Contacts of the helix formed by residues 188 - 210 (chain B) in PDB entry 5DTM
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 ALA 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU* 2.9 16.5 + - - +
187B LYS* 1.3 76.7 - - - +
189B ASP* 1.3 63.1 + - - +
190B ILE 3.6 0.7 - - - +
191B PRO* 3.4 18.8 - - + +
192B ALA* 3.1 25.1 + - - +
220B ARG* 3.9 0.7 - - - -
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Residues in contact with ASP 189 (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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187B LYS 3.5 0.2 + - - -
188B ALA* 1.3 70.4 - - - +
190B ILE* 1.4 75.7 + - + +
192B ALA* 3.8 2.4 - - - +
193B LYS* 3.0 35.5 + - - +
220B ARG* 3.4 29.7 + - - +
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Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 3.5 55.0 - - + +
125B LEU* 4.0 4.9 - - + +
189B ASP* 1.4 88.9 - - + +
191B PRO* 1.4 71.0 - - + +
193B LYS* 3.2 7.9 + - + +
194B TYR* 3.0 38.8 + - + +
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Residues in contact with PRO 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.1 18.4 - - + +
133B PRO* 5.8 0.9 - - + -
165B GLY* 3.5 29.7 - - - +
166B VAL* 3.7 16.5 - - + +
186B GLU* 3.9 9.4 - - + +
188B ALA* 3.4 32.8 - - + +
190B ILE* 1.4 91.0 - - + +
192B ALA* 1.4 49.9 + - - +
194B TYR* 3.2 2.3 + - - +
195B ALA* 2.8 34.7 + - - +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 4.0 16.9 - - + +
188B ALA 3.1 20.1 + - - +
189B ASP 3.8 3.1 - - - +
191B PRO* 1.4 75.8 - - - +
193B LYS* 1.3 60.4 + - - +
195B ALA* 3.4 20.0 + - - +
196B GLU* 3.5 15.8 + - - +
219B GLU 5.3 0.7 - - - +
220B ARG* 4.0 37.7 - - + +
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Residues in contact with LYS 193 (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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189B ASP* 3.0 23.0 + - - +
190B ILE* 3.2 6.7 + - + +
192B ALA* 1.3 74.6 - - - +
194B TYR* 1.4 64.2 + - + +
196B GLU* 3.3 32.8 + - - +
197B THR* 3.8 7.3 + - - -
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Residues in contact with TYR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER* 3.3 28.9 - - - -
119B VAL* 3.8 25.8 - - + -
120B THR* 4.0 6.3 + - - -
121B ASP* 3.1 45.1 + - - +
124B LYS* 3.8 12.6 + - + +
125B LEU* 4.2 11.0 - - + -
166B VAL* 3.7 12.6 - - + -
190B ILE* 3.0 39.6 + - + +
191B PRO 3.7 6.5 - - - +
193B LYS* 1.4 73.9 - - + +
195B ALA* 1.4 57.8 + - - +
197B THR* 3.1 11.1 + - - +
198B MET* 2.9 30.7 + - - +
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 6.1 0.2 - - - +
165B GLY 4.2 3.4 - - - +
166B VAL* 3.5 27.5 + - - +
167B GLY 4.5 0.4 - - - +
186B GLU* 6.0 0.9 - - + -
191B PRO 2.8 16.6 + - - +
192B ALA* 3.4 15.9 - - - +
193B LYS 3.3 0.2 - - - -
194B TYR* 1.4 71.8 - - - +
196B GLU* 1.4 56.3 + - + +
198B MET* 3.5 1.3 - - - +
199B ASP* 2.9 31.4 + - - +
218B LEU* 3.6 24.0 - - + +
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Residues in contact with GLU 196 (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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192B ALA 3.6 16.0 - - - +
193B LYS* 3.3 18.6 + - - +
194B TYR 3.2 0.4 - - - -
195B ALA* 1.4 78.0 - - - +
197B THR* 1.4 59.0 + - - +
