Contacts of the helix formed by residues 141 - 160 (chain B) in PDB entry 3E2A
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 LYS 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 4.1 13.2 - - + +
138B SER* 2.8 18.0 + - - +
140B GLU* 1.3 99.9 + - + +
142B ARG* 1.3 62.3 + - - +
143B ALA 3.3 3.2 + - - -
144B ASP* 3.4 11.6 + - + +
145B MET* 3.2 19.9 + - - +
218B GLU* 3.0 35.1 + - - +
219B ASN* 3.4 31.9 + - - +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MET* 3.9 19.2 - - + +
127B TRP* 5.7 6.0 - - - +
134B LEU* 2.9 37.0 + - + +
135B GLY* 3.4 22.6 + - - -
137B LEU* 3.0 33.1 + - + -
138B SER 3.2 9.4 + - - +
139B PRO* 3.5 32.0 + - - +
141B LYS* 1.3 77.2 - - - +
143B ALA* 1.3 56.5 + - - +
145B MET* 3.3 2.8 + - - +
146B LEU* 2.8 30.1 + - - +
221B LEU* 3.6 15.0 - - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.8 5.5 - - + +
105B HIS* 3.5 37.2 - - + +
108B MET* 3.6 25.7 - - - -
139B PRO 4.7 1.6 + - - +
140B GLU 5.2 3.5 + - - +
141B LYS 3.3 0.4 - - - -
142B ARG* 1.3 78.9 - - - +
144B ASP* 1.3 58.5 + - - +
146B LEU* 3.2 2.9 + - - +
147B THR* 2.8 34.2 + - - +
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Residues in contact with ASP 144 (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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99B THR* 3.9 35.2 - - - +
100B ASN 4.0 6.1 + - - -
105B HIS* 5.7 1.4 + - - -
140B GLU 5.6 2.3 + - - +
141B LYS* 3.4 12.3 + - + +
142B ARG 3.4 0.2 - - - -
143B ALA* 1.3 80.3 - - - +
145B MET* 1.3 60.4 + - - +
147B THR* 3.5 9.0 + - - -
148B LYS* 3.3 32.3 + - + +
184B ASN* 5.9 1.0 + - - -
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.7 15.3 - - + -
134B LEU* 3.7 12.8 - - + -
137B LEU* 3.3 31.6 - - + -
141B LYS 3.2 7.1 + - - +
142B ARG 3.5 5.8 - - - +
143B ALA 3.2 0.2 - - - -
144B ASP* 1.3 73.9 - - - +
146B LEU* 1.3 64.7 + - - +
148B LYS* 3.1 24.3 + - + +
149B ILE* 2.9 31.6 + - + +
212B LEU* 4.1 34.3 - - + +
215B LEU* 4.7 6.5 - - + -
219B ASN* 4.1 22.2 - - - +
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Residues in contact with LEU 146 (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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104B ILE* 4.3 7.2 - - + -
108B MET* 3.6 37.2 - - + -
123B ILE* 3.9 26.0 - - + +
126B ILE* 3.9 26.9 - - + -
127B TRP* 4.0 28.3 - - + +
134B LEU* 4.1 15.0 - - + +
142B ARG 2.8 19.2 + - - +
143B ALA 3.6 5.2 - - - +
145B MET* 1.3 73.4 - - - +
147B THR* 1.3 53.2 + - - +
149B ILE* 4.3 5.4 - - + -
150B ASN* 2.8 36.8 + - + +
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Residues in contact with THR 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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68B ASN* 6.0 0.4 - - - +
97B GLY* 4.8 2.2 - - - -
98B HIS 3.1 40.4 + - - +
99B THR* 4.7 2.0 - - + +
101B CYS* 4.5 4.1 + - + +
104B ILE* 3.6 28.7 - - + +
143B ALA 2.8 24.6 + - - -
144B ASP* 3.6 14.6 + - - +
145B MET 3.2 0.2 - - - -
146B LEU* 1.3 75.2 - - - +
148B LYS* 1.3 61.0 + - + +
150B ASN* 3.5 4.1 + - - +
151B VAL* 3.3 24.3 + - - +
180B VAL* 4.6 9.9 - - + -
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Residues in contact with LYS 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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144B ASP* 3.3 21.3 + - + +
