Contacts of the helix formed by residues 254 - 284 (chain A) in PDB entry 2XFR
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 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 2.8 29.7 + - - +
253A LEU* 1.3 81.8 - - - +
255A GLU* 1.3 58.5 + - - +
256A LYS* 3.7 6.6 + - - +
257A GLY 3.1 13.0 + - - -
258A ARG* 2.9 28.7 + - - +
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Residues in contact with GLU 255 (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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224A HIS* 4.4 10.3 + - - -
227A TRP* 3.9 27.4 - - + -
254A SER* 1.3 74.7 - - - +
256A LYS* 1.3 59.1 + - + +
258A ARG* 3.4 30.2 + - - +
259A PHE* 3.0 27.7 + - - +
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Residues in contact with LYS 256 (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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215A PHE* 6.1 0.2 - - - -
227A TRP* 3.0 57.0 - - + +
228A GLU 3.7 25.5 + - - +
230A PRO* 6.6 0.4 - - - -
254A SER* 3.3 6.8 + - - +
255A GLU* 1.3 76.8 - - + +
257A GLY* 1.3 66.4 + - - +
259A PHE* 3.4 4.3 + - - +
260A PHE* 3.0 24.4 + - - +
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 6.2 0.2 - - - -
245A PHE* 4.2 14.4 - - - -
251A THR 3.8 11.7 - - - -
252A TYR 3.8 8.5 - - - -
254A SER* 3.1 19.2 + - - -
256A LYS* 1.3 77.7 - - - +
258A ARG* 1.3 55.8 + - - +
260A PHE* 3.3 4.5 + - - +
261A LEU* 2.9 35.0 + - - +
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR 3.8 5.6 + - - +
253A LEU* 2.9 27.1 + - - +
254A SER* 2.9 23.9 + - - +
255A GLU* 3.5 31.6 - - - +
257A GLY* 1.3 71.9 - - - +
259A PHE* 1.3 66.7 + - - +
261A LEU 3.9 0.2 - - - -
262A ALA* 2.9 27.0 + - - +
315A TYR* 3.5 24.9 - - + +
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PHE* 3.8 30.7 - + - -
218A ALA* 3.8 32.8 - - + -
219A ALA* 3.9 10.5 - - - -
222A VAL* 3.8 24.9 - - + -
227A TRP* 3.5 35.2 - + + -
255A GLU 3.0 18.0 + - - +
256A LYS 3.7 4.5 - - - +
257A GLY 3.3 0.2 - - - -
258A ARG* 1.3 76.1 - - - +
260A PHE* 1.3 59.1 + - - +
262A ALA* 3.5 5.4 + - + +
263A TRP* 2.9 32.8 + - + +
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Residues in contact with PHE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 3.7 47.8 - + + -
206A CYS* 3.8 17.7 - - - -
215A PHE* 4.0 22.0 - + + -
228A GLU 5.4 1.6 - - - +
229A PHE* 3.5 31.2 - + + -
230A PRO* 3.5 35.4 - - + -
245A PHE* 4.6 2.5 - + - -
256A LYS 3.0 18.1 + - - +
257A GLY* 3.8 3.1 - - - +
259A PHE* 1.3 77.7 - - - +
261A LEU* 1.3 69.6 + - + +
263A TRP* 3.2 12.7 + + - +
264A TYR* 2.9 35.0 + + + +
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Residues in contact with LEU 261 (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 PHE* 3.8 35.2 - - + -
245A PHE* 3.9 19.3 - - + -
252A TYR* 3.9 18.6 - - + +
257A GLY 2.9 20.3 + - - +
260A PHE* 1.3 79.1 - - + +
262A ALA* 1.3 55.7 + - - +
264A TYR* 3.9 4.6 - - + +
265A SER* 2.7 35.7 + - - -
310A LEU* 4.0 31.0 - - + +
315A TYR* 3.6 36.9 - - + +
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Residues in contact with ALA 262 (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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258A ARG 2.9 18.4 + - - +
259A PHE* 3.8 6.3 - - + +
261A LEU* 1.3 74.0 - - - +
263A TRP* 1.3 56.5 + - - +
265A SER* 3.3 5.8 + - - -
