A PHE* 4.0 13.7 - - + -
139A VAL* 4.5 2.9 - - + -
149A GLY 3.0 12.9 + - - +
150A ALA* 3.5 9.6 - - - +
152A ILE* 1.3 74.3 - - - +
154A ALA* 1.3 64.4 + - - +
156A THR* 3.0 2.3 + - - -
157A PHE* 3.0 46.4 + - + +
162A VAL* 3.8 26.7 - - + -
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Residues in contact with ALA 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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150A ALA 3.0 13.3 + - - +
151A GLU* 3.1 8.9 + - - +
153A LEU* 1.3 77.7 - - - +
155A ASP* 1.3 64.4 + - - +
156A THR 3.3 0.7 + - - -
157A PHE 3.5 17.0 + - - +
158A LYS* 3.8 6.1 + - - +
160A TYR 5.1 1.3 - - - +
162A VAL* 3.7 22.7 - - + -
-2B LEU* 3.9 25.4 - - + +
-1B GLY* 4.3 17.3 - - - +
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Residues in contact with ASP 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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148A ARG* 4.6 14.0 + - - -
151A GLU* 2.9 20.7 + - - +
152A ILE* 3.6 16.8 - - + +
153A LEU 3.2 0.2 - - - -
154A ALA* 1.3 78.5 - - - +
156A THR* 1.3 58.8 + - - +
158A LYS* 3.2 22.6 - - - +
-1B GLY* 5.6 3.6 - - - -
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Residues in contact with THR 156 (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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86A THR* 3.8 29.4 + - + +
88A LEU* 3.7 18.0 - - + +
116A VAL* 3.8 30.6 - - + +
152A ILE* 2.6 23.1 + - - +
153A LEU* 3.0 7.7 + - - -
155A ASP* 1.3 82.5 - - - +
157A PHE* 1.3 76.2 + - + +
158A LYS* 3.4 5.9 + - - +
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Residues in contact with PHE 157 (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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81A VAL* 3.5 42.8 - - + -
83A CYS* 3.7 27.4 - - + -
86A THR* 3.8 31.2 - - + -
88A LEU* 3.9 18.4 - - + -
137A PHE* 3.7 27.1 - + + -
153A LEU* 3.0 39.1 + - + +
154A ALA 3.6 5.9 - - - +
156A THR* 1.3 80.7 - - + +
158A LYS* 1.3 61.9 + - - +
159A ASP 3.2 3.1 - - - -
160A TYR* 3.1 27.0 + + + +
162A VAL* 4.8 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