Contacts of the helix formed by residues 262 - 285 (chain B) in PDB entry 1X9H
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 HIS 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 3.8 2.7 - - - -
62B TRP* 4.3 10.5 - + + +
158B LYS* 4.3 17.0 - - + +
164B GLU* 5.5 2.2 - - - -
236B HIS* 4.4 11.2 - + - -
260B GLU* 3.1 39.2 + - + +
261B MET* 1.3 77.3 - - - +
263B PRO* 1.3 78.4 - - + +
264B LYS* 3.2 18.7 - - + +
265B GLY* 2.9 34.8 + - - -
266B VAL* 2.9 20.6 + - - +
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Residues in contact with PRO 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 3.8 26.4 - - + -
62B TRP* 5.5 0.7 - - + +
142B LEU* 5.3 1.3 - - + -
143B THR* 6.0 0.2 - - + -
146B LEU* 3.9 22.2 - - + -
157B VAL 3.4 14.1 - - - +
158B LYS* 3.3 35.7 - - + +
160B PRO* 4.1 12.3 - - + -
262B HIS* 1.3 87.9 - - + +
264B LYS* 1.3 57.2 + - - +
266B VAL* 4.0 0.4 - - + +
267B LEU* 2.9 42.0 + - + +
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Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LYS 4.8 1.0 + - - +
160B PRO* 3.6 22.3 - - + +
161B GLU 5.9 0.2 - - - +
162B GLY 3.3 32.5 - - - +
163B LEU* 3.9 8.6 - - - +
164B GLU* 3.2 37.9 + - - +
262B HIS* 3.2 15.1 + - + +
263B PRO* 1.3 78.4 - - - +
265B GLY* 1.3 55.8 + - - +
268B SER* 2.6 41.8 + - - +
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Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLU* 5.7 2.9 - - - -
259B VAL* 4.1 2.6 - - - +
260B GLU* 3.3 26.8 + - - -
262B HIS* 2.9 21.6 + - - -
264B LYS* 1.3 73.8 - - - +
266B VAL* 1.3 60.7 + - - +
268B SER* 3.8 4.8 - - - -
269B PHE* 3.0 30.0 + - - +
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Residues in contact with VAL 266 (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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54B LEU* 4.0 22.4 - - + -
58B PHE* 3.7 23.1 - - + -
142B LEU* 5.2 3.8 - - + -
193B VAL* 4.6 4.3 - - + -
259B VAL* 4.4 7.4 - - + -
260B GLU 3.4 3.8 + - - +
261B MET* 3.7 32.8 - - + -
262B HIS 2.9 17.6 + - - +
263B PRO 4.0 2.2 - - - +
265B GLY* 1.3 73.6 - - - +
267B LEU* 1.3 61.9 + - + +
269B PHE* 3.4 1.5 + - - +
270B LEU* 2.9 52.7 + - + +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 3.5 15.5 - - + -
15B ILE* 4.8 5.8 - - + -
138B LEU* 4.0 33.4 - - + -
139B PRO* 4.2 24.0 - - + -
142B LEU* 4.1 22.2 - - + -
143B THR* 4.5 15.5 - - + -
160B PRO* 4.9 4.3 - - + -
163B LEU* 3.6 26.0 - - + -
263B PRO* 2.9 24.6 + - + +
266B VAL* 1.3 78.6 - - + +
268B SER* 1.3 58.1 + - - +
270B LEU* 4.7 0.4 - - - -
271B ARG* 2.8 32.1 + - - +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 3.6 7.9 - - - +
164B GLU* 3.0 40.5 + - - +
264B LYS 2.6 23.1 + - - -
265B GLY* 3.8 4.9 - - - -
266B VAL 3.3 0.2 - - - -
267B LEU* 1.3 78.0 - - - +
269B PHE* 1.3 61.6 + - - +
271B ARG* 3.4 19.8 + - - +
272B ASP* 3.1 29.9 + - - +
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Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 5.4 11.2 - - + -
174B LEU* 4.8 11.9 - - + -
193B VAL* 3.9 22.4 - - + -
197B VAL* 4.0 9.0 - - + -
232B LEU* 4.0 21.1 - - + -
257B TYR* 4.4 21.5 - + + -
258B ALA 5.1 4.7 - - - -
259B VAL* 3.8 31.4 - - + -
265B GLY 3.0 18.8 + - - +
266B VAL* 3.8 2.0 - - - +
268B SER* 1.3 77.6 - - - +
270B LEU* 1.3 69.9 + - + +
272B ASP* 3.1 13.6 + - + +
