Contacts of the helix formed by residues 147 - 171 (chain B) in PDB entry 1JS6
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 SER 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PRO* 3.7 9.4 - - - +
354A GLY 5.3 2.9 - - - -
145B GLN* 3.3 3.2 - - - +
146B GLY* 1.3 79.4 - - - +
148B ALA* 1.3 61.8 + - - +
149B SER* 3.7 2.3 + - - -
150B GLU* 2.8 34.6 + - - +
151B ALA* 2.9 26.7 + - - +
302B HIS* 4.0 3.1 - - - -
309B PHE* 4.7 8.5 - - - -
312B SER* 3.5 13.0 + - - -
602B PLP 3.1 21.9 + - - -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER* 1.3 72.3 - - - +
149B SER* 1.3 58.0 + - - +
151B ALA* 3.2 1.7 + - - +
152B THR* 2.9 34.1 + - - -
194B SER* 5.1 1.3 - - - -
271B ASP* 4.7 3.1 - - - +
273B ALA* 3.9 6.1 - - + -
298B ASN* 3.4 22.6 - - - +
300B ASN* 3.3 25.5 + - - +
312B SER* 3.4 4.1 + - - -
602B PLP 2.8 31.1 + - + +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU 5.3 2.7 - - - -
352A PRO* 4.6 4.0 - - - -
353A LEU* 3.1 29.8 - - - +
147B SER* 3.1 5.5 - - - -
148B ALA* 1.3 79.1 - - - +
150B GLU* 1.3 61.8 + - - +
152B THR* 3.7 2.5 + - - -
153B LEU* 3.2 21.3 + - - +
194B SER* 3.1 35.6 - - - +
197B ARG* 5.8 1.1 - - - -
602B PLP 2.9 23.2 + - - -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 4.4 13.2 - - - +
351A LEU* 5.3 2.4 - - + +
352A PRO* 3.3 33.8 - - + +
145B GLN* 4.6 10.5 - - - +
146B GLY* 3.3 15.6 + - - +
147B SER* 2.8 37.7 + - - +
149B SER* 1.3 74.6 - - - +
151B ALA* 1.3 67.1 + - - +
153B LEU* 3.1 7.8 + - + +
154B VAL* 2.8 30.0 + - + +
309B PHE* 6.0 0.2 - - - -
351B LEU* 4.9 15.3 - - + +
352B PRO* 5.1 9.7 - - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN* 4.1 13.3 - - + +
147B SER 2.9 12.0 + - - +
148B ALA 3.5 2.7 - - - +
150B GLU* 1.3 77.1 - - - +
152B THR* 1.3 63.2 + - - +
154B VAL* 3.2 3.4 + - - +
155B ALA* 3.0 23.0 + - - +
269B HIS* 4.6 2.2 - - - -
298B ASN* 3.3 40.4 - - + +
314B MET* 3.8 23.0 - - - +
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA 2.9 17.0 + - - -
149B SER* 3.8 6.7 - - - -
151B ALA* 1.3 76.3 - - - +
153B LEU* 1.3 61.9 + - - +
155B ALA* 3.2 4.3 + - - +
156B LEU* 3.0 21.5 + - - +
194B SER* 4.3 8.5 + - - +
195B VAL* 4.4 19.0 - - + +
198B ALA* 4.1 17.3 - - + -
238B PHE* 4.0 3.9 - - + -
240B VAL* 4.4 20.2 - - + -
269B HIS* 3.6 23.5 + - + -
271B ASP* 4.6 11.1 + - - +
298B ASN* 5.2 0.3 + - - -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 6.1 1.1 - - + -
201A ILE* 6.1 0.7 - - + -
351A LEU* 5.0 9.4 - - + +
149B SER 3.2 12.2 + - - +
150B GLU* 3.1 9.7 + - + +
152B THR* 1.3 78.6 - - - +
154B VAL* 1.3 64.1 + - - +
156B LEU* 3.3 4.3 + - + +
157B LEU* 3.0 43.5 + - + +
198B ALA* 3.8 38.3 - - + +
201B ILE* 3.8 36.3 - - + -
202B GLY 4.6 2.0 - - - +
351B LEU* 3.5 26.7 - - + -
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN* 3.9 20.4 - - - +
150B GLU* 2.8 20.7 + - + +
151B ALA* 3.5 6.3 - - - +
153B LEU* 1.3 75.3 - - - +
155B ALA* 1.3 63.8 + - - +
157B LEU* 3.2 5.1 + - - +
