Contacts of the helix formed by residues 134 - 156 (chain F) in PDB entry 5JRE
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 134 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F GLU* 2.9 50.8 + - - +
130F LEU* 4.1 4.1 + - - -
132F LYS* 3.4 5.8 - - + +
133F GLY* 1.3 73.8 - - - +
135F ILE* 1.3 59.9 + - - +
136F GLU* 3.5 10.2 + - - +
137F TYR* 3.3 34.2 + - - +
138F ALA* 3.9 3.3 + - - +
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Residues in contact with ILE 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F LEU* 4.7 10.7 - - + +
133F GLY 3.3 6.3 + - - +
134F ASN* 1.3 73.1 - - - +
136F GLU* 1.3 75.8 + - + +
138F ALA* 3.1 8.7 + - + +
139F LYS* 3.0 49.7 + - + +
180F ILE* 3.7 20.9 - - + +
183F LYS* 3.4 61.7 - - + +
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Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F ASN* 3.3 8.4 + - - +
135F ILE* 1.3 86.9 - - + +
137F TYR* 1.3 62.6 + - - +
139F LYS* 3.4 26.2 + - - +
140F LYS* 3.0 25.1 + - - +
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Residues in contact with TYR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F TYR* 3.6 24.8 - + - -
93F ILE* 4.0 12.1 - - + +
122F ILE 5.1 0.7 - - - -
125F LYS* 3.3 44.1 - - + +
126F SER* 4.0 21.1 - - - -
129F GLU* 3.6 22.2 - - + -
134F ASN* 3.3 29.4 + - - +
135F ILE 3.2 0.2 - - - -
136F GLU* 1.3 77.1 - - - +
138F ALA* 1.3 59.1 + - - +
140F LYS* 3.3 14.5 + - + +
141F ALA* 2.9 28.0 + - + +
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F SER* 4.4 17.3 - - - +
130F LEU* 5.3 10.8 - - + -
134F ASN 3.9 3.8 + - - +
135F ILE* 3.1 15.4 + - + +
137F TYR* 1.3 77.0 - - - +
139F LYS* 1.3 59.8 + - - +
141F ALA* 3.3 8.9 + - - +
142F LYS* 2.9 27.9 + - - +
176F LEU* 3.8 19.4 - - + +
180F ILE* 3.7 15.9 - - + +
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Residues in contact with LYS 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 6.4 2.7 - - - -
135F ILE* 3.0 37.3 + - + +
136F GLU* 3.7 31.2 + - - +
138F ALA* 1.3 72.9 - - - +
140F LYS* 1.3 66.0 + - - +
142F LYS* 3.4 4.8 + - - +
143F GLN* 3.3 26.7 + - - +
180F ILE* 4.0 35.0 - - + -
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Residues in contact with LYS 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F TYR* 4.2 4.8 + - - +
96F ASN* 2.6 39.8 + - - +
136F GLU* 3.0 16.1 + - - +
137F TYR* 3.6 16.4 - - + +
139F LYS* 1.3 75.7 - - - +
141F ALA* 1.3 66.2 + - - +
143F GLN* 3.2 9.8 + - + +
144F ASP* 2.8 55.5 + - - +
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Residues in contact with ALA 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F TYR* 3.6 15.7 + - - +
122F ILE* 3.9 15.7 - - + -
126F SER* 3.2 26.5 - - - +
137F TYR* 2.9 19.4 + - + +
138F ALA 3.3 5.1 + - - +
140F LYS* 1.3 75.1 - - - +
142F LYS* 1.3 57.7 + - - +
144F ASP* 3.3 1.6 + - - +
145F LEU* 2.8 35.0 + - - +
176F LEU* 3.9 5.6 - - + -
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Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 5.6 6.8 - - - +
131A ILE* 4.2 19.8 - - + +
138F ALA 2.9 13.4 + - - +
139F LYS* 3.5 10.8 - - - +