199B ASP* 3.6 8.6 - - - +
200B ARG* 3.3 40.9 + - - +
218B LEU* 6.1 1.6 - - - +
220B ARG* 6.0 2.3 - - - +
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Residues in contact with THR 197 (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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117B HIS 4.5 2.9 - - - +
118B SER* 3.6 31.0 - - - +
193B LYS 3.8 7.6 + - - -
194B TYR* 3.1 12.6 + - - -
196B GLU* 1.4 75.0 - - - +
198B MET* 1.4 55.3 + - - +
200B ARG* 3.2 32.5 + - - +
201B GLU* 2.8 44.2 + - + +
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Residues in contact with MET 198 (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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111B LEU* 4.8 3.8 - - + +
114B VAL* 3.4 19.8 - - + +
115B TYR* 3.7 24.7 - - + +
118B SER* 3.4 28.2 + - - -
119B VAL* 4.3 5.2 - - + -
166B VAL* 3.3 39.5 - - + +
168B GLN* 3.8 29.4 - - + -
171B LEU* 3.9 17.5 - - + -
194B TYR 2.9 18.0 + - - +
195B ALA 3.3 4.0 + - - +
197B THR* 1.4 74.3 - - - +
199B ASP* 1.3 57.2 + - - +
202B PHE* 2.9 33.2 + - - +
218B LEU* 5.0 0.7 - - + -
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Residues in contact with ASP 199 (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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171B LEU* 4.9 0.4 - - - -
195B ALA 2.9 19.4 + - - +
196B GLU* 3.6 9.4 - - - +
197B THR 3.2 0.2 - - - -
198B MET* 1.3 76.0 - - - +
200B ARG* 1.3 63.3 + - - +
202B PHE* 4.6 0.4 - - - -
203B ARG* 2.8 46.1 + - - +
216B TYR* 2.7 41.4 + - - +
218B LEU* 4.1 18.2 + - + +
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU* 3.3 19.7 + - - +
197B THR* 3.2 51.9 + - - +
199B ASP* 1.3 78.2 - - + +
201B GLU* 1.3 64.6 + - + +
203B ARG* 3.5 6.4 + - - +
204B LYS* 3.0 24.9 + - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 3.9 13.2 - - + +
117B HIS* 3.3 31.1 - - + +
118B SER* 3.4 23.3 - - - +
197B THR* 2.8 27.5 + - + +
200B ARG* 1.3 74.3 + - + +
202B PHE* 1.3 57.7 + - - +
204B LYS* 2.8 36.1 + - - +
205B TRP* 2.8 44.9 + - + -
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Residues in contact with PHE 202 (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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107B LEU* 4.5 4.0 - - + -
110B ILE* 4.3 11.2 - - + -
111B LEU* 4.0 23.3 - - + -
114B VAL* 3.7 11.1 - - + +
171B LEU* 3.7 43.5 - - + -
175B ALA* 4.0 5.6 - - + -
198B MET 2.9 19.6 + - - +
199B ASP 3.7 2.9 - - - +
201B GLU* 1.3 76.2 - - - +
203B ARG* 1.3 56.7 + - - +
205B TRP* 3.8 0.5 - - - +
206B MET* 2.9 67.5 + - + +
213B HIS* 3.7 27.8 - + + -
216B TYR* 3.4 29.8 - + - +
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Residues in contact with ARG 203 (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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199B ASP* 2.8 36.8 + - - +
200B ARG* 3.9 5.6 - - - +
202B PHE* 1.3 73.7 - - - +
204B LYS* 1.3 61.4 + - - +
206B MET* 4.0 1.7 - - - +
207B LYS* 3.1 30.7 + - + +
213B HIS* 3.7 32.9 + - - +
215B GLU* 5.9 2.0 - - - +
216B TYR* 3.1 51.0 + - - +
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Residues in contact with LYS 204 (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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117B HIS* 4.6 6.3 - - - -
