Contacts of the strand formed by residues 179 - 189 (chain E) in PDB entry 2JG8
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 GLN 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148E SER* 3.4 4.9 - - - -
149E SER* 2.8 64.3 + - - +
151E GLY 3.0 8.5 + - - -
153E LEU* 4.5 3.2 - - - +
172E ASP* 2.9 40.1 + - - +
174E ALA* 3.8 14.9 - - + +
177E THR* 5.8 0.9 - - + -
178E PHE* 1.3 76.1 - - - +
180E VAL* 1.3 62.9 + - - +
181E THR* 4.6 6.2 - - - -
1224E CA 2.3 34.8 - - - -
165F CYS 3.5 10.2 - - - +
166F GLY* 4.5 2.5 - - - -
173F GLN* 5.8 5.4 - - - +
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Residues in contact with VAL 180 (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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178D VAL 5.7 1.0 - - - +
146E HIS* 4.4 2.5 - - + -
147E ALA 3.3 12.6 - - - +
148E SER* 4.7 2.2 - - - +
172E ASP* 4.6 3.1 - - - +
179E GLN* 1.3 78.2 - - - +
181E THR* 1.3 70.1 + - - +
164F PHE* 4.0 24.0 - - + -
165F CYS 3.6 15.4 + - - +
166F GLY* 4.6 4.1 - - - +
174F VAL 4.2 9.9 - - - +
175F ASN* 3.8 39.5 - - + +
176F SER* 3.5 23.4 + - - +
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Residues in contact with THR 181 (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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178D VAL* 3.9 11.3 - - - +
145E TYR* 4.4 12.4 + - + +
146E HIS* 3.3 5.2 - - - -
147E ALA* 2.9 42.0 + - + +
153E LEU* 4.2 22.4 - - + +
170E PHE* 5.8 1.6 - - - +
171E CYS 5.3 0.3 - - - -
172E ASP* 2.7 43.4 + - + +
179E GLN* 4.2 5.7 + - - +
180E VAL* 1.3 77.3 - - - +
182E THR* 1.3 71.9 + - - +
176F SER* 4.7 0.4 - - - -
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Residues in contact with THR 182 (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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142D GLN* 3.6 16.0 + - + +
178D VAL* 3.8 17.4 - - + +
180D SER* 3.5 30.7 - - - +
144E THR* 4.5 2.3 + - - -
145E TYR* 3.0 23.7 + - - -
146E HIS* 3.5 12.7 + - - -
170E PHE* 4.3 5.7 - - - +
181E THR* 1.3 85.7 + - - +
183E GLY* 1.3 65.4 + - - +
143F HIS* 5.1 3.1 - - + -
176F SER* 3.4 23.6 - - - +
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Residues in contact with GLY 183 (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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142D GLN* 3.9 9.0 - - - -
144E THR* 3.2 7.0 + - - -
145E TYR* 3.0 45.3 + - - +
170E PHE* 3.7 19.5 - - - -
182E THR* 1.3 79.1 + - - +
184E GLY* 1.3 58.1 + - - -
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Residues in contact with GLY 184 (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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140D THR* 6.2 0.2 - - - -
142D GLN* 3.1 19.8 + - - +
213D VAL* 3.9 5.2 - - - +
215D SER* 4.7 2.9 - - - -
142E TYR* 3.9 17.7 - - - -
143E PHE 3.1 12.1 - - - -
144E THR* 4.1 0.4 - - - -
157E LEU* 5.4 0.9 - - - -
170E PHE* 3.8 9.1 - - - -
183E GLY* 1.3 74.7 - - - -
185E MET* 1.3 74.2 + - - +
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Residues in contact with MET 185 (chain E).
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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96D SER* 3.5 28.3 - - - -
98D ILE* 4.5 2.0 - - + -
115D ILE* 3.8 17.7 - - - -
213D VAL* 3.9 13.9 - - + -
215D SER* 4.2 0.9 - - - -
142E TYR* 3.4 8.6 - - - -
143E PHE* 2.8 42.0 + - + +
157E LEU* 3.5 20.9 - - + -
167E VAL* 4.1 3.4 - - + -
168E VAL* 3.6 42.4 - - + -
184E GLY* 1.3 80.4 - - - +
186E VAL* 1.3 68.4 + - - +
187E LEU* 3.7 21.4 + - + -
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Residues in contact with VAL 186 (chain E).
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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94D ALA* 3.9 19.5 - - + -
95D PHE 3.5 20.6 - - - +
96D SER* 2.8 19.0 + - - +
115D ILE* 4.2 0.2 - - - +
116D THR* 2.7 42.2 + - + -
215D SER* 4.1 4.2 + - - -
216D GLY 4.2 10.3 - - - +
217D PHE* 4.2 12.1 - - + -
140E LEU* 4.2 6.5 - - + -
141E TYR 3.3 9.9 - - - +
142E TYR* 3.8 17.0 - - + -
185E MET* 1.3 80.4 - - - +
187E LEU* 1.3 58.8 + - - +
220E LEU* 4.4 7.6 - - + -
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Residues in contact with LEU 187 (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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115D ILE* 3.9 10.5 - - + -
116D THR* 3.6 1.6 - - - -
139E GLY 3.7 0.9 - - - +
140E LEU* 3.5 5.3 - - - -
141E TYR* 2.8 41.4 + - - +
143E PHE* 4.0 18.4 - - + -
157E LEU* 4.3 15.0 - - + -
159E ARG* 3.6 40.4 - - + +
167E VAL* 4.1 7.0 - - + -
185E MET* 3.7 22.2 + - + -
186E VAL* 1.3 76.2 - - - +
188E LYS* 1.3 61.4 + - - +
189E LEU* 3.7 12.0 + - + -
195E VAL* 3.9 31.0 - - + -
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Residues in contact with LYS 188 (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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92D ARG* 5.9 2.6 - - - +
116D THR* 3.8 13.1 + - + +
118D GLN* 3.4 27.5 + - - +
139E GLY* 3.6 9.0 - - - +
140E LEU* 4.0 17.0 - - + +
159E ARG* 3.2 23.6 + - - +
187E LEU* 1.3 70.3 - - - +
189E LEU* 1.3 66.9 + - - +
190E GLU* 4.9 12.4 - - + +
193E GLU* 4.0 2.9 - - - +
223E ASP* 4.7 19.5 - - - +
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Residues in contact with LEU 189 (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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133E PHE* 3.9 14.6 - - + -
135E CYS* 3.9 19.1 - - + -
138E PRO* 3.3 4.2 - - - +
139E GLY* 2.8 39.0 + - - +
141E TYR* 3.7 16.2 - - + -
143E PHE* 3.7 30.7 - - + -
159E ARG* 3.7 19.1 - - + -
187E LEU* 4.0 9.6 - - + -
188E LYS* 1.3 85.4 - - - +
190E GLU* 1.3 66.4 + - - +
193E GLU* 3.4 17.5 - - + +
195E VAL* 3.7 18.4 - - + -
223E ASP* 5.4 0.2 - - - +
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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