Contacts of the helix formed by residues 146 - 157 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ASN 3.0 27.7 + - - -
123B ALA* 3.7 0.6 - - - +
124B THR* 2.9 47.9 + - + +
141B LEU* 5.5 2.8 - - - +
142B SER 5.1 1.3 - - - +
145B THR* 1.3 80.1 - - - +
147B GLN* 1.3 61.5 + - - +
148B ARG* 3.9 5.1 - - - +
149B GLY 2.9 18.7 + - - -
150B ALA* 3.5 18.4 + - - +
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Residues in contact with GLN 147 (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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146B ASN* 1.3 73.9 - - - +
148B ARG* 1.3 64.8 + - - +
149B GLY 3.0 4.7 + - - -
150B ALA* 3.3 3.7 + - - +
151B GLU* 2.7 63.3 + - - +
164B THR* 4.8 17.0 + - - +
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Residues in contact with ARG 148 (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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120B ASP* 3.8 20.6 - - + +
122B ASN* 3.7 22.7 - - + +
123B ALA* 3.5 19.9 - - + +
146B ASN* 3.6 3.2 + - - +
147B GLN* 1.3 78.6 - - - +
149B GLY* 1.3 55.8 + - - +
151B GLU* 4.0 13.7 - - - +
152B ILE* 3.1 27.5 + - + +
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Residues in contact with GLY 149 (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 MET* 3.8 16.3 - - - +
123B ALA* 3.8 10.7 - - - +
124B THR 3.7 10.3 - - - -
125B LEU* 3.9 7.5 - - - +
146B ASN* 2.9 18.3 + - - -
148B ARG* 1.3 75.4 - - - +
150B ALA* 1.3 60.0 + - - +
151B GLU 3.2 0.2 - - - -
152B ILE* 3.0 17.9 + - - +
153B LEU* 3.1 10.9 + - - +
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Residues in contact with ALA 150 (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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125B LEU* 3.7 11.4 - - + +
139B VAL* 3.8 25.8 - - + -
145B THR* 4.6 0.2 - - + -
146B ASN 3.5 17.4 + - - +
147B GLN* 3.3 7.1 + - - +
149B GLY* 1.3 70.9 - - - +
151B GLU* 1.3 63.9 + - + +
153B LEU* 3.4 10.2 - - - +
154B ALA* 3.3 17.2 + - - +
162B VAL* 4.7 6.4 - - + +
164B THR* 4.1 20.4 - - + -
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Residues in contact with GLU 151 (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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147B GLN* 2.7 59.8 + - - +
148B ARG* 4.0 11.8 - - - +
150B ALA* 1.3 71.9 - - + +
152B ILE* 1.3 58.7 - - - +
153B LEU 3.0 4.9 - - - -
154B ALA* 3.0 27.3 + - - +
155B ASP* 3.2 8.3 + - - +
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Residues in contact with ILE 152 (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 LEU* 4.7 1.2 - - - +
116B VAL* 5.2 0.2 - - - +
118B MET* 4.1 23.6 - - + -
120B ASP* 6.1 2.0 - - + -
123B ALA* 5.0 2.5 - - + -
148B ARG* 3.1 20.5 + - + +
149B GLY* 3.0 10.1 + - - +
151B GLU* 1.3 76.2 - - - +
153B LEU* 1.3 59.7 + - - +
155B ASP* 3.8 7.8 + - - +
156B THR* 3.0 23.0 + - - -
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Residues in contact with LEU 153 (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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81B VAL* 4.6 4.7 - - + -
88B LEU* 3.4 34.1 - - + +
125B LEU* 4.3 12.1 - - + -
130B VAL* 4.1 27.1 - - + -
137B PHE* 4.4 18.6 - - + -
139B VAL* 4.4 6.1 - - + -
149B GLY 3.1 9.1 + - - +
150B ALA* 3.4 10.8 - - - +
152B ILE* 1.3 76.9 - - - +
154B ALA* 1.3 53.9 + - - +
156B THR* 2.7 24.6 + - - -
157B PHE* 2.8 40.3 + - + -
162B VAL* 4.4 21.1 - - + -
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Residues in contact with ALA 154 (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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150B ALA 3.3 9.7 + - - +
151B GLU* 3.0 15.2 + - - +
153B LEU* 1.3 83.5 - - - +
155B ASP* 1.3 60.4 + - - +
156B THR 3.2 0.5 + - - -
157B PHE* 3.7 3.1 - - - +
158B LYS* 3.4 23.6 + - - +
162B VAL* 4.9 17.5 - - + -
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Residues in contact with ASP 155 (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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151B GLU 3.2 7.6 + - - +
152B ILE* 4.0 11.0 - - - +
154B ALA* 1.3 77.7 - - - +
156B THR* 1.3 60.8 + - - +
158B LYS* 3.5 30.2 + - - +
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Residues in contact with THR 156 (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 THR* 3.8 22.6 + - + +
88B LEU* 3.7 10.3 - - + +
116B VAL* 2.8 47.4 - - + +
152B ILE 3.0 14.1 + - - -
153B LEU* 2.7 22.9 + - - -
155B ASP* 1.3 75.6 - - - +
157B PHE* 1.3 73.6 + - + +
158B LYS* 3.5 8.4 + - - +
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Residues in contact with PHE 157 (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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81B VAL* 3.8 34.5 - - + -
83B CYS* 3.5 29.2 - - + -
86B THR* 3.7 30.1 - - + -
88B LEU* 4.1 10.3 - - + -
137B PHE* 3.5 36.3 - + + -
153B LEU* 2.8 41.7 + - + +
154B ALA* 3.4 5.3 + - - +
156B THR* 1.3 81.7 - - + +
158B LYS* 1.3 64.6 + - - +
159B ASP 2.9 5.4 + - - -
160B TYR* 3.1 23.1 + + + +
162B VAL* 5.1 2.9 - - + +
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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