Contacts of the helix formed by residues 168 - 189 (chain B) in PDB entry 3GNI
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 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE* 4.6 13.4 - - - -
166B GLY 4.2 0.2 + - - -
167B MET* 1.3 76.4 - - - +
169B GLU* 1.3 66.0 + - - +
170B LEU* 3.4 4.0 - - + +
171B ALA* 3.1 29.7 + - - +
172B ILE* 3.3 17.0 + - - +
348B PHE* 6.0 0.4 - - - -
393B LEU* 3.8 37.5 + - + +
394B LEU* 5.9 0.2 - - - +
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Residues in contact with GLU 169 (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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167B MET 3.8 0.6 + - - -
168B ASN* 1.3 71.8 - - - +
170B LEU* 1.3 65.6 + - - +
172B ILE* 3.2 11.7 + - + +
173B ALA* 3.1 20.4 + - - +
348B PHE* 3.2 20.6 - - + -
349B SER* 2.6 51.1 + - - -
352B PHE* 3.8 19.7 - - + -
378B PHE* 3.5 16.5 - - + -
381B GLN* 3.5 23.2 + - - +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASN* 3.4 2.3 - - + +
169B GLU* 1.3 77.2 - - - +
171B ALA* 1.3 63.3 + - - +
173B ALA* 3.2 3.3 + - - +
174B TYR* 3.2 45.9 + - + +
381B GLN* 3.8 45.1 + - + +
382B ILE* 4.7 1.8 - - + -
389B ALA* 6.3 0.9 - - + -
393B LEU* 3.9 28.9 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B MET* 4.6 11.4 - - + -
168B ASN* 3.1 30.0 + - - +
170B LEU* 1.3 79.1 - - - +
172B ILE* 1.3 56.6 + - - +
174B TYR* 3.3 4.3 + - - +
175B ILE* 2.9 39.1 + - + +
390B LEU* 4.2 14.5 - - + +
393B LEU* 3.5 19.4 - - + +
394B LEU* 5.2 4.5 - - + -
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B MET* 3.6 29.2 - - + +
168B ASN 3.3 9.2 + - - +
169B GLU* 3.2 14.6 + - - +
171B ALA* 1.3 71.9 - - - +
173B ALA* 1.3 60.2 + - - +
175B ILE* 3.9 6.2 - - - +
176B LEU* 2.8 54.8 + - + +
269B ALA* 4.9 0.9 - - - -
272B LEU* 3.7 40.8 - - + +
273B ALA* 3.7 13.0 - - + +
348B PHE* 5.1 1.3 - - + -
352B PHE* 4.2 14.8 - - + -
378B PHE* 4.2 10.3 - - + -
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU 3.1 11.8 + - - +
170B LEU 3.2 9.4 + - - +
172B ILE* 1.3 74.9 - - - +
174B TYR* 1.3 63.8 + - - +
177B GLN* 3.0 27.2 + - - +
378B PHE* 3.7 24.7 - - + +
379B PHE* 3.5 10.2 - - + -
381B GLN* 3.9 20.0 - - + +
382B ILE* 3.8 16.2 - - + -
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Residues in contact with TYR 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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170B LEU* 3.2 48.9 + - + +
171B ALA 3.3 6.0 + - - +
173B ALA* 1.3 77.4 - - - +
175B ILE* 1.3 62.4 + - - +
177B GLN* 3.8 8.7 - - - +
178B GLY* 3.5 13.2 + - - -
209B VAL* 3.8 10.7 - - + +
382B ILE* 3.5 47.6 - - + +
386B ALA* 3.4 38.9 + - + -
389B ALA* 3.5 27.5 - - + +
390B LEU* 3.9 20.0 - - + -
393B LEU* 4.1 12.3 - - + -
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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
----------------------------------------------------------
155B ALA* 4.8 4.7 - - + -
167B MET* 3.8 30.1 - - + -
171B ALA* 2.9 23.1 + - + +
172B ILE* 3.9 5.6 - - - +
174B TYR* 1.3 77.4 - - - +
176B LEU* 1.3 62.5 + - - +
178B GLY 3.3 2.8 + - - -
179B VAL* 3.3 17.8 + - - +
201B ILE* 3.8 30.1 - - + -
203B ILE* 3.9 24.0 - - + -
209B VAL* 3.5 13.3 - - + +