273B VAL* 2.9 48.1 + - + +
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Residues in contact with LEU 270 (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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11B TRP* 3.9 18.3 - - + -
54B LEU* 4.0 22.7 - - + -
138B LEU* 4.0 8.7 - - + -
193B VAL* 4.2 15.9 - - + +
196B ARG* 3.6 36.2 + - + +
197B VAL* 4.3 9.0 - - + -
200B GLU* 4.7 3.5 - - - +
266B VAL* 2.9 44.1 + - + +
267B LEU* 4.2 2.0 - - - +
269B PHE* 1.3 86.4 - - + +
271B ARG* 1.3 60.3 + - - +
273B VAL* 3.3 8.2 + - + +
274B GLY* 2.9 24.4 + - - -
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.1 38.5 - - + +
9B LEU* 4.5 7.4 + - - +
11B TRP* 3.4 23.6 - - + +
12B GLU* 5.9 1.0 - - - +
163B LEU* 3.9 18.4 - - + +
164B GLU 2.8 30.1 + - - -
165B PRO 3.5 2.8 + - - -
166B PRO* 3.5 24.9 - - - +
267B LEU 2.8 19.1 + - - +
268B SER* 3.4 19.4 + - - +
270B LEU* 1.3 76.6 - - - +
272B ASP* 1.3 87.6 + - - +
274B GLY* 3.1 3.5 + - - -
275B ILE* 3.0 34.6 + - - +
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PRO 4.6 0.3 - - - +
166B PRO* 3.3 10.0 - - - +
167B ASN* 3.0 34.4 + - + +
170B LEU* 5.5 3.5 - - + +
171B ILE* 3.6 22.9 - - + +
174B LEU* 5.1 6.1 - - + -
268B SER* 3.1 12.5 + - - +
269B PHE* 3.1 14.0 + - + +
271B ARG* 1.3 105.5 + - - +
273B VAL* 1.3 57.5 + - + +
275B ILE* 3.3 3.9 + - - +
276B ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.2 14.1 - - + -
197B VAL* 4.0 33.2 - - + -
200B GLU* 4.1 14.1 - - + -
201B PHE* 4.0 16.8 - - + -
269B PHE* 2.9 47.3 + - + +
270B LEU* 3.5 12.1 - - + +
271B ARG 3.2 0.2 - - - -
272B ASP* 1.3 73.9 - - - +
274B GLY* 1.3 59.2 + - - +
276B ALA* 3.2 7.4 + - - +
277B SER* 2.9 29.0 + - - -
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Residues in contact with GLY 274 (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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8B TYR* 3.7 18.2 - - - -
200B GLU* 3.6 22.4 + - - -
270B LEU 2.9 11.1 + - - -
271B ARG 3.1 4.4 + - - -
273B VAL* 1.3 76.9 - - - +
275B ILE* 1.3 62.2 + - - +
277B SER* 2.8 19.4 + - - -
278B VAL* 3.0 15.4 + - - +
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Residues in contact with ILE 275 (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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5B LEU* 4.0 27.3 - - + +
8B TYR* 4.0 11.0 - - + -
9B LEU* 3.7 27.1 - - + -
166B PRO* 4.3 7.2 - - + -
171B ILE* 4.0 23.8 - - + -
271B ARG* 3.0 35.5 + - - +
272B ASP 3.3 6.0 + - - +
274B GLY* 1.3 73.3 - - - +
276B ALA* 1.3 59.1 + - - +
278B VAL* 3.2 3.8 + - - +
279B LYS* 2.8 54.3 + - + +
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Residues in contact with ALA 276 (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 ILE* 3.8 26.7 - - + +
174B LEU* 3.9 19.5 - - + -
175B VAL* 3.5 17.7 - - + +
201B PHE* 4.1 7.6 - - + -
272B ASP 2.9 17.0 + - - +
273B VAL* 3.5 6.7 - - - +
275B ILE* 1.3 77.6 - - - +
277B SER* 1.3 58.3 + - - +
279B LYS 3.3 0.3 + - - -
280B LEU* 2.9 27.7 + - - +
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Residues in contact with SER 277 (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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200B GLU* 3.6 23.8 + - - +
201B PHE* 3.6 28.2 - - - -
204B ASN* 2.9 25.1 + - - +
205B ALA* 3.7 8.0 - - - +