200B ARG 3.0 18.4 + - - +
201B GLU* 2.8 38.5 + - - +
203B ARG* 1.3 77.1 - - - +
205B TRP* 1.3 88.3 + - - +
207B LYS* 3.3 7.9 + - - +
208B TRP* 2.9 27.6 + - + +
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Residues in contact with TRP 205 (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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9B LEU* 5.8 0.2 - - + -
18B ALA* 3.5 24.2 - - + -
20B TYR* 3.4 17.9 - + - -
40B THR* 4.8 2.5 - - + -
110B ILE* 4.6 5.2 - - + -
113B GLN* 3.3 36.3 - - + +
114B VAL* 4.2 19.7 - - + -
117B HIS* 3.9 23.3 + + - -
201B GLU* 2.8 52.7 + - + +
202B PHE 4.1 2.0 - - - +
204B LYS* 1.3 85.9 - - - +
206B MET* 1.3 59.7 + - - +
208B TRP* 3.0 37.2 + + + +
209B TYR* 3.0 58.8 + + + -
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Residues in contact with MET 206 (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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102B PRO* 3.9 13.5 - - + -
107B LEU* 5.1 0.4 - - - -
110B ILE* 3.8 28.5 - - + -
175B ALA* 4.2 2.0 - - + -
202B PHE* 2.9 58.5 + - + +
203B ARG 4.0 2.9 - - - +
205B TRP* 1.3 72.1 - - - +
207B LYS* 1.3 55.4 + - + +
209B TYR* 3.4 2.8 + - - -
210B GLY 2.9 8.3 + - - -
211B LYS* 2.8 52.9 + - + +
212B LYS 3.3 28.0 - - - +
213B HIS* 3.8 25.1 - - + -
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Residues in contact with LYS 207 (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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13B VAL* 3.3 15.2 - - - +
15B ALA* 3.9 11.5 - - + +
203B ARG* 3.1 21.4 + - + +
204B LYS* 3.5 7.2 - - - +
206B MET* 1.3 73.9 - - + +
208B TRP* 1.4 64.0 + - - +
210B GLY* 3.1 11.7 + - - +
211B LYS 5.2 1.1 - - - -
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Residues in contact with TRP 208 (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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9B LEU* 3.3 33.0 + - + -
10B LYS 3.2 18.4 - - - -
11B SER* 2.6 38.2 + - - +
12B PRO* 3.3 14.2 - - + +
13B VAL* 3.7 1.2 - - - +
15B ALA* 4.0 5.8 - - + +
16B GLU 3.2 23.1 - - - -
17B PRO 4.3 0.4 - - - -
18B ALA* 3.3 18.8 - - + +
40B THR* 3.6 23.3 - - + -
44B VAL* 3.9 7.0 - - + -
78B TYR* 3.5 19.5 - + - -
204B LYS* 2.9 16.0 + - + +
205B TRP* 3.0 29.3 + + + +
207B LYS* 1.4 75.6 - - - +
209B TYR* 1.4 92.5 + + - +
210B GLY 3.5 0.2 + - - -
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO* 4.2 9.8 - - + +
13B VAL* 4.1 8.5 - - - +
40B THR* 3.4 11.7 - - + +
44B VAL* 4.0 17.3 - - + -
106B LEU* 3.8 25.6 - - + -
109B HIS* 2.9 23.7 + + - -
110B ILE* 3.6 26.0 - - + -
113B GLN* 2.7 29.5 + - - -
205B TRP* 3.0 40.3 + + + +
206B MET 4.0 1.6 - - - +
208B TRP* 1.4 97.7 - + - +
210B GLY* 1.3 60.2 + - - +
211B LYS* 3.8 28.8 - - + -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.7 20.8 - - - +
99B ASN* 3.3 27.5 - - - +
100B THR 4.0 1.9 + - - -
206B MET 2.9 5.0 + - - -
207B LYS* 3.1 14.2 + - - -
209B TYR* 1.3 79.5 - - - +
211B LYS* 1.3 64.2 + - - +
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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
------------------------------------------------------------
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