145B MET* 3.1 23.9 + - + +
147B THR* 1.3 75.2 - - + +
149B ILE* 1.3 65.8 + - - +
151B VAL* 3.3 6.1 + - - +
152B ALA* 3.2 19.2 + - - +
180B VAL* 4.3 15.3 - - + -
189B VAL* 6.5 0.2 - - - -
191B GLN* 3.4 34.5 - - - +
212B LEU* 3.8 27.7 - - + +
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Residues in contact with ILE 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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126B ILE* 3.7 12.6 - - + -
130B HIS* 3.2 49.8 - - + +
133B LEU* 3.8 36.1 - - + -
134B LEU* 4.5 7.9 - - + -
145B MET* 2.9 26.2 + - + +
146B LEU* 3.9 5.8 - - + +
148B LYS* 1.3 74.4 - - - +
150B ASN* 1.3 63.9 + - - +
152B ALA* 3.2 5.6 + - - +
153B GLU* 2.9 22.7 + - + +
209B ILE* 4.7 3.8 - - + -
212B LEU* 3.8 22.7 - - + -
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Residues in contact with ASN 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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67B ALA 3.1 26.7 + - - -
68B ASN* 3.3 17.8 + - - +
104B ILE* 4.1 17.0 - - + +
123B ILE* 3.1 20.7 - - + +
126B ILE* 3.8 8.0 - - + +
146B LEU* 2.8 26.0 + - + +
147B THR* 3.5 8.1 + - - +
148B LYS 3.2 0.2 - - - -
149B ILE* 1.3 72.9 - - - +
151B VAL* 1.3 64.3 + - - +
153B GLU* 3.0 7.9 + - - +
154B GLN* 2.8 53.1 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 4.0 8.7 - - - +
95B ILE* 4.2 6.7 - - + +
96B CYS 4.6 0.2 - - - -
97B GLY* 3.5 34.1 - - - +
147B THR 3.3 13.9 + - - +
148B LYS 3.3 8.6 + - - +
150B ASN* 1.3 77.9 - - - +
152B ALA* 1.3 62.9 + - - +
154B GLN* 3.3 7.9 + - - +
155B VAL* 3.1 23.6 + - + +
178B GLY* 3.4 40.6 - - - +
179B TRP 3.6 7.2 - - - +
180B VAL* 3.9 5.6 - - + -
191B GLN* 3.9 10.3 - - + -
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Residues in contact with ALA 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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148B LYS 3.2 9.3 + - - +
149B ILE* 3.2 9.5 + - - +
151B VAL* 1.3 78.9 - - - +
153B GLU* 1.3 62.3 + - - +
155B VAL* 3.3 3.6 + - - +
156B TYR* 3.1 22.2 + - - +
191B GLN* 5.1 5.4 - - + +
193B VAL* 3.7 28.5 - - + +
205B TYR* 4.0 6.5 - - + -
208B ALA* 4.7 3.8 - - + -
209B ILE* 4.0 23.1 - - + -
212B LEU* 4.9 4.0 - - + -
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Residues in contact with GLU 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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126B ILE* 3.8 37.3 - - + +
129B LYS* 2.8 25.9 + - - +
130B HIS* 2.3 33.5 + - - +
149B ILE* 2.9 17.9 + - + +
150B ASN 3.0 7.2 + - - +
152B ALA* 1.3 76.9 - - + +
154B GLN* 1.3 58.3 + - - +
156B TYR* 3.3 9.6 - - - +
157B ASN* 2.9 34.5 + - - +
205B TYR* 2.6 25.6 + - + -
209B ILE* 4.3 0.7 - - + +
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Residues in contact with GLN 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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68B ASN 3.5 19.7 - - - +
69B GLN* 3.6 17.7 + - - +
70B VAL* 2.9 28.0 + - - +
95B ILE* 3.5 19.3 - - + +
126B ILE* 3.5 20.8 - - - +
150B ASN* 2.8 48.2 + - - +
151B VAL* 3.8 3.8 - - - +
153B GLU* 1.3 73.7 - - - +
155B VAL* 1.3 62.2 + - - +
157B ASN* 3.3 19.9 + - - +
158B LEU* 2.8 29.3 + - - +