140F LYS 3.2 0.2 - - - -
141F ALA* 1.3 75.9 - - - +
143F GLN* 1.3 61.7 + - + +
145F LEU* 3.3 4.2 + - - +
146F GLU* 2.7 65.9 + - - +
173F ILE* 4.6 7.7 - - + +
176F LEU* 3.5 17.6 - - + +
177F ILE* 3.4 36.1 - - + -
180F ILE* 4.1 15.5 - - + -
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Residues in contact with GLN 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LYS 3.3 15.4 + - - +
140F LYS* 3.2 10.4 + - + +
142F LYS* 1.3 80.9 - - + +
144F ASP* 1.3 61.9 + - - +
146F GLU* 3.3 15.9 + - - +
147F SER* 3.0 31.6 + - - -
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Residues in contact with ASP 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.4 34.3 - - + +
92F TYR* 2.6 36.5 + - + +
96F ASN* 5.0 1.1 - - - -
122F ILE* 5.9 0.7 - - + -
140F LYS* 2.8 42.7 + - - +
141F ALA 3.6 3.8 - - - +
143F GLN* 1.3 76.8 - - - +
145F LEU* 1.3 62.5 + - + +
147F SER* 3.3 5.4 + - - -
148F LEU* 3.0 24.1 + - - +
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Residues in contact with LEU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 6.1 0.4 - - + -
119F ALA* 3.8 29.4 - - + +
122F ILE* 3.9 33.0 - - + -
123F LEU 5.1 0.4 - - - +
141F ALA 2.8 19.0 + - - +
142F LYS 3.9 1.8 - - - +
144F ASP* 1.3 73.0 - - - +
146F GLU* 1.3 59.0 + - - +
148F LEU* 3.5 17.0 - - + +
149F TYR* 2.9 28.8 + - - +
169F VAL* 4.0 4.3 - - + +
172F ILE* 3.7 29.2 - - + -
173F ILE* 3.7 21.4 - - + +
176F LEU* 4.0 22.0 - - + -
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Residues in contact with GLU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.8 31.3 + - + +
124A ARG* 4.3 12.8 + - - +
142F LYS* 2.7 56.6 + - - +
143F GLN* 3.5 17.1 - - - +
144F ASP 3.2 0.2 - - - -
145F LEU* 1.3 74.0 - - - +
147F SER* 1.3 63.6 + - - +
149F TYR* 3.3 5.0 + - - +
150F LEU* 3.0 29.5 + - - +
173F ILE* 4.0 22.0 - - + +
177F ILE* 4.9 0.2 - - - +
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Residues in contact with SER 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1E GLY* 3.3 35.8 + - - +
0E SER 4.3 0.2 - - - -
1E MET* 3.6 15.3 - - - -
143F GLN 3.0 16.1 + - - -
144F ASP* 3.5 10.7 + - - -
146F GLU* 1.3 76.6 - - - +
148F LEU* 1.3 56.2 + - - +
150F LEU* 3.3 8.0 + - - +
151F ASP* 2.9 35.5 + - - +
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.9 14.5 - - + +
2E LEU* 3.7 35.7 - - + -
115F ILE* 4.0 17.3 - - + +
118F ILE* 3.8 33.9 - - + -
119F ALA* 5.1 1.1 - - + -
144F ASP 3.0 14.0 + - - +
145F LEU* 3.5 23.6 - - + +
147F SER* 1.3 75.0 - - - +
149F TYR* 1.3 58.3 + - - +
151F ASP* 3.2 5.6 + - - +
152F LEU* 2.9 39.9 + - + +
169F VAL* 4.7 14.6 - - + -
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Residues in contact with TYR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.7 31.0 - - + +
38A TYR* 4.4 26.9 - + + -
124A ARG* 6.0 2.7 - - - -
145F LEU 2.9 17.6 + - - +
146F GLU* 3.4 6.7 - - - +
147F SER 3.2 0.2 - - - -
148F LEU* 1.3 76.3 - - - +
150F LEU* 1.3 58.1 + - - +
152F LEU* 3.3 7.3 + - - +
153F LEU* 2.9 53.8 + - + +
166F LEU* 3.5 40.1 - - + +
167F ASP* 5.5 0.2 - - - -
169F VAL* 4.0 17.3 - - + -
