Contacts of the helix formed by residues 251 - 275 (chain A) in PDB entry 4FDI
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 ARG 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 2.9 48.7 + - - +
51A GLU* 3.3 34.7 + - - +
53A SER* 4.4 5.6 - - - +
55A GLU* 3.9 12.6 - - - +
249A SER* 2.8 12.6 + - - +
250A GLN* 1.3 79.1 - - - +
252A GLY* 1.3 62.7 + - - +
253A ARG 3.9 0.5 + - - -
254A TYR* 4.0 18.1 + - + +
255A GLY* 3.7 14.8 + - - +
258A VAL* 4.8 7.5 - - - +
297A PRO 4.0 8.5 - - - +
298A GLU 4.5 0.5 - - - +
300A GLY 4.6 1.8 + - - -
301A GLY* 3.6 9.7 - - - -
302A SER* 3.5 21.6 - - - +
445B GLY 3.6 19.9 + - - +
446B ARG* 3.5 18.6 + - - +
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Residues in contact with GLY 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A SER* 3.6 7.9 + - - -
250A GLN 3.4 4.9 + - - -
251A ARG* 1.3 77.1 - - - +
253A ARG* 1.3 65.2 + - - -
255A GLY* 3.1 10.4 + - - -
256A ASP* 3.1 20.1 + - - +
298A GLU* 3.4 13.9 - - - -
446B ARG* 3.8 12.3 - - - +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.3 20.2 + - - +
199A LYS 2.9 26.9 + - - -
200A THR 3.3 12.5 + - - -
201A GLY* 3.5 21.4 - - - -
238A PRO* 6.2 1.4 - - - +
239A VAL* 3.4 32.8 + - + +
240A TYR* 5.0 1.6 - - - +
241A ALA* 5.4 0.2 - - - +
246A LEU* 4.7 7.6 - - + +
252A GLY* 1.3 71.4 - - - -
254A TYR* 1.3 62.4 + - - +
256A ASP* 3.2 29.5 + - + +
257A ALA 3.3 4.9 + - - -
298A GLU* 3.1 25.5 + - + +
299A GLN* 3.3 28.0 - - - +
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Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP 3.5 5.9 + - - -
41A MET* 3.3 22.7 - - - +
45A ASP* 2.7 27.6 + - - -
235A THR* 3.3 33.9 - - - -
239A VAL* 3.8 12.1 - - + +
251A ARG* 4.1 17.5 - - - +
252A GLY 3.3 0.4 - - - -
253A ARG* 1.3 75.8 - - - +
255A GLY* 1.3 63.1 + - - +
257A ALA* 3.3 6.2 + - - +
258A VAL* 3.2 40.6 + - + +
297A PRO 4.9 0.9 - - - +
298A GLU 3.0 19.7 + - - +
299A GLN 3.8 3.1 - - - -
300A GLY* 3.6 33.2 - - - +
301A GLY* 3.3 24.9 - - - -
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Residues in contact with GLY 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 4.4 1.9 - - - +
249A SER* 3.2 23.8 - - - -
251A ARG* 3.7 17.6 + - - -
252A GLY 3.1 4.6 + - - -
254A TYR* 1.3 77.6 - - - +
256A ASP* 1.3 59.4 + - - +
258A VAL* 3.2 10.1 + - - +
259A ARG* 2.9 34.3 + - - +
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Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA* 4.1 15.0 - - + -
245A PHE* 3.4 16.0 - - - +
246A LEU* 3.5 10.8 - - + +
247A GLY* 2.8 27.1 + - - -
248A THR* 3.3 4.4 + - - -
249A SER* 3.1 31.2 + - - +
252A GLY 3.1 10.6 + - - +
253A ARG* 3.2 19.9 + - - +
255A GLY* 1.3 77.0 - - - +
257A ALA* 1.3 61.3 + - - +
259A ARG* 3.4 4.7 + - - +
260A GLU* 3.1 22.3 + - - +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 3.9 18.4 - - + +
235A THR* 4.1 4.5 - - + -
239A VAL* 3.7 17.3 - - + -
240A TYR 3.4 25.1 - - - +
241A ALA* 4.2 3.5 - - - +
253A ARG 3.3 1.2 + - - -
254A TYR 3.3 10.1 + - - +
256A ASP* 1.3 76.1 - - - +
258A VAL* 1.3 61.1 + - - +
260A GLU* 3.2 4.8 + - - +
261A ILE* 2.8 36.2 + - - +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 3.9 22.7 - - + -
45A ASP 4.4 6.1 - - - +
