Contacts of the helix formed by residues 163 - 188 (chain B) in PDB entry 1NRJ
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 PRO 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ALA 4.5 1.8 - - - +
162B ARG* 1.3 92.3 - - + +
164B PRO* 1.3 73.3 - - + +
165B SER* 4.6 6.3 - - - +
166B LYS* 3.1 30.8 + - + +
167B ILE* 3.1 19.9 + - - +
225B GLU* 5.7 0.2 - - - +
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Residues in contact with PRO 164 (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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153B CYS* 3.9 23.8 - - + -
162B ARG 3.5 3.3 - - - +
163B PRO* 1.3 85.1 - - + +
165B SER* 1.3 56.2 + - - +
167B ILE* 3.4 4.6 + - + +
168B LYS* 3.0 29.6 + - - +
223B ALA* 3.8 21.9 - - - +
224B PHE* 4.0 2.0 - - - -
225B GLU* 3.8 48.2 - - + +
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PRO* 4.6 5.5 - - - +
164B PRO* 1.3 79.1 - - - +
166B LYS* 1.3 68.6 + - - +
168B LYS* 3.5 7.2 + - - +
169B ASP* 3.0 39.9 + - - +
223B ALA* 5.4 1.5 + - - -
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 5.0 6.2 - - + +
162B ARG* 5.2 3.6 - - + -
163B PRO* 3.1 36.1 + - + +
165B SER* 1.3 82.5 + - - +
167B ILE* 1.3 59.6 + - - +
169B ASP* 3.8 11.2 - - + +
170B ALA* 2.9 30.8 + - - +
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 4.2 13.2 - - + -
118B SER* 4.0 25.8 - - - +
120B VAL 6.0 1.6 - - - +
122B PRO* 5.5 5.8 - - + -
125B LEU* 4.6 8.7 - - + +
151B ILE* 4.9 1.3 - - + -
153B CYS* 3.7 30.7 - - + -
162B ARG* 3.6 32.3 - - + +
163B PRO 3.1 8.4 + - - +
164B PRO* 3.6 6.5 - - + +
166B LYS* 1.3 74.4 - - - +
168B LYS* 1.3 64.2 + - - +
170B ALA* 3.3 6.3 + - - +
171B LEU* 2.9 41.6 + - + +
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 4.2 7.9 - - + -
164B PRO 3.0 16.7 + - - +
165B SER* 3.8 6.7 - - - +
166B LYS 3.3 0.2 - - - -
167B ILE* 1.3 78.0 - - - +
169B ASP* 1.3 67.4 + - - +
171B LEU* 3.4 8.8 + - - +
172B GLU* 3.0 20.1 + - - +
214B PHE* 3.5 41.6 - - + +
221B VAL* 3.1 34.2 + - - +
222B VAL* 4.7 1.8 - - - +
223B ALA* 4.0 23.1 - - + +
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B SER* 3.0 27.0 + - - +
166B LYS* 3.8 12.9 - - + +
168B LYS* 1.3 82.9 - - - +
170B ALA* 1.3 61.2 + - - +
172B GLU* 3.4 16.2 + - - +
173B SER* 3.1 27.2 + - - -
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Residues in contact with ALA 170 (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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122B PRO* 3.8 24.2 - - + +
123B LYS* 6.2 0.9 - - + -
125B LEU* 3.8 21.3 - - + +
166B LYS 2.9 19.2 + - - +
167B ILE 3.6 4.0 - - - +
169B ASP* 1.3 75.8 - - - +
171B LEU* 1.3 66.1 + - - +
173B SER* 3.5 6.2 + - - -
174B GLU* 3.0 24.4 + - - +
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Residues in contact with LEU 171 (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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114B PHE* 5.0 6.3 - - + -
116B VAL* 5.0 3.4 - - + -
125B LEU* 4.1 20.6 - - + -
128B THR* 3.9 26.7 - - + +
129B ALA* 4.2 17.4 - - - +
132B LEU* 4.4 18.2 - - + -
151B ILE* 4.3 22.7 - - + -
167B ILE* 2.9 34.6 + - + +
168B LYS 3.7 4.9 - - - +
170B ALA* 1.3 77.4 - - - +
172B GLU* 1.3 52.5 + - - +
174B GLU* 3.3 3.9 + - - +
175B ILE* 2.8 40.7 + - + +
214B PHE* 4.4 9.4 - - + -
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Residues in contact with GLU 172 (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 LYS* 3.0 18.1 + - - +
169B ASP* 3.6 16.2 - - - +
170B ALA 3.3 0.2 - - - -
171B LEU* 1.3 75.3 - - - +
173B SER* 1.3 63.3 + - - +
175B ILE* 3.3 3.6 + - - +
176B GLN* 3.1 21.0 + - - +
212B PHE* 3.8 31.6 - - + +
213B LYS* 3.4 26.2 + - + +
214B PHE* 2.9 45.0 + - + +
215B ALA* 4.5 1.4 + - - +
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Residues in contact with SER 173 (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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169B ASP 3.1 14.8 + - - -
170B ALA* 3.7 6.7 - - - -
172B GLU* 1.3 80.1 - - - +
174B GLU* 1.3 61.6 + - - +
176B GLN* 3.4 9.0 + - - +
177B LYS* 3.3 30.3 + - - +
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Residues in contact with GLU 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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123B LYS 5.7 1.6 - - - +
125B LEU* 4.0 10.3 + - + +
126B THR* 2.9 37.0 + - - +
129B ALA* 3.6 24.9 - - + -
170B ALA 3.0 18.4 + - - +
171B LEU* 3.9 2.0 - - - +
173B SER* 1.3 73.7 - - - +
175B ILE* 1.3 66.9 + - - +
177B LYS* 3.2 21.9 + - - +
178B VAL* 3.0 21.0 + - + +
181B ARG* 2.9 25.1 + - - -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 3.8 23.3 - - + +
132B LEU* 4.0 23.6 - - + -
133B VAL* 3.6 30.7 - - + +
136B LEU* 4.9 1.1 - - + -
171B LEU* 2.8 23.4 + - + +
172B GLU 3.3 5.1 + - - +
174B GLU* 1.3 74.8 - - - +
176B GLN* 1.3 63.2 + - - +
