Contacts of the helix formed by residues 144 - 156 (chain D) in PDB entry 2JG1
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 144 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ASN* 3.0 28.3 + - - +
143D GLN* 1.3 75.9 - - - +
145D TYR* 1.3 65.6 + - - +
146D TYR 3.4 2.2 - - - -
147D ALA* 3.0 17.2 + - + +
148D GLN* 2.8 52.1 + - - +
171D THR* 4.5 7.0 - - + -
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Residues in contact with TYR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 3.7 23.8 - - + -
58D PHE* 3.7 3.3 - + - -
114D ALA* 2.6 45.4 + - + -
117D PHE* 3.3 27.5 - + - +
118D ILE* 3.7 16.7 - - + +
137D LEU* 4.0 11.6 - - + +
141D LEU* 3.6 32.8 - - + -
142D ASN* 3.0 19.8 + - + +
143D GLN 3.3 2.0 - - - -
144D ASP* 1.3 80.4 + - - +
146D TYR* 1.3 61.9 + - - +
148D GLN* 3.3 19.9 + - - +
149D ILE* 3.1 35.8 + - + +
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Residues in contact with TYR 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 5.2 0.4 + - + -
7D LEU* 3.6 21.8 + - + +
133D ILE* 3.5 30.9 - - + +
134D SER 3.6 9.9 + - - -
135D GLY 2.7 32.9 + - - -
136D SER 3.7 7.1 + - - -
137D LEU* 3.6 25.8 - - + +
143D GLN 4.8 1.6 + - - +
144D ASP 3.4 0.8 - - - -
145D TYR* 1.3 75.0 - - - +
147D ALA* 1.3 60.3 + - - +
149D ILE* 3.2 16.7 + - + +
150D ILE* 2.9 40.7 + - + +
162D LEU* 4.5 4.7 - - + -
164D CYS* 4.4 12.8 - - + -
168D THR* 3.8 27.6 - - + -
172D VAL* 3.7 17.7 - - + -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D ASP* 3.0 25.4 + - + +
146D TYR* 1.3 77.6 - - - +
148D GLN* 1.3 54.5 + - - +
150D ILE* 3.4 4.3 + - - +
151D GLU* 2.9 31.3 + - - +
171D THR* 5.3 6.7 - - + +
172D VAL* 4.4 5.6 - - + +
175D ASN* 3.7 42.7 - - + +
177D TYR* 4.4 0.6 - - - +
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Residues in contact with GLN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 3.9 22.4 - - + +
142D ASN* 4.7 4.6 - - - +
144D ASP* 2.8 47.0 + - - +
145D TYR* 3.4 24.5 - - - +
147D ALA* 1.3 76.0 - - + +
149D ILE* 1.3 61.6 + - - +
151D GLU* 3.4 8.1 - - - +
152D ARG* 3.0 49.1 + - - +
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 3.7 21.3 - - + -
7D LEU* 4.2 4.7 - - + -
117D PHE* 4.4 9.0 - - + -
118D ILE* 4.2 15.5 - - + -
121D PHE* 3.5 28.6 - - + -
133D ILE* 3.8 21.5 - - + -
145D TYR* 3.1 39.9 + - + +
146D TYR* 3.2 21.7 + - + +
148D GLN* 1.3 75.0 - - - +
150D ILE* 1.3 63.3 + - - +
152D ARG* 3.1 19.9 + - - +
153D CYS* 3.2 12.7 + - - -
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 4.3 9.9 - - + -
146D TYR* 2.9 27.1 + - + +
147D ALA* 4.0 3.6 - - - +
149D ILE* 1.3 68.2 - - - +
151D GLU* 1.3 60.2 + - - +
153D CYS* 3.2 7.9 + - - +
154D GLN* 2.9 30.7 + - + +
160D VAL* 4.2 25.8 - - + -
162D LEU* 4.5 11.0 - - + -
172D VAL* 3.7 34.8 - - + -
177D TYR* 3.3 25.8 - - + +
178D LYS 3.5 20.2 - - - +
179D PRO* 4.1 5.8 - - + -
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Residues in contact with GLU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 2.9 14.5 + - - +
148D GLN* 3.4 15.5 - - - +
150D ILE* 1.3 76.3 - - - +
152D ARG* 1.3 73.5 + - - +
154D GLN* 3.2 3.1 + - - +
155D ASN* 2.9 48.1 + - - +
177D TYR* 3.8 50.1 + - + +
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 3.3 29.3 - - + +
121D PHE* 4.0 19.5 - - + -
122D GLU* 2.8 40.1 + - + -
125D MSE 4.0 7.2 - - + +
148D GLN* 3.0 47.4 + - - +
149D ILE* 3.1 8.4 + - - +
151D GLU* 1.3 96.4 + - - +
153D CYS* 1.3 62.5 + - - +
155D ASN* 3.6 16.0 - - - +
156D LYS* 3.6 25.6 + - - +
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Residues in contact with CYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PHE* 3.5 26.7 - - - -
125D MSE 4.0 13.0 - - - -
131D VAL* 4.0 10.5 - - - -
149D ILE* 3.2 17.2 + - - -
150D ILE* 3.2 8.1 + - - +
152D ARG* 1.3 73.6 - - - +
154D GLN* 1.3 62.4 + - + +
156D LYS* 3.1 3.5 + - - -
157D GLY 3.0 8.1 + - - -
158D VAL* 2.9 44.1 + - + +
160D VAL* 3.6 24.7 - - + -
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Residues in contact with GLN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ILE* 2.9 22.6 + - + +
151D GLU 3.6 4.5 - - - +
153D CYS* 1.3 77.5 - - + +
155D ASN* 1.3 63.0 + - - +
156D LYS 3.1 1.0 + - - -
157D GLY* 3.2 13.3 + - - +
158D VAL 5.0 1.8 - - - +
160D VAL* 6.4 0.2 - - + -
177D TYR* 4.2 23.3 - - + -
178D LYS* 2.9 37.0 + - - +
179D PRO 5.5 0.2 - - - -
180D THR* 5.3 5.1 + - - -
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Residues in contact with ASN 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D GLU* 2.9 39.3 + - - +
152D ARG* 3.6 21.6 - - - +
153D CYS 3.3 0.4 - - - -
154D GLN* 1.3 76.3 - - - +
156D LYS* 1.3 68.8 + - + +
157D GLY 3.6 0.2 - - - -
177D TYR* 4.8 9.3 - - - -
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Residues in contact with LYS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLU 5.8 0.7 - - - -
125D MSE 3.7 36.1 - - + +
126D GLU* 4.9 9.4 - - - +
152D ARG 3.6 16.1 + - - +
153D CYS 3.1 4.6 + - - +
154D GLN 3.1 0.6 - - - -
155D ASN* 1.3 86.2 - - + +
157D GLY* 1.3 64.8 + - - +
158D VAL* 3.3 12.6 + - + +
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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