Contacts of the helix formed by residues 262 - 285 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.7 4.9 - - - -
62A TRP* 4.3 10.5 - + + +
158A LYS* 4.1 20.9 - - + -
236A HIS* 4.3 17.1 - + - -
260A GLU* 3.1 33.1 + - + +
261A MET* 1.3 78.6 - - - +
263A PRO* 1.3 79.0 - - + +
264A LYS* 3.6 19.3 + - + +
265A GLY* 3.0 36.3 + - - -
266A VAL* 2.8 21.7 + - - +
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Residues in contact with PRO 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.8 24.7 - - + -
62A TRP* 5.7 0.4 - - - +
142A LEU* 5.1 2.9 - - + -
146A LEU* 3.8 22.0 - - + -
157A VAL 3.4 16.2 - - - +
158A LYS* 3.3 31.0 - - + +
160A PRO* 3.9 15.0 - - + -
262A HIS* 1.3 87.2 - - + +
264A LYS* 1.3 56.1 + - - +
266A VAL* 4.5 0.7 - - + -
267A LEU* 2.9 41.9 + - + +
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS 4.8 0.8 + - - -
160A PRO* 3.7 20.6 - - + +
161A GLU* 2.9 34.4 + - - +
162A GLY 3.4 24.2 - - - +
163A LEU* 3.9 14.1 - - - +
164A GLU* 3.4 30.9 + - + +
262A HIS* 3.3 17.1 + - + +
263A PRO* 1.3 77.7 - - - +
265A GLY* 1.3 55.2 + - - +
268A SER* 2.7 42.9 + - - +
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Residues in contact with GLY 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 5.9 1.6 - - - -
259A VAL* 4.2 1.7 - - - +
260A GLU* 3.3 28.6 + - - -
262A HIS* 3.0 20.8 + - - -
264A LYS* 1.3 76.9 - - - +
266A VAL* 1.3 57.8 + - - +
268A SER* 3.5 5.1 + - - -
269A PHE* 3.0 30.5 + - - +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.1 22.9 - - + -
58A PHE* 3.8 21.8 - - + -
142A LEU* 5.1 3.8 - - + -
193A VAL* 4.5 4.9 - - + -
259A VAL* 4.4 8.1 - - + -
260A GLU 3.7 4.3 - - - +
261A MET* 3.7 31.4 - - + -
262A HIS 2.8 18.4 + - - +
263A PRO 3.9 2.2 - - - +
265A GLY* 1.3 73.7 - - - +
267A LEU* 1.3 61.2 + - + +
269A PHE* 3.4 1.1 + - - +
270A LEU* 2.9 56.1 + - + +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.5 14.3 - - + -
15A ILE* 4.7 2.2 - - + -
138A LEU* 3.8 34.8 - - + -
139A PRO* 4.1 27.1 - - + -
142A LEU* 4.0 21.8 - - + -
143A THR* 4.6 9.0 - - + -
160A PRO* 4.1 20.6 - - + -
163A LEU* 3.7 22.7 - - + -
263A PRO* 2.9 25.1 + - + +
266A VAL* 1.3 73.4 - - + +
268A SER* 1.3 56.0 + - - +
270A LEU* 4.7 0.7 - - - -
271A ARG* 2.9 30.8 + - - +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.7 6.6 - - - +
164A GLU* 3.0 46.8 + - - +
264A LYS* 2.7 23.3 + - - +
265A GLY* 3.7 5.4 - - - -
267A LEU* 1.3 73.9 - - - +
269A PHE* 1.3 65.3 + - - +
271A ARG* 3.3 22.9 + - - +
272A ASP* 3.1 22.6 + - - -
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 4.0 26.9 - - + -
174A LEU* 5.0 6.1 - - + -
193A VAL* 3.9 22.9 - - + -
197A VAL* 4.0 9.9 - - + -
232A LEU* 4.0 21.1 - - + -
257A TYR* 4.5 14.6 - + + -
258A ALA 5.0 5.2 - - - -
259A VAL* 3.8 31.6 - - + -
265A GLY 3.0 17.9 + - - +
266A VAL 3.8 2.2 - - - +
268A SER* 1.3 76.9 - - - +