170F SER* 3.8 21.3 + - - -
173F ILE* 4.2 9.2 - - + -
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER* 6.1 1.8 - - - +
38A TYR* 3.5 58.1 - - + +
-1E GLY 5.4 4.3 - - - +
146F GLU 3.0 16.5 + - - +
147F SER* 3.6 10.1 - - - +
149F TYR* 1.3 74.3 - - + +
151F ASP* 1.3 61.5 + - - +
153F LEU* 3.4 18.2 + - + +
154F TYR* 2.9 29.9 + - - +
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Residues in contact with ASP 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1E GLY 4.4 1.7 - - - +
0E SER* 3.4 20.5 + - - -
1E MET* 2.7 33.0 + - - +
2E LEU* 2.9 29.7 + - + -
5E LEU* 3.6 22.3 - - + +
147F SER 2.9 16.5 + - - +
148F LEU 3.2 8.3 + - - +
150F LEU* 1.3 76.9 - - - +
152F LEU* 1.3 62.0 + - - +
154F TYR* 3.2 12.9 + - - +
155F ILE* 3.2 18.1 + - - +
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Residues in contact with LEU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 4.2 10.5 - - + -
112F LEU* 4.6 13.7 - - + +
115F ILE* 4.7 8.5 - - + -
116F GLY* 5.0 12.8 - - - +
148F LEU* 2.9 38.3 + - + +
149F TYR* 3.7 2.0 - - - +
151F ASP* 1.3 72.7 - - - +
153F LEU* 1.3 66.9 + - - +
155F ILE* 3.3 33.1 + - + +
156F GLU 3.8 2.9 + - - -
157F LEU* 3.8 25.4 + - + +
165F LYS* 5.5 0.4 - - + -
166F LEU* 3.5 27.1 - - + +
169F VAL* 4.3 20.0 - - + -
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Residues in contact with LEU 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS* 3.5 44.2 - - + +
34A LYS* 3.7 47.8 - - + +
35A SER* 4.3 8.5 - - - +
38A TYR* 5.2 0.2 - - + -
149F TYR* 2.9 47.9 + - + +
150F LEU* 3.5 21.1 - - + +
152F LEU* 1.3 76.0 - - - +
154F TYR* 1.3 61.4 + - - +
156F GLU* 3.1 12.1 + - - -
157F LEU 4.9 0.2 + - - -
166F LEU* 3.6 15.4 - - + +
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Residues in contact with TYR 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS* 4.6 9.1 - - - +
5E LEU* 3.6 34.5 - - + -
6E ASP* 2.4 30.5 + - - -
9E LYS* 3.0 62.6 + - + +
150F LEU 2.9 14.1 + - - +
151F ASP* 3.2 10.3 + - - +
153F LEU* 1.3 75.7 - - - +
155F ILE* 1.3 60.8 + - - +
156F GLU* 3.2 3.8 + - - +
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Residues in contact with ILE 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 4.1 11.7 - - + -
5E LEU* 4.0 12.1 - - + -
8E LEU* 3.9 25.8 - - + -
9E LYS* 3.8 27.5 - - + +
12E TYR* 3.6 33.7 - - + -
13E GLN* 2.9 22.5 + - - -
112F LEU* 4.0 15.5 - - + -
151F ASP 3.2 15.5 + - - +
152F LEU* 3.5 16.4 - - + +
153F LEU 3.2 0.6 - - - -
154F TYR* 1.3 75.0 - - - +
156F GLU* 1.3 57.8 + - - +
157F LEU* 3.8 13.5 - - + -
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Residues in contact with GLU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 5.7 0.7 - - - -
28A ARG* 6.4 2.7 - - + -
31A LYS* 4.6 21.5 - - + -
9E LYS* 3.5 18.4 - - - +
12E TYR* 3.7 0.2 - - - -
13E GLN* 2.8 22.7 + - - +
152F LEU 3.8 0.6 + - - -
153F LEU 3.1 14.0 + - - +
154F TYR 3.2 16.8 - - - +
155F ILE* 1.3 78.3 - - - +
157F LEU* 1.3 66.9 + - - +
158F LYS* 3.5 11.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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