158B ALA* 2.9 22.3 + - - +
314B MET* 4.5 9.0 - - + -
322B LEU* 3.6 31.2 - - + -
326B PHE* 4.0 12.3 - - + -
349B TRP 3.7 10.3 - - - +
351B LEU* 3.9 31.2 - - + +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA 3.0 10.0 + - - +
152B THR 3.2 8.5 + - - +
154B VAL* 1.3 76.5 - - - +
156B LEU* 1.3 57.1 + - - +
158B ALA* 3.1 9.3 + - - +
159B ALA* 2.8 28.6 + - - +
238B PHE* 3.9 13.6 - - + -
267B TRP* 4.1 7.0 - - - +
269B HIS* 3.7 15.0 - - - +
296B SER* 3.6 24.0 - - - +
314B MET* 3.9 8.7 - - + -
322B LEU* 6.3 0.2 - - - -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B THR 3.0 9.8 + - - +
153B LEU* 3.7 10.5 - - + +
155B ALA* 1.3 75.6 - - - +
157B LEU* 1.3 58.7 + - + +
159B ALA* 3.2 1.7 + - - +
160B ARG* 2.7 36.2 + - + +
185B ALA* 4.7 4.3 - - + -
195B VAL* 5.1 2.7 - - + +
198B ALA* 4.0 8.7 - - + +
199B GLY* 3.9 27.6 - - - +
202B GLY* 4.1 25.8 - - - -
204B VAL* 4.4 11.9 - - + -
237B PHE* 3.9 15.9 - - + -
238B PHE* 3.6 41.6 - - + -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 3.6 29.8 - - + -
153B LEU* 3.0 36.4 + - + +
154B VAL 3.7 4.0 - - - +
156B LEU* 1.3 76.8 - - + +
158B ALA* 1.3 63.0 + - - +
160B ARG* 3.6 39.9 + - - +
161B THR* 3.0 28.2 + - - -
201B ILE* 5.6 0.9 - - + -
202B GLY* 4.4 14.1 - - - -
325B ALA* 3.7 4.6 - - + +
326B PHE* 4.4 13.9 - - + -
351B LEU* 3.7 24.2 - - + -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL 2.9 13.4 + - - +
155B ALA* 3.4 9.0 - - - +
157B LEU* 1.3 76.8 - - - +
159B ALA* 1.3 63.6 + - - +
161B THR* 3.8 2.1 - - - +
162B LYS* 3.0 25.1 + - - +
267B TRP* 3.7 16.6 - - + -
321B ASP 3.5 22.3 - - - +
322B LEU* 4.2 15.0 - - + +
325B ALA* 3.5 15.4 - - + +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA 2.8 13.4 + - - +
156B LEU 3.4 7.6 - - - +
158B ALA* 1.3 75.1 - - - +
160B ARG* 1.3 66.0 + - - +
162B LYS* 3.1 4.9 + - - +
163B VAL* 3.0 24.1 + - - +
237B PHE* 3.9 13.9 - - + +
238B PHE* 3.8 12.1 - - + -
267B TRP* 3.6 39.2 - - + -
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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
----------------------------------------------------------
160A ARG* 4.9 2.0 - - - +
180A LEU* 6.3 0.2 - - - +
200A LEU 3.7 8.9 + - - -
201A ILE* 2.8 33.5 + - - +
202A GLY 4.9 5.1 + - - -
203A GLY* 4.5 5.8 - - - +
156B LEU* 2.7 21.9 + - + +
157B LEU* 3.6 22.7 + - - +
159B ALA* 1.3 73.1 - - - +
161B THR* 1.3 71.5 + - - +
163B VAL* 3.1 6.6 - - - +
164B VAL* 3.1 29.1 + - + +
176B GLN* 5.4 7.5 + - - -
180B LEU* 3.6 33.5 - - + +
183B LEU* 4.0 8.5 - - + -
201B ILE 4.6 1.0 + - - -
202B GLY* 2.8 45.8 + - - -
204B VAL* 4.5 3.8 - - + -
237B PHE* 3.5 16.3 - - + -
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 3.0 18.4 + - - -
158B ALA 3.8 3.6 - - - +
160B ARG* 1.3 85.6 + - - +
162B LYS* 1.3 63.4 + - - +
164B VAL* 3.3 6.7 + - - +
165B ARG* 3.1 57.8 + - + +
324B GLY 4.1 0.7 - - - +
325B ALA* 3.8 26.6 + - - +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA 3.0 18.5 + - - +