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Residues in contact with VAL 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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95B ILE* 3.5 15.2 - - + +
151B VAL 3.1 16.3 + - - +
152B ALA* 3.7 6.7 - - - +
154B GLN* 1.3 74.1 - - - +
156B TYR* 1.3 53.3 + - - +
158B LEU* 3.2 3.6 + - + +
159B GLY* 2.8 32.6 + - - -
176B LEU* 3.9 26.6 - - + +
177B HIS 3.4 22.4 - - - +
178B GLY* 3.4 15.7 - - - -
193B VAL* 3.7 33.2 - - + +
195B ALA* 5.3 0.7 - - + -
201B LEU* 3.8 6.6 - - + +
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Residues in contact with TYR 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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128A PHE* 4.8 12.0 - + - -
231A SO4 4.6 3.5 + - - -
129B LYS* 4.7 6.5 - - - -
152B ALA 3.1 13.7 + - - +
153B GLU* 3.3 17.0 - - - +
154B GLN 3.2 0.2 - - - -
155B VAL* 1.3 76.9 - - - +
157B ASN* 1.3 62.7 + - - +
159B GLY* 3.2 2.8 + - - -
160B ARG* 3.0 65.8 + - - +
193B VAL* 4.9 0.6 - - - +
198B ARG* 3.8 11.1 + - - -
201B LEU* 3.9 18.8 - - + +
202B GLU* 2.3 35.9 + - - -
205B TYR* 3.6 54.7 - + + -
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Residues in contact with ASN 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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121A LEU* 5.0 0.2 - - - +
125A ASP* 5.2 0.2 - - - +
70B VAL* 3.2 30.8 + - + +
71B ILE* 5.2 1.2 - - - +
72B HIS* 3.2 32.1 + - + +
126B ILE* 5.5 3.0 - - - +
153B GLU* 2.9 24.4 + - - +
154B GLN* 3.3 25.1 + - - +
156B TYR* 1.3 73.5 - - - +
158B LEU* 1.3 62.6 + - - +
160B ARG* 3.1 26.9 + - - +
161B THR* 3.3 15.1 + - - +
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Residues in contact with LEU 158 (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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40B ILE* 4.6 1.8 - - + -
70B VAL* 4.0 17.7 - - + +
81B VAL* 3.8 40.2 - - + -
93B ILE* 3.5 35.2 - - + +
95B ILE* 3.8 21.1 - - + -
154B GLN 2.8 19.5 + - - +
155B VAL* 3.4 5.4 - - + +
157B ASN* 1.3 71.7 - - - +
159B GLY* 1.3 61.9 + - - +
161B THR* 2.9 29.7 + - + -
164B VAL* 3.4 10.9 - - + +
176B LEU* 4.1 22.0 - - + -
177B HIS 5.7 0.4 - - - +
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Residues in contact with GLY 159 (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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155B VAL 2.8 11.3 + - - -
156B TYR 3.2 0.2 + - - -
158B LEU* 1.3 75.2 - - - +
160B ARG* 1.3 56.6 + - - +
161B THR 3.4 0.2 - - - -
164B VAL* 4.1 3.1 - - - +
165B LYS* 3.4 19.1 - - - +
168B TRP* 3.6 16.2 - - - -
176B LEU* 3.4 21.9 - - - +
198B ARG* 4.2 1.0 - - - -
201B LEU* 3.5 23.2 - - - +
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.4 40.7 + - + +
124A ARG* 4.1 1.2 - - - +
125A ASP* 2.9 29.1 + - - -
128A PHE* 4.0 10.7 - - - -
231A SO4 2.9 43.6 + - - +
72B HIS* 3.5 7.1 - - - -
129B LYS* 6.1 0.4 - - - +
156B TYR* 3.0 52.9 + - - +
157B ASN* 3.1 26.4 + - - +
159B GLY* 1.3 77.6 - - - +
161B THR* 1.3 65.1 + - - +
162B SER 3.6 1.0 + - - -
165B LYS* 4.0 17.0 - - - -
198B ARG* 4.0 11.0 - - - +
201B LEU* 4.2 3.1 - - + -
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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
------------------------------------------------------------
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