Contacts of the helix formed by residues 256 - 286 (chain A) in