270A LEU* 1.3 68.8 + - + +
272A ASP* 3.2 10.5 + - - +
273A VAL* 3.0 46.3 + - + +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 4.0 15.7 - - + -
54A LEU* 4.0 12.1 - - + -
138A LEU* 3.8 22.9 - - + -
193A VAL* 4.2 12.8 - - + -
196A ARG* 3.7 34.7 + - + +
197A VAL* 4.3 11.2 - - + +
200A GLU* 4.7 3.7 - - + +
266A VAL* 2.9 44.2 + - + +
267A LEU 4.2 2.2 - - - +
269A PHE* 1.3 86.0 - - + +
271A ARG* 1.3 60.0 + - - +
273A VAL* 3.6 8.2 - - + +
274A GLY* 2.8 25.3 + - - -
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 3.2 33.8 - - + +
9A LEU* 4.9 1.1 - - - +
11A TRP* 3.6 23.3 - - + -
12A GLU* 4.2 9.9 + - - -
163A LEU* 4.0 18.6 - - + +
164A GLU* 2.8 32.0 + - - +
165A PRO 3.5 8.7 + - - -
166A PRO* 3.7 19.8 - - - +
267A LEU 2.9 19.4 + - - +
268A SER* 3.3 24.5 + - - +
269A PHE 3.2 0.2 - - - -
270A LEU* 1.3 75.9 - - - +
272A ASP* 1.3 78.3 + - - +
274A GLY* 3.2 2.6 + - - -
275A ILE* 3.0 50.5 + - - +
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PRO 4.8 0.3 - - - +
166A PRO* 3.2 14.9 - - - +
167A ASN* 3.0 41.6 + - - +
170A LEU* 3.7 21.3 - - + +
171A ILE* 3.7 22.4 - - + +
174A LEU* 4.7 2.0 - - + -
268A SER* 3.1 14.0 + - - +
269A PHE* 3.2 9.0 + - - +
271A ARG* 1.3 85.0 + - - +
273A VAL* 1.3 56.6 + - - +
275A ILE* 3.3 0.9 + - - -
276A ALA* 2.9 29.7 + - - +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 3.9 19.5 - - + -
197A VAL* 4.1 32.3 - - + -
200A GLU* 4.1 17.5 - - + -
201A PHE* 4.1 14.0 - - + -
269A PHE* 3.0 47.1 + - + +
270A LEU* 3.6 11.9 - - + +
271A ARG 3.3 0.2 - - - -
272A ASP* 1.3 72.1 - - - +
274A GLY* 1.3 66.4 - - - +
276A ALA* 3.3 2.6 + - - +
277A SER* 2.9 23.4 + - - -
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Residues in contact with GLY 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 3.6 19.7 - - - -
200A GLU* 3.5 23.1 + - - -
270A LEU 2.8 12.3 + - - -
271A ARG 3.2 4.4 + - - -
273A VAL* 1.3 76.5 - - - +
275A ILE* 1.3 61.4 + - - +
277A SER* 2.8 19.5 + - - -
278A VAL* 3.1 13.5 + - - +
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.9 20.2 - - + -
8A TYR* 3.9 16.8 - - + -
9A LEU* 4.0 22.0 - - + -
166A PRO* 4.2 14.4 - - + -
171A ILE* 4.0 19.5 - - + -
271A ARG* 3.0 42.5 + - - +
272A ASP 3.8 4.0 - - - +
274A GLY* 1.3 76.1 - - - +
276A ALA* 1.3 58.3 + - - +
278A VAL* 3.2 6.9 + - - +
279A LYS* 2.9 45.5 + - + +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.8 26.6 - - + +
174A LEU* 3.8 21.8 - - + -
175A VAL* 3.5 16.9 - - + +
201A PHE* 4.2 7.7 - - + -
272A ASP 2.9 17.6 + - - +
273A VAL 3.6 4.7 - - - +
275A ILE* 1.3 76.8 - - - +
277A SER* 1.3 57.8 + - - +
279A LYS* 3.3 0.6 + - - -
280A LEU* 2.9 27.4 + - - +
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLU* 3.6 28.2 + - - +
201A PHE* 3.6 23.7 - - - -
204A ASN* 2.9 24.8 + - - -
205A ALA* 3.6 10.7 + - - +
273A VAL 2.9 14.9 + - - -