178B VAL* 3.2 6.7 + - - +
179B ILE* 3.1 25.0 + - + +
212B PHE* 3.6 40.2 - - + -
214B PHE* 4.0 18.2 - - + -
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Residues in contact with GLN 176 (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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172B GLU 3.1 11.9 + - - +
173B SER* 3.7 10.3 - - - +
174B GLU 3.2 0.2 - - - -
175B ILE* 1.3 77.8 - - - +
177B LYS* 1.3 63.1 + - + +
179B ILE* 3.3 10.6 + - - +
180B GLU* 3.1 43.8 + - + +
211B GLY* 3.5 13.3 - - - -
212B PHE* 2.7 42.3 + - + +
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Residues in contact with LYS 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 SER* 3.3 17.5 + - - +
174B GLU* 3.2 25.5 + - - +
176B GLN* 1.3 77.0 - - + +
178B VAL* 1.4 57.5 + - - +
180B GLU* 3.4 6.4 + - - +
181B ARG* 3.0 56.2 + - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B THR* 4.5 1.3 - - + +
129B ALA* 4.4 12.8 - - + -
130B GLU* 3.9 27.4 - - + +
133B VAL* 4.2 14.6 - - + -
174B GLU* 3.0 20.6 + - - +
175B ILE* 3.2 9.2 + - - +
177B LYS* 1.4 75.3 - - - +
179B ILE* 1.3 60.1 + - + +
181B ARG* 3.4 23.3 + - - +
182B ARG* 3.0 59.9 + - + +
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Residues in contact with ILE 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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133B VAL* 4.2 11.9 - - + -
175B ILE* 3.1 34.4 + - + +
176B GLN* 3.7 10.8 - - - +
178B VAL* 1.3 75.9 - - + +
180B GLU* 1.3 62.1 + - + +
182B ARG* 3.4 2.6 + - - +
183B LYS* 3.0 29.6 + - + +
203B LEU* 3.7 34.8 - - + +
206B LEU* 4.9 14.1 - - + +
212B PHE* 4.2 21.5 - - + -
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Residues in contact with GLU 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 GLN* 3.1 41.4 + - + +
177B LYS* 3.9 6.7 - - - +
178B VAL 3.3 0.2 - - - -
179B ILE* 1.3 74.9 - - + +
181B ARG* 1.3 65.9 + - - +
183B LYS* 3.3 7.4 + - - +
184B LYS* 3.0 24.9 + - - +
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Residues in contact with ARG 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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126B THR* 3.8 18.3 + - - +
130B GLU* 5.5 0.8 + - - -
174B GLU* 2.9 27.3 + - - -
177B LYS* 3.0 38.2 + - - +
178B VAL* 3.7 21.4 - - - +
180B GLU* 1.3 74.1 - - - +
182B ARG* 1.3 64.4 + - + +
184B LYS* 3.3 5.0 + - - +
185B SER* 3.1 24.9 + - - -
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Residues in contact with ARG 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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130B GLU* 3.8 32.1 + - - +
133B VAL* 3.9 12.3 - - - +
134B ASP* 2.9 37.9 + - - -
178B VAL* 3.0 32.4 + - + +
179B ILE* 3.9 4.7 - - - +
181B ARG* 1.3 77.4 - - + +
183B LYS* 1.3 62.0 + - - +
185B SER* 3.7 6.5 + - - -
186B LEU* 3.3 31.4 + - + +
203B LEU* 4.1 28.3 - - + +
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Residues in contact with LYS 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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179B ILE* 3.0 19.7 + - + +
180B GLU* 3.7 8.3 - - - +
181B ARG 3.2 0.2 - - - -
182B ARG* 1.3 76.1 - - - +
184B LYS* 1.3 65.3 + - - +
186B LEU* 3.3 16.2 + - - +
187B ASN* 3.2 29.8 + - - +
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Residues in contact with LYS 184 (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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180B GLU 3.0 16.2 + - - +
181B ARG* 3.9 5.6 - - - +
183B LYS* 1.3 76.4 - - + +
185B SER* 1.3 65.9 + - - +
187B ASN* 3.5 7.7 + - + +
188B GLU* 3.3 19.6 + - - +
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Residues in contact with SER 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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181B ARG 3.1 16.9 + - - -
182B ARG* 3.9 7.2 - - - -
184B LYS* 1.3 77.8 - - - +
186B LEU* 1.3 61.2 + - - +
188B GLU* 3.3 25.1 + - - +
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Residues in contact with LEU 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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182B ARG* 3.3 22.1 + - + +
183B LYS* 3.7 8.7 - - - +
184B LYS 3.3 0.4 - - - -
185B SER* 1.3 80.3 - - - +
187B ASN* 1.3 62.4 + - - +
188B GLU 4.5 2.6 - - - -
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Residues in contact with ASN 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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183B LYS* 3.2 24.7 + - - +
184B LYS* 3.8 10.5 - - - +
186B LEU* 1.3 79.2 - - - +
188B GLU* 1.3 63.2 + - - +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LYS 3.3 10.2 + - - +
185B SER* 3.3 21.5 + - - +
186B LEU 4.5 2.9 - - - -
187B ASN* 1.3 84.5 - - - +
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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