273B VAL 2.9 15.2 + - - -
274B GLY* 2.8 20.1 + - - -
276B ALA* 1.3 77.0 - - - +
278B VAL* 1.3 56.1 + - - +
280B LEU 3.5 0.5 + - - -
281B ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 278 (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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2B SER* 4.2 9.4 - - - +
4B LEU* 4.1 14.8 - - + -
5B LEU* 4.2 28.5 - - + +
8B TYR* 3.8 24.0 - - + -
204B ASN* 4.0 10.8 - - - +
274B GLY 3.0 13.5 + - - +
275B ILE* 3.6 9.2 - - - +
277B SER* 1.3 74.7 - - - +
279B LYS* 1.3 66.2 + - + +
281B ALA* 3.2 8.3 + - - +
282B GLU* 3.1 22.4 + - + +
288B PRO* 4.3 13.5 - - + +
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Residues in contact with LYS 279 (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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5B LEU* 5.7 7.9 - - + -
171B ILE* 3.9 25.4 - - + -
172B HIS* 3.8 23.4 - - - +
175B VAL* 3.9 11.9 - - + -
275B ILE* 2.8 32.6 + - + +
276B ALA 3.6 4.5 - - - +
278B VAL* 1.3 80.1 - - + +
280B LEU* 1.3 61.7 + - - +
282B GLU* 3.2 17.9 + - - +
283B ILE* 3.1 28.7 + - + +
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Residues in contact with LEU 280 (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 VAL* 4.0 22.4 - - + +
178B PHE* 4.0 15.0 - - + -
179B GLN* 3.6 37.9 - - + +
201B PHE* 3.9 26.5 - - + -
205B ALA* 4.1 7.6 - - + -
207B ILE* 4.0 18.4 - - + -
276B ALA 2.9 17.3 + - - +
277B SER 3.8 4.5 - - - +
279B LYS* 1.3 73.0 - - - +
281B ALA* 1.3 60.8 + - - +
283B ILE* 3.2 7.3 + - + -
284B ARG* 2.9 45.5 + - + +
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Residues in contact with ALA 281 (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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204B ASN 3.3 26.0 - - - +
205B ALA* 4.2 4.2 - - - +
277B SER 3.0 11.5 + - - +
278B VAL 3.2 10.3 + - - +
280B LEU* 1.3 76.7 - - - +
282B GLU* 1.3 56.8 + - - +
284B ARG* 3.1 2.9 + - - -
285B GLY 2.9 24.8 + - - -
286B VAL* 3.0 34.1 + - + +
288B PRO* 3.7 13.5 - - + -
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Residues in contact with GLU 282 (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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278B VAL* 3.1 11.4 + - + +
279B LYS* 3.2 20.0 + - - +
281B ALA* 1.3 74.3 - - - +
283B ILE* 1.3 67.3 + - + +
285B GLY* 3.1 14.6 + - - -
286B VAL 4.3 3.6 + - - -
288B PRO* 5.7 0.8 - - - +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.6 30.3 - - + -
179B GLN* 4.1 19.7 - - - +
279B LYS* 3.1 13.4 + - + +
280B LEU* 3.2 10.3 + - + +
282B GLU* 1.3 81.5 - - + +
284B ARG* 1.3 60.2 + - + +
285B GLY* 3.4 0.7 + - - -
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLU* 4.9 2.0 + - - -
179B GLN* 4.6 3.1 - - - +
181B ARG* 3.6 5.5 - - - +
205B ALA 2.9 30.5 + - - -
206B LYS* 3.5 18.2 + - - +
207B ILE* 3.7 22.6 - - - +
280B LEU* 2.9 39.6 + - + +
281B ALA 3.1 4.5 + - - +
283B ILE* 1.3 76.3 - - + +
285B GLY* 1.3 62.0 + - - +
286B VAL* 3.5 20.4 + - + +
505B SO4 3.0 49.9 + - - +
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA 2.9 4.0 + - - -
282B GLU* 3.1 13.3 + - - -
283B ILE 3.2 1.2 + - - -
284B ARG* 1.3 79.6 - - - +
286B VAL* 1.3 61.1 + - - +
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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