159B ALA* 3.6 5.6 - - - +
161B THR* 1.3 79.2 - - - +
163B VAL* 1.3 57.0 + - - +
165B ARG* 3.5 13.4 + - - +
166B ARG* 3.2 42.2 + - - +
265B ASP* 5.9 1.2 + - - -
267B TRP* 4.4 13.1 - - + -
295B ASP* 4.9 8.3 + - - -
318B ARG* 5.0 4.0 - - - +
321B ASP* 3.0 44.1 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA 3.0 13.8 + - - +
160B ARG* 3.1 20.2 - - - +
162B LYS* 1.3 75.1 - - - +
164B VAL* 1.3 70.1 + - - +
166B ARG* 3.5 31.1 - - - +
167B LEU* 3.1 40.1 + - + +
183B LEU* 4.0 23.6 - - + -
235B ILE* 4.6 11.4 - - + -
236B PRO 5.3 0.7 - - - +
237B PHE* 4.2 22.0 - - + -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ARG* 3.1 32.7 + - + +
161B THR* 3.7 7.2 - - - +
163B VAL* 1.3 78.9 - - + +
165B ARG* 1.3 64.3 + - + +
167B LEU* 3.6 2.5 + - - +
168B GLN* 3.1 44.9 + - + +
176B GLN* 4.2 36.1 - - + +
179B VAL* 4.0 26.9 - - + -
180B LEU* 4.7 3.8 - - + -
183B LEU* 4.8 0.2 - - + -
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B THR* 3.1 41.2 + - + +
162B LYS* 3.7 13.3 - - - +
164B VAL* 1.3 76.9 - - + +
166B ARG* 1.3 60.9 + - - +
168B GLN* 3.1 12.0 + - - +
169B ALA* 2.8 29.3 + - - +
320B THR 5.5 1.4 + - - -
324B GLY* 2.8 41.8 + - - -
327B LYS* 4.2 6.9 + - - +
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LYS* 3.2 35.4 + - - +
163B VAL* 3.5 29.9 - - - +
165B ARG* 1.3 78.5 - - - +
167B LEU* 1.3 72.7 + - + +
169B ALA* 3.0 9.7 + - + +
170B ALA* 3.0 24.9 + - + +
265B ASP* 3.3 36.5 + - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 3.1 34.3 + - + +
164B VAL 4.0 4.3 - - - +
165B ARG 3.3 0.2 - - - -
166B ARG* 1.3 88.5 - - + +
168B GLN* 1.3 56.8 + - - +
170B ALA* 3.8 7.5 - - + +
171B SER* 3.2 17.2 + - - -
174B LEU* 2.9 32.9 - - + +
179B VAL* 3.4 35.7 - - + -
235B ILE* 3.9 25.4 - - + -
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Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 3.1 33.7 + - + +
165B ARG* 3.1 9.1 + - - +
166B ARG 3.1 0.8 - - - -
167B LEU* 1.3 76.9 - - + +
169B ALA* 1.3 62.2 + - - +
170B ALA 2.9 6.0 + - - -
171B SER 4.2 6.5 - - - +
172B PRO* 3.1 29.2 - - + +
173B GLY 5.3 0.9 - - - +
174B LEU* 2.6 37.4 + - + +
175B THR* 4.1 0.8 - - - +
176B GLN* 3.9 15.8 - - - +
179B VAL* 5.4 1.3 - - + -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ARG 2.8 16.2 + - - +
166B ARG* 3.0 11.4 + - + +
168B GLN* 1.3 77.3 - - - +
170B ALA* 1.3 59.4 + - - +
172B PRO* 4.3 8.1 - - - +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 3.0 15.8 + - + +
167B LEU* 3.8 9.9 - - + +
168B GLN 2.9 1.4 - - - -
169B ALA* 1.3 77.6 - - - +
171B SER* 1.3 58.4 + - - +
172B PRO* 2.7 20.5 - - - +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU 3.2 10.1 + - - -
168B GLN 3.5 3.4 - - - +
170B ALA* 1.3 80.4 + - - +
172B PRO* 1.3 67.5 - - - +
173B GLY 2.9 4.3 + - - -
174B LEU* 3.1 29.3 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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