Contacts of the helix formed by residues 171 - 196 (chain B) in PDB entry 4DJH
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 THR 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ALA* 4.2 6.7 - - - +
167B LEU 4.4 8.3 - - - +
168B ASP* 3.8 16.8 - - - +
169B PHE 3.0 3.2 + - - -
170B ARG* 1.3 81.4 - - - +
172B PRO* 1.3 77.9 - - - +
173B LEU* 2.9 7.6 + - - +
174B LYS* 3.1 33.7 + - - +
175B ALA* 3.2 10.9 + - - +
1302B OLC 5.4 0.2 + - - -
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Residues in contact with PRO 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 3.3 41.1 - - + +
92B THR* 3.9 1.1 - - - +
93B ALA 4.2 9.6 - - - +
96B ILE* 3.8 22.2 - - + +
171B THR* 1.3 86.7 - - - +
173B LEU* 1.3 56.2 + - - +
175B ALA* 3.3 6.5 + - + +
176B LYS* 2.9 37.7 + - + +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR* 2.9 8.1 + - - +
172B PRO* 1.3 76.7 - - - +
174B LYS* 1.3 74.7 + - + +
176B LYS* 2.8 33.6 + - + +
177B ILE* 3.0 33.3 + - + +
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Residues in contact with LYS 174 (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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168B ASP* 3.3 21.5 - - - +
169B PHE* 3.3 35.0 - - + +
171B THR* 3.1 13.9 + - - +
173B LEU* 1.3 84.2 - - + +
175B ALA* 1.3 57.0 + - - +
177B ILE* 3.4 17.7 + - + +
178B ILE* 3.1 32.9 + - + +
1302B OLC 3.5 10.3 - - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA* 3.8 18.8 - - - +
96B ILE* 3.1 27.4 - - + -
97B TYR* 4.1 22.4 - - + +
171B THR 3.2 10.5 + - - +
172B PRO 3.5 6.1 - - - +
173B LEU 3.0 0.8 - - - -
174B LYS* 1.3 76.1 - - - +
176B LYS* 1.3 58.4 + - - +
178B ILE* 3.3 2.4 + - - +
179B ASN* 2.9 32.6 + - - +
1302B OLC 4.5 3.9 + - - +
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.9 21.5 - - + -
172B PRO* 2.9 27.0 + - + +
173B LEU* 2.8 25.6 + - + +
175B ALA* 1.3 74.1 - - - +
177B ILE* 1.3 65.9 + - + +
179B ASN* 3.3 7.4 + - - +
180B ILE* 2.9 33.9 + - + +
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Residues in contact with ILE 177 (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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173B LEU* 3.0 37.3 + - + +
174B LYS* 3.6 20.2 - - + +
176B LYS* 1.3 76.5 - - + +
178B ILE* 1.3 65.2 + - + +
180B ILE* 3.2 14.0 + - + +
181B CYS* 3.2 29.6 + - - -
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 3.6 24.7 - - + +
151B MET* 3.8 33.0 - - + -
174B LYS* 3.1 15.3 + - + +
175B ALA 3.7 3.8 - - - +
176B LYS 3.2 0.2 - - - -
177B ILE* 1.3 78.0 - - + +
179B ASN* 1.3 66.0 + - - +
181B CYS* 3.0 18.6 + - - +
182B ILE* 3.1 15.9 + - + +
1302B OLC 3.6 62.6 - - + +
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Residues in contact with ASN 179 (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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96B ILE* 2.8 41.5 + - - +
97B TYR* 3.4 21.1 - - - -
99B PHE* 5.4 2.6 - - - -
100B ASN* 3.2 36.8 + - - +
148B THR* 4.4 0.3 - - - +
175B ALA 2.9 11.9 + - - +
176B LYS* 3.4 11.3 - - - +
178B ILE* 1.3 75.6 - - - +
180B ILE* 1.3 65.0 + - + +
182B ILE* 2.9 24.0 + - - +
183B TRP* 3.2 16.2 + - + -
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Residues in contact with ILE 180 (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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176B LYS* 2.9 26.5 + - + +
177B ILE* 3.2 12.5 + - + +
179B ASN* 1.3 75.8 - - + +