272B LEU* 4.1 19.7 - - + -
390B LEU* 4.0 22.2 - - + -
394B LEU* 5.3 2.0 - - + -
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Residues in contact with LEU 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 ILE* 2.8 42.1 + - + +
175B ILE* 1.3 71.9 - - + +
177B GLN* 1.3 59.7 + - - +
179B VAL* 3.8 16.1 - - + +
180B LEU* 3.0 32.4 + - - +
265B VAL* 4.2 24.4 - - + +
268B THR* 4.4 10.8 - - + -
269B ALA* 3.8 15.5 - - + +
272B LEU* 4.0 18.4 - - + -
352B PHE* 5.0 0.2 - - + -
355B PHE* 3.6 30.5 - - + -
378B PHE* 4.5 4.7 - - + -
379B PHE* 4.1 12.3 - - + -
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Residues in contact with GLN 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 ALA 3.0 18.8 + - - +
174B TYR* 3.8 10.8 - - - +
176B LEU* 1.3 77.0 - - - +
178B GLY* 1.3 57.5 + - - +
180B LEU* 3.2 2.9 + - - +
181B LYS* 2.9 53.6 + - - +
374B LEU* 3.7 21.8 + - + +
379B PHE* 3.7 21.9 + - + +
382B ILE* 4.2 35.0 - - - +
386B ALA* 5.6 3.3 - - - +
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASN* 3.3 39.9 - - - +
174B TYR 3.5 5.5 + - - -
175B ILE 3.3 8.0 + - - -
177B GLN* 1.3 75.3 - - - +
179B VAL* 1.3 64.9 + - - +
181B LYS* 3.5 3.3 + - - -
182B ALA* 3.2 17.2 + - - +
209B VAL* 4.0 11.2 - - - -
211B LEU 6.0 0.2 - - - -
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Residues in contact with VAL 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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175B ILE 3.3 14.4 + - - +
176B LEU* 3.8 17.3 - - + +
178B GLY* 1.3 74.3 - - - +
180B LEU* 1.3 58.8 + - + +
182B ALA* 3.4 7.2 + - - +
183B LEU* 3.0 39.0 + - + +
196B VAL* 3.9 26.2 - - + -
201B ILE* 3.7 39.5 - - + -
209B VAL* 4.2 3.1 - - + +
211B LEU* 4.4 17.0 - - + -
265B VAL* 4.6 6.7 - - + -
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Residues in contact with LEU 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 LEU 3.0 20.5 + - - +
177B GLN 3.2 4.4 + - - +
179B VAL* 1.3 75.3 - - + +
181B LYS* 1.3 59.2 + - - +
183B LEU* 3.3 10.9 + - + +
184B ASP* 2.9 30.0 + - - +
262B ILE* 4.3 2.0 - - + -
265B VAL* 3.8 32.3 - - + -
355B PHE* 4.3 4.9 - - + -
370B ALA* 3.7 26.9 - - + +
373B LEU* 3.7 32.1 - - + -
374B LEU* 3.7 13.6 - - + +
379B PHE* 3.7 27.8 - - + -
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Residues in contact with LYS 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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127B HIS* 3.6 16.7 + - + +
129B ASN* 3.5 23.1 - - - +
177B GLN* 2.9 47.6 + - + +
178B GLY* 3.5 2.2 + - - +
180B LEU* 1.3 74.7 - - - +
182B ALA* 1.3 62.0 + - - +
184B ASP* 3.4 5.1 - - - +
185B TYR* 3.3 16.6 + - - +
374B LEU* 4.1 21.5 - - + +
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Residues in contact with ALA 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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127B HIS* 3.8 11.1 - - - -
129B ASN* 3.6 22.7 - - + +
130B ILE* 3.8 13.6 - - + +
178B GLY 3.2 13.4 + - - +
179B VAL 3.5 8.7 - - - +
181B LYS* 1.3 76.3 - - - +
183B LEU* 1.3 56.6 + - - +
185B TYR* 3.3 4.7 + - - +
186B ILE* 2.9 34.0 + - - +
211B LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 3.0 25.1 + - + +