55A GLU* 5.2 3.1 - - + +
56A THR* 3.7 27.4 - - + -
59A LEU* 5.8 0.8 - - + +
235A THR* 3.8 14.4 - - + -
251A ARG* 4.8 6.3 - - - +
254A TYR* 3.2 39.4 + - + +
255A GLY* 3.2 10.5 + - - +
257A ALA* 1.3 77.1 - - - +
259A ARG* 1.3 58.1 + - + +
261A ILE* 3.8 6.3 - - - +
262A ASP* 2.8 29.3 + - - +
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 3.9 44.9 + - + +
57A PRO* 6.1 3.0 - - - +
244A PRO 4.8 1.0 + - - -
245A PHE* 3.6 26.8 - - + +
248A THR* 2.8 52.6 + - - +
249A SER* 4.3 2.0 - - - -
255A GLY 2.9 20.9 + - - +
256A ASP 3.7 5.2 - - - +
258A VAL* 1.3 74.8 - - + +
260A GLU* 1.3 59.0 + - - +
262A ASP* 3.7 6.9 - - - +
263A ASP* 2.9 30.3 + - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ALA 4.7 0.2 - - - +
206A THR* 3.8 27.2 + - + -
207A GLN* 2.9 25.0 + - - +
240A TYR 4.6 0.5 - - - +
241A ALA* 3.2 12.0 - - - +
242A SER* 2.5 53.2 + - - -
245A PHE* 3.6 27.2 - - + -
256A ASP 3.1 10.7 + - - +
257A ALA* 3.2 7.8 + - - +
259A ARG* 1.3 74.6 - - - +
261A ILE* 1.3 56.3 + - - +
263A ASP* 3.5 2.3 + - - +
264A SER* 2.7 37.2 + - - -
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 3.5 31.6 - - + -
41A MET* 4.7 4.3 - - + -
59A LEU* 5.7 2.0 - - + -
206A THR* 4.2 17.0 - - + -
230A TRP* 4.3 6.7 - - + -
232A VAL* 4.0 18.6 - - + -
234A ALA* 4.1 14.1 - - + -
235A THR* 3.7 31.2 - - + +
257A ALA 2.8 24.1 + - - +
258A VAL* 3.8 5.4 - - - +
260A GLU* 1.3 69.2 - - - +
262A ASP* 1.3 60.5 + - - +
264A SER* 3.3 6.7 + - - -
265A ILE* 2.9 40.6 + - + +
285A PHE* 5.3 0.2 - - + -
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU 4.6 0.2 - - - +
56A THR* 3.3 31.4 - - + -
57A PRO* 3.2 11.4 - - - +
58A ASN* 3.1 40.9 + - - +
59A LEU* 2.7 38.0 + - + +
258A VAL 2.8 18.8 + - - +
259A ARG* 3.7 7.2 - - - +
261A ILE* 1.3 73.8 - - - +
263A ASP* 1.3 60.4 + - - +
265A ILE* 3.2 7.1 + - - +
266A GLY 2.9 23.6 + - - -
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 3.7 14.2 + - - +
207A GLN* 5.3 2.9 + - - -
210A LEU* 5.5 0.9 - - - +
245A PHE* 3.7 28.0 - - + -
259A ARG 2.9 18.3 + - - +
260A GLU 3.7 4.2 - - - +
262A ASP* 1.3 77.9 + - - +
264A SER* 1.3 63.9 + - - +
266A GLY* 3.2 2.9 + - - -
267A LYS* 2.9 54.6 + - - +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 3.7 13.9 - - - +
207A GLN* 4.3 7.4 + - - -
210A LEU* 3.5 34.3 - - - +
230A TRP* 3.8 20.4 - - - -
260A GLU 2.7 22.1 + - - -
261A ILE* 3.5 5.6 - - - -
263A ASP* 1.3 76.7 + - - +
265A ILE* 1.3 62.3 + - - +
267A LYS 3.1 2.8 + - - -
268A ILE* 3.0 25.9 + - - +
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.9 24.7 - - + -
38A MET* 4.2 2.0 - - + -
58A ASN* 5.5 3.1 - - + +
59A LEU* 3.9 21.1 - - + +
62A MET* 4.8 1.8 - - - -
230A TRP* 3.6 20.6 - - + -
261A ILE* 2.9 34.8 + - + +
262A ASP* 3.2 5.4 + - - +
264A SER* 1.3 72.3 - - - +
266A GLY* 1.3 65.0 + - - +
268A ILE* 3.2 8.8 + - + +
269A LEU* 3.0 37.3 + - + +
285A PHE* 3.7 34.8 - - + -
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 3.5 29.4 - - - +
262A ASP 2.9 11.1 + - - -
263A ASP 3.2 4.9 + - - -
265A ILE* 1.3 75.7 - - - +
267A LYS* 1.3 56.5 + - - +
269A LEU* 3.3 8.6 + - - +
270A GLU* 2.9 38.1 + - - +