181B CYS* 1.3 65.5 + - - +
183B TRP* 3.0 12.7 + - + +
184B LEU* 2.9 37.8 + - + +
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Residues in contact with CYS 181 (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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177B ILE* 3.2 24.8 + - - -
178B ILE* 3.0 11.5 + - - +
180B ILE* 1.3 78.6 - - - +
182B ILE* 1.3 53.6 + - - +
184B LEU* 2.9 13.9 + - - +
185B LEU* 2.6 36.7 + - - +
1302B OLC 3.5 29.4 - - + -
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Residues in contact with ILE 182 (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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97B TYR* 5.4 0.2 - - + -
100B ASN* 4.5 2.2 - - - +
144B THR* 3.7 28.0 - - + +
147B PHE* 3.5 52.7 - - + +
148B THR* 3.7 15.9 - - - +
151B MET* 4.2 11.9 - - + -
178B ILE* 3.1 15.7 + - + +
179B ASN* 2.9 19.8 + - - +
181B CYS* 1.3 75.3 - - - +
183B TRP* 1.3 55.3 + - - +
185B LEU* 3.6 6.0 - - - +
186B SER* 2.7 38.5 + - - +
1302B OLC 4.0 14.1 - - + +
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Residues in contact with TRP 183 (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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100B ASN* 2.8 38.1 + - - +
103B LEU* 4.0 26.0 - - + +
104B ALA* 4.8 4.9 - - + -
107B LEU* 4.0 26.7 - - + -
140B TYR* 3.5 51.4 - + + -
141B ASN 5.7 0.4 - - - -
144B THR* 3.5 27.1 - - + +
179B ASN 3.2 18.0 + - - -
180B ILE* 3.0 11.9 + - + +
182B ILE* 1.3 73.7 - - - +
184B LEU* 1.3 57.9 + - + +
186B SER* 4.3 2.2 - - - -
187B SER* 2.7 35.7 + - - -
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 2.9 30.6 + - + +
181B CYS* 2.9 16.0 + - - +
183B TRP* 1.3 76.4 - - + +
185B LEU* 1.3 66.3 + - - +
187B SER* 3.2 22.2 + - - +
188B SER* 3.9 2.3 + - - -
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Residues in contact with LEU 185 (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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147B PHE* 3.1 37.2 - - + -
181B CYS 2.6 20.5 + - - +
182B ILE* 3.6 4.3 - - - +
184B LEU* 1.3 72.9 - - - +
186B SER* 1.3 64.4 + - - +
187B SER 3.0 1.4 + - - -
188B SER* 2.9 32.1 + - - +
1302B OLC 4.9 14.1 - - + -
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Residues in contact with SER 186 (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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140B TYR* 3.7 24.6 - - - -
143B PHE* 3.4 20.7 + - - +
144B THR* 3.3 28.8 + - - -
147B PHE* 4.1 2.1 - - - -
182B ILE* 2.7 28.6 + - - +
183B TRP 3.9 1.1 - - - -
185B LEU* 1.3 73.7 - - - +
187B SER* 1.3 56.5 + - - +
188B SER 3.0 0.7 - - - -
189B VAL* 3.0 12.1 + - - +
190B GLY* 2.8 23.4 + - - -
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Residues in contact with SER 187 (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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140B TYR* 2.5 29.0 + - - -
183B TRP 2.7 17.8 + - - -
184B LEU* 3.2 21.1 - - - +
185B LEU 3.0 1.6 + - - -
186B SER* 1.3 73.8 - - - +
188B SER* 1.3 60.2 + - - +
190B GLY 3.6 0.9 - - - +
191B ILE* 2.8 47.4 + - - +
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Residues in contact with SER 188 (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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184B LEU 3.9 2.2 + - - -
185B LEU* 2.9 25.9 + - - +
186B SER 4.3 0.2 + - - -
187B SER* 1.3 79.4 - - - +
189B VAL* 1.3 68.4 + - - +