266A ASN* 2.7 53.6 + - - +
315A TYR* 3.6 12.6 - - + -
320A ARG* 4.8 7.0 - - - +
468A LEU* 5.2 4.3 - - + -
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Residues in contact with TRP 263 (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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187A TYR* 5.5 1.3 - - - -
206A CYS* 3.9 24.5 - - + -
211A LEU* 3.3 34.8 - - + -
214A ASP* 2.9 24.1 + - + -
215A PHE* 3.6 30.4 - + + +
218A ALA* 3.9 20.2 - - + -
229A PHE* 3.7 23.8 - + - -
259A PHE* 2.9 25.0 + - + +
260A PHE* 3.2 17.2 + + - +
262A ALA* 1.3 75.7 - - - +
264A TYR* 1.3 83.7 + + - +
266A ASN* 3.8 6.4 - - - +
267A ASN* 3.0 46.4 + - - +
270A LYS* 6.1 2.5 - - - -
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Residues in contact with TYR 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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187A TYR* 2.7 74.7 + + - +
203A GLU 3.9 0.3 + - - -
204A PHE* 3.4 17.0 - + - -
205A ILE 3.0 28.7 + - - -
206A CYS* 3.8 26.9 - - + -
260A PHE* 2.9 26.5 + + + +
261A LEU* 3.9 6.7 - - + +
263A TRP* 1.3 89.1 - + + +
265A SER* 1.3 61.5 + - - +
267A ASN 3.5 3.8 + - - -
268A LEU 3.7 1.6 + - - -
310A LEU 3.4 20.0 - - - -
311A THR 2.7 29.2 + - - -
313A GLY* 3.7 6.3 - - - -
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Residues in contact with SER 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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261A LEU 2.7 22.5 + - - -
262A ALA* 3.3 6.8 + - - -
264A TYR* 1.3 77.8 - - - +
266A ASN* 1.4 68.4 + - - +
268A LEU* 3.2 13.3 + - - +
269A ILE* 3.3 21.8 + - - +
313A GLY 3.2 27.3 - - - +
315A TYR* 3.3 27.1 - - - +
320A ARG* 4.8 2.8 + - - -
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Residues in contact with ASN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ALA* 2.7 38.9 + - - +
263A TRP* 3.8 6.9 - - - +
265A SER* 1.4 74.9 + - - +
267A ASN* 1.3 58.5 + - - +
269A ILE* 3.1 10.7 + - - +
270A LYS* 2.9 38.2 + - - +
320A ARG* 4.9 0.7 + - - -
464A ILE* 3.5 30.3 - - + +
468A LEU* 3.6 35.5 - - - +
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.7 22.9 - - + +
187A TYR* 3.8 15.2 + - - +
211A LEU* 4.0 9.3 - - - +
214A ASP* 3.4 22.3 + - - +
263A TRP* 3.0 48.0 + - - +
265A SER 3.2 0.6 - - - -
266A ASN* 1.3 78.2 - - - +
268A LEU* 1.3 57.1 + - - +
270A LYS* 3.3 28.2 + - - +
271A HIS* 3.0 27.9 + - - +
274A ARG* 4.9 2.4 + - - -
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Residues in contact with LEU 268 (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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121A TYR* 4.4 4.7 - - - +
135A LEU* 3.9 15.0 - - + +
179A LEU 5.4 0.4 - - - +
185A MET* 3.6 31.2 - - + +
186A ARG* 3.8 31.6 - - - +
187A TYR* 3.5 32.8 - - + -
264A TYR 3.7 1.9 + - - +
265A SER 3.2 6.7 + - - +
266A ASN 3.2 0.6 - - - -
267A ASN* 1.3 76.2 - - - +
269A ILE* 1.3 61.4 + - + +
271A HIS* 3.3 9.5 + - + +
272A GLY 2.9 24.8 + - - -
312A ALA 3.7 8.1 - - - +
313A GLY* 3.7 27.8 - - - +
314A TYR* 4.6 3.4 - - + -
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Residues in contact with ILE 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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185A MET* 4.7 2.0 - - + -
265A SER* 3.3 17.7 + - - +
266A ASN* 3.1 21.7 + - - +
268A LEU* 1.3 77.0 - - + +