180B LEU* 3.7 12.3 - - + +
182B ALA* 1.3 73.6 - - - +
184B ASP* 1.3 55.8 + - - +
186B ILE* 4.3 5.4 - - + -
187B HIS* 2.8 51.4 + - + +
193B HIS* 3.8 29.6 - - + -
196B VAL* 3.9 13.9 - - + -
211B LEU* 4.0 11.9 - - + -
261B ASP* 4.0 19.5 - - + +
262B ILE* 4.6 4.3 - - + -
265B VAL* 3.5 32.1 - - + -
370B ALA* 4.3 4.5 - - + -
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Residues in contact with ASP 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 LEU 2.9 13.9 + - - +
181B LYS* 3.4 13.7 - - - +
182B ALA 3.3 0.2 - - - -
183B LEU* 1.3 76.0 - - - +
185B TYR* 1.3 56.8 + - - +
187B HIS* 3.7 3.6 - - - +
188B HIS* 2.9 62.2 + - - -
370B ALA* 4.0 9.9 + - + +
371B SER* 3.5 32.0 + - - -
374B LEU* 4.6 8.0 - - + +
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Residues in contact with TYR 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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93A GLU* 2.9 28.8 + - - -
96A LYS* 3.2 13.7 + - - -
124B LEU 3.7 0.2 + - - -
125B PHE* 3.7 29.8 - + + -
126B ASN 3.1 29.0 + - - -
127B HIS* 3.6 30.3 - + + +
130B ILE* 3.7 15.9 - - + -
181B LYS 3.3 4.4 + - - +
182B ALA 3.5 6.5 - - - +
184B ASP* 1.3 75.9 - - - +
186B ILE* 1.3 69.7 + - + +
188B HIS* 3.2 8.3 + - + +
189B MET* 3.1 46.6 + - + +
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Residues in contact with ILE 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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125B PHE* 3.7 18.2 - - + -
130B ILE* 3.8 21.5 - - + -
182B ALA 2.9 25.5 + - - +
183B LEU* 3.9 6.1 - - + +
185B TYR* 1.3 73.3 - - + +
187B HIS* 1.3 64.2 + - + +
189B MET* 3.4 13.6 + - - +
191B TYR* 3.1 48.3 + - + +
193B HIS* 4.2 19.5 - - + +
211B LEU* 4.1 25.1 - - + -
214B LEU* 4.5 4.5 - - + -
217B ASN* 4.0 16.6 - - - +
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Residues in contact with HIS 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 LEU* 2.8 42.8 + - + +
184B ASP* 3.8 4.3 - - - +
186B ILE* 1.3 73.3 - - + +
188B HIS* 1.3 66.6 + - - +
189B MET 3.1 1.3 - - - -
190B GLY* 3.1 14.2 + - - -
191B TYR 3.2 21.5 - - - +
258B ALA* 3.4 40.7 - - + +
261B ASP* 2.6 33.8 + - + +
262B ILE* 4.4 12.1 - - + +
370B ALA* 4.5 10.1 + - - +
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Residues in contact with HIS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 2.9 51.3 + - - +
185B TYR* 3.2 7.4 + - - +
187B HIS* 1.3 76.6 - - - +
189B MET* 1.3 63.7 + - + +
190B GLY* 3.2 3.7 + - - -
226B ARG* 5.8 3.1 + - - -
371B SER* 5.2 5.4 - - - -
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Residues in contact with MET 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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51A LYS* 5.8 5.6 - - - +
93A GLU* 3.9 11.4 - - - +
96A LYS* 3.3 35.9 - - - +
100A GLN* 5.5 6.6 + - - -
125B PHE* 4.0 10.1 - - + -
185B TYR* 3.1 43.4 + - + +
186B ILE 3.5 9.4 - - - +
187B HIS 3.1 0.4 - - - -
188B HIS* 1.3 80.8 - - + +
190B GLY* 1.3 61.4 + - - +
191B TYR* 3.3 24.9 - - + -
221B ILE* 4.3 10.8 - - - +
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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