192B SER* 2.8 21.8 + - - -
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Residues in contact with VAL 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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139B TYR* 4.1 20.6 - - + +
143B PHE* 3.4 52.9 - - + -
186B SER* 3.2 14.4 - - - +
188B SER* 1.3 86.3 + - - +
190B GLY* 1.3 64.9 + - - +
191B ILE 3.4 0.4 - - - -
192B SER* 3.3 8.1 + - - +
193B ALA* 3.1 24.1 + - - +
226B MET* 5.7 10.5 - - + -
230B VAL* 5.3 4.9 - - + -
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Residues in contact with GLY 190 (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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136B SER* 3.1 27.7 - - - -
139B TYR* 4.7 1.8 - - - -
140B TYR* 3.6 31.6 - - - -
186B SER 2.8 16.4 + - - -
189B VAL* 1.3 80.7 - - - +
191B ILE* 1.3 60.0 + - - +
193B ALA* 3.4 8.1 - - - +
194B ILE* 3.4 3.3 + - - +
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Residues in contact with ILE 191 (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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140B TYR* 3.8 13.7 - - + +
187B SER* 2.8 33.9 + - - +
190B GLY* 1.3 72.3 - - - +
192B SER* 1.3 61.7 + - - +
193B ALA 3.0 1.8 - - - -
194B ILE* 2.8 32.8 + - + +
195B VAL* 2.9 21.2 + - + +
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Residues in contact with SER 192 (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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188B SER 2.8 25.8 + - - -
189B VAL* 3.3 11.6 + - - +
191B ILE* 1.3 79.7 - - - +
193B ALA* 1.3 53.1 + - - +
195B VAL* 3.1 10.5 + - - +
196B LEU* 2.6 50.3 + - - +
226B MET* 5.1 10.0 - - - +
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Residues in contact with ALA 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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132B LYS 4.2 4.0 - - - +
135B LEU* 4.3 2.7 - - + +
136B SER* 3.8 21.3 - - - +
139B TYR* 4.1 15.9 - - + -
189B VAL 3.1 21.7 + - - +
190B GLY 3.4 7.4 - - - +
192B SER* 1.3 75.9 + - - +
194B ILE* 1.3 55.8 - - - +
197B GLY* 2.6 34.0 + - - -
212B LEU* 4.1 16.1 - - + +
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Residues in contact with ILE 194 (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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132B LYS* 3.7 30.6 - - + +
133B ILE* 5.2 4.9 - - + +
136B SER* 3.7 27.8 - - - +
140B TYR* 5.6 3.6 - - + -
190B GLY 3.4 5.6 + - - +
191B ILE* 2.8 22.9 + - + +
193B ALA* 1.3 79.3 - - - +
195B VAL* 1.3 64.6 + - + +
197B GLY 3.9 3.5 + - - +
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Residues in contact with VAL 195 (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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191B ILE* 2.9 26.1 + - + +
192B SER* 3.1 12.5 + - - +
194B ILE* 1.3 85.1 - - + +
196B LEU* 1.3 71.7 + - + +
197B GLY 3.6 4.7 + - - +
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Residues in contact with LEU 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 SER* 2.6 30.2 + - - +
193B ALA 3.7 0.2 - - - -
195B VAL* 1.3 83.0 - - + +
197B GLY* 1.3 62.5 - - - +
211B SER 3.7 0.2 - - - +
212B LEU* 3.3 16.2 - - + -
213B GLN* 2.7 54.5 + - - +
214B PHE* 3.5 34.1 - - + -
215B PRO* 5.9 2.5 - - + -
226B MET* 4.5 11.0 - - + -
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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