270A LYS* 1.3 56.5 - - - +
272A GLY 3.4 1.2 + - - -
273A ASP* 2.9 27.6 + - + +
322A GLY 5.7 0.2 - - - +
325A THR* 3.9 28.9 - - - +
326A ILE* 4.0 24.9 - - + +
329A MET* 3.7 35.0 - - + +
464A ILE* 3.8 17.5 - - + -
467A ILE* 4.0 12.6 - - + -
468A LEU* 4.6 2.9 - - + -
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Residues in contact with LYS 270 (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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214A ASP* 4.9 7.9 + - - -
263A TRP* 6.1 2.0 - - - -
266A ASN* 2.9 23.1 + - - +
267A ASN* 3.3 28.3 + - - +
269A ILE* 1.3 73.5 - - - +
271A HIS* 1.3 64.4 + - - +
273A ASP* 3.3 6.1 + - - +
274A ARG* 3.0 50.0 + - - +
464A ILE* 4.3 25.6 - - + -
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Residues in contact with HIS 271 (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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121A TYR* 4.8 0.9 - - - -
132A TYR* 2.8 36.2 + + - -
133A LEU 5.1 0.2 - - - -
135A LEU* 3.4 20.8 - - + +
138A ASP* 2.6 38.4 + - - +
152A TYR* 4.8 0.9 - + - -
179A LEU* 2.9 27.7 + - + -
185A MET* 4.8 4.3 - - + -
267A ASN 3.0 19.3 + - - +
268A LEU* 3.4 14.4 - - + +
270A LYS* 1.3 74.3 - - - +
272A GLY* 1.3 65.9 + - - +
274A ARG* 3.5 11.4 - - - +
275A ILE* 3.2 45.0 + - + +
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Residues in contact with GLY 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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179A LEU* 3.9 26.7 - - - -
185A MET* 4.0 7.0 - - - -
268A LEU 2.9 14.6 + - - -
269A ILE 3.8 2.2 - - - -
271A HIS* 1.3 77.2 - - - +
273A ASP* 1.3 56.9 + - - +
275A ILE* 4.0 0.3 - - - +
276A LEU* 2.9 36.1 + - - +
329A MET* 4.1 8.5 - - - -
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Residues in contact with ASP 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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269A ILE* 2.9 18.0 + - + +
270A LYS* 3.7 8.1 - - - +
272A GLY* 1.3 76.4 - - - +
274A ARG* 1.3 58.1 + - - +
277A ASP* 3.0 28.2 + - - +
329A MET* 3.7 23.4 - - + +
332A ARG* 3.1 26.2 + - - -
333A HIS* 2.8 30.2 + - - -
461A GLU* 4.2 12.3 - - - +
462A ILE 4.9 3.9 - - - +
467A ILE* 5.5 5.6 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.4 10.9 + - - +
138A ASP* 2.9 36.4 + - - +
139A ASN* 3.5 29.7 - - - +
149A VAL* 3.9 10.4 - - + +
267A ASN* 5.3 1.4 + - - -
270A LYS* 3.0 40.5 + - - +
271A HIS* 3.5 24.5 - - - +
273A ASP* 1.3 78.9 + - - +
275A ILE* 1.3 68.3 + - + +
277A ASP* 3.5 7.1 + - - +
278A GLU* 3.4 25.1 + - - +
332A ARG* 5.8 0.2 - - - +
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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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90A PHE* 5.7 0.4 - - + -
132A TYR* 4.4 0.7 - - - +
138A ASP* 4.3 3.1 - - - +
149A VAL* 3.9 20.2 - - + -
152A TYR* 3.8 31.0 - - + -
156A MET* 4.4 9.6 - - + +
177A VAL* 3.7 27.1 - - + -
178A GLY 5.2 0.9 - - - +
179A LEU* 3.7 15.3 - - + -
271A HIS* 3.2 50.8 + - + +
274A ARG* 1.3 75.5 - - + +
276A LEU* 1.3 60.2 + - - +
278A GLU* 3.2 9.6 + - + +
279A ALA* 2.9 25.1 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.3 22.4 - - + -
179A LEU* 5.2 1.8 - - + -
272A GLY* 2.9 22.8 + - - +
275A ILE* 1.3 74.6 - - - +
277A ASP* 1.3 58.5 + - - +
279A ALA* 3.7 3.8 - - + +
280A ASN* 2.8 31.9 + - - +