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Residues in contact with LYS 267 (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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210A LEU* 4.0 27.4 - - + -
214A LEU* 3.9 10.3 - - + +
263A ASP* 2.9 43.9 + - - +
264A SER 3.6 7.2 - - - +
266A GLY* 1.3 72.6 - - - +
268A ILE* 1.3 65.3 + - - +
270A GLU* 3.8 16.1 - - - +
271A LEU* 3.1 23.4 + - - +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.8 32.3 - - + -
36A LEU* 4.6 7.9 - - + -
210A LEU* 3.8 12.3 - - + -
213A ALA* 4.0 14.8 - - + -
214A LEU* 4.1 11.0 - - + -
217A ILE* 4.0 11.1 - - + +
230A TRP* 3.9 44.0 - - + -
264A SER 3.0 18.6 + - - +
265A ILE* 3.2 10.5 + - + +
267A LYS* 1.3 76.9 - - - +
269A LEU* 1.3 66.8 + - + +
271A LEU* 3.2 12.8 + - - +
272A LEU* 3.3 16.0 + - + +
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Residues in contact with LEU 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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36A LEU* 5.4 3.4 - - + -
58A ASN 4.9 4.7 - - - +
62A MET* 4.0 35.7 - - + +
65A GLU* 5.3 1.6 - - - +
265A ILE* 3.0 30.1 + - + +
266A GLY* 3.7 6.3 - - - +
268A ILE* 1.3 81.1 - - + +
270A GLU* 1.3 60.4 + - - +
272A LEU* 3.3 11.6 + - + +
273A GLN* 3.3 27.3 + - - +
283A VAL* 3.8 32.8 - - + -
325A TRP* 4.0 31.7 - - + +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 4.6 7.6 - - - +
61A ARG* 5.8 1.0 + - - -
266A GLY 2.9 25.5 + - - +
267A LYS* 3.8 17.3 - - - +
268A ILE 3.3 0.2 - - - -
269A LEU* 1.3 74.4 - - - +
271A LEU* 1.3 58.9 + - - +
273A GLN* 3.3 13.7 + - - +
274A ASP* 2.9 43.3 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.6 50.9 - - + +
217A ILE* 3.9 17.3 - - + -
218A LYS* 4.0 18.2 - - + -
267A LYS 3.1 14.2 + - - +
268A ILE 3.2 9.2 + - - +
270A GLU* 1.3 76.6 - - - +
272A LEU* 1.3 58.0 + - - +
274A ASP* 3.2 11.2 + - + +
275A LEU* 2.9 52.0 + - + +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.8 24.7 - - + -
217A ILE* 3.9 12.8 - - + -
226A PHE* 3.9 21.1 - - + -
268A ILE 3.3 14.9 + - - +
269A LEU* 3.5 12.8 - - + +
270A GLU 3.3 0.2 - - - -
271A LEU* 1.3 77.2 - - - +
273A GLN* 1.3 58.4 + - - +
275A LEU* 4.9 0.4 - - - -
276A HIS 3.3 2.3 + - - -
277A VAL* 3.0 53.4 + - + +
278A ALA* 3.0 16.5 + - + -
281A THR* 3.8 13.9 - - + +
283A VAL* 3.9 19.1 - - + -
325A TRP* 4.3 9.4 - - + -
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Residues in contact with GLN 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 4.5 13.8 + - - +
269A LEU* 3.3 16.1 + - - +
270A GLU* 3.3 18.0 + - - +
272A LEU* 1.3 74.1 - - - +
274A ASP* 1.3 63.3 + - - +
275A LEU 3.2 0.4 - - - -
276A HIS* 3.1 28.3 + - - +
278A ALA* 3.7 21.1 - - + -
325A TRP* 4.4 16.9 - - + -
327A PRO* 5.6 2.6 - - - +
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 2.9 30.1 + - - +
271A LEU* 3.2 14.8 + - + +
273A GLN* 1.3 78.3 - - - +
275A LEU* 1.3 61.0 + - + +
276A HIS* 3.3 18.5 - - - -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.9 19.3 - - + -
218A LYS* 4.2 21.8 - - + +
221A ALA* 4.4 15.1 - - + +
271A LEU* 2.9 48.4 + - + +
272A LEU 4.3 2.7 - - - +
274A ASP* 1.3 76.7 - - + +
276A HIS* 1.3 73.5 + - - +
277A VAL* 3.2 12.5 + - + +
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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