274A GLY* 2.8 19.4 + - - -
276A ALA* 1.3 76.5 - - - +
278A VAL* 1.3 55.3 + - - +
280A LEU 3.5 0.6 + - - +
281A ALA* 3.1 24.1 + - - +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 4.4 5.8 - - - +
4A LEU* 4.0 17.9 - - + -
5A LEU* 3.9 24.5 - - + -
8A TYR* 3.8 22.4 - - + -
204A ASN* 4.0 10.1 - - - +
274A GLY 3.1 14.0 + - - +
275A ILE* 3.2 9.6 + - - +
277A SER* 1.3 74.4 - - - +
279A LYS* 1.3 64.1 + - - +
281A ALA* 3.2 8.8 + - - +
282A GLU* 3.1 35.0 + - - +
288A PRO* 4.2 16.2 - - + -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.6 25.5 - - + +
171A ILE* 4.7 7.2 - - + -
172A HIS* 6.0 7.4 - - + -
175A VAL* 4.0 13.0 - - + -
275A ILE* 2.9 39.1 + - + +
276A ALA* 3.7 5.2 - - - +
278A VAL* 1.3 75.7 - - - +
280A LEU* 1.3 61.7 + - - +
282A GLU* 3.2 25.8 + - - +
283A ILE* 3.1 30.1 + - + +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 4.2 15.6 - - + +
178A PHE* 4.1 15.0 - - + -
179A GLN* 3.6 39.7 - - + +
201A PHE* 3.9 26.7 - - + -
205A ALA* 4.1 7.4 - - + -
207A ILE* 4.0 18.6 - - + -
276A ALA 2.9 16.4 + - - +
277A SER 3.8 4.7 - - - +
279A LYS* 1.3 74.1 - - - +
281A ALA* 1.3 63.7 + - - +
283A ILE* 3.2 12.9 + - + -
284A ARG* 2.9 39.5 + - + +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASN 3.3 25.4 - - - +
205A ALA* 4.1 4.6 - - - +
277A SER 3.1 11.9 + - - +
278A VAL 3.2 10.1 + - - +
280A LEU* 1.3 75.1 - - - +
282A GLU* 1.3 57.8 + - - +
284A ARG* 3.2 2.8 + - - -
285A GLY 2.9 24.4 + - - -
286A VAL* 3.0 35.6 + - + +
288A PRO* 3.8 13.0 - - + -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 4.9 6.8 - - - -
5A LEU* 4.3 10.7 - - - +
278A VAL* 3.1 27.4 + - + +
279A LYS* 3.4 29.6 + - - +
280A LEU 3.2 0.2 - - - -
281A ALA* 1.3 77.4 - - + +
283A ILE* 1.3 64.2 + - + +
285A GLY* 3.1 13.7 + - - -
286A VAL 4.7 2.7 - - - +
288A PRO* 5.5 6.8 - - + +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 3.4 32.8 - - + -
179A GLN* 3.8 21.8 - - - +
279A LYS* 3.1 15.9 + - + +
280A LEU* 3.5 11.4 - - + +
282A GLU* 1.3 77.5 - - + +
284A ARG* 1.3 60.1 + - + +
285A GLY 3.4 0.7 + - - -
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLN* 4.7 2.9 - - - +
181A ARG* 3.7 5.1 - - - +
205A ALA 2.9 34.5 + - - -
206A LYS* 3.4 21.4 + - - +
207A ILE* 3.6 20.6 - - - +
280A LEU* 2.9 40.6 + - + +
281A ALA 3.2 5.1 + - - +
283A ILE* 1.3 74.4 - - + +
285A GLY* 1.3 60.5 + - - +
286A VAL* 3.7 19.1 + - + +
504A SO4 2.9 49.7 + - - +
226B GLU* 4.5 3.6 + - - -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ALA 2.9 4.5 + - - -
282A GLU* 3.1 12.8 + - - -
283A ILE 3.2 1.0 + - - -
284A ARG* 1.3 79.3 - - - +
286A VAL* 1.3 62.8 + - - +
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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
------------------------------------------------------------
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