290A LEU* 4.7 13.0 - - + +
291A ALA 4.7 1.3 - - - +
292A ILE* 3.8 22.7 - - + -
329A MET* 4.1 5.4 - - + -
330A LEU* 3.4 32.8 - - + -
333A HIS* 3.8 29.1 - - + +
335A ALA* 4.3 14.1 - - + -
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Residues in contact with ASP 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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273A ASP 3.0 19.4 + - - +
274A ARG* 3.7 7.9 - - - +
275A ILE 3.2 0.4 - - - -
276A LEU* 1.3 75.5 - - - +
278A GLU* 1.3 63.0 + - + +
280A ASN* 3.4 1.2 + - - -
281A LYS* 3.1 30.7 + - - +
332A ARG* 3.7 18.8 + - - +
333A HIS* 3.6 8.0 - - + -
457A ARG* 2.9 41.5 + - - -
458A SER* 3.6 12.0 + - - -
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Residues in contact with GLU 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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149A VAL* 3.6 27.0 - - + +
150A GLN* 6.3 0.2 - - - -
153A ALA* 3.8 25.8 - - + +
156A MET* 4.5 5.4 - - + -
274A ARG 3.4 14.3 + - - +
275A ILE* 3.2 8.4 + - + +
277A ASP* 1.3 79.3 - - + +
279A ALA* 1.3 62.5 + - - +
281A LYS* 3.3 26.7 + - - +
282A VAL* 3.0 27.5 + - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A MET* 3.7 30.6 - - + +
177A VAL* 3.9 16.2 - - + -
275A ILE 2.9 14.0 + - - +
276A LEU* 3.2 8.9 + - + +
278A GLU* 1.3 76.3 - - - +
280A ASN* 1.3 62.4 + - - +
282A VAL* 3.2 2.7 + - - -
283A PHE* 3.0 31.2 + - + -
290A LEU* 3.6 16.5 - - + +
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Residues in contact with ASN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU 2.8 19.5 + - - +
277A ASP 3.7 3.1 - - - +
279A ALA* 1.3 73.2 - - - +
281A LYS* 1.3 56.3 + - - +
283A PHE 3.4 0.5 + - - -
284A LEU* 2.9 30.1 + - - +
290A LEU* 3.5 11.1 - - + +
333A HIS* 4.0 16.1 + - + +
455A LEU* 3.7 16.3 - - - +
456A PRO 3.0 22.6 + - - -
457A ARG* 2.9 29.3 + - - -
458A SER* 3.0 33.4 + - - +
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 4.4 2.9 + - - -
277A ASP* 3.1 27.0 + - - +
278A GLU* 3.3 31.7 + - - +
280A ASN* 1.3 78.0 - - - +
282A VAL* 1.3 64.3 + - + +
284A LEU* 3.7 17.0 - - + +
457A ARG* 3.3 36.4 - - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 4.0 16.2 - - + +
156A MET* 3.6 32.1 - - + +
157A THR* 3.5 21.3 - - - +
160A ARG* 2.9 50.9 + - + +
278A GLU* 3.0 20.9 + - - +
279A ALA 3.2 7.2 + - - +
281A LYS* 1.3 78.3 - - + +
283A PHE* 1.3 75.0 + - + +
284A LEU 3.3 2.3 + - - +
286A TYR* 4.7 0.5 - - - -
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Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 5.0 0.4 - - - -
156A MET* 4.1 24.5 - - + -
159A PHE* 4.0 18.6 - + - -
160A ARG* 4.0 23.6 - - + -
167A LEU* 4.5 13.7 - - + -
175A ILE* 3.9 42.4 - - + -
279A ALA* 3.0 28.6 + - - +
280A ASN 3.7 1.8 - - - -
282A VAL* 1.3 89.7 - - + +
284A LEU* 1.3 65.9 + - - +
285A GLY 3.2 0.2 + - - -
286A TYR* 3.0 24.5 + + - +
288A VAL* 4.1 13.5 - - + -
290A LEU* 4.0 14.4 - - + -
455A LEU* 3.8 20.0 - - + +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASN* 2.9 15.4 + - - +
281A LYS* 3.7 12.8 - - + +
282A VAL 3.3 2.8 - - - +
283A PHE* 1.3 78.2 - - - +
285A GLY* 1.3 59.7 + - - +
286A TYR* 3.4 11.8 + - - -
455A LEU* 3.4 14.4 - - - +
456A PRO* 3.7 1.8 - - + +
457A ARG* 3.3 53.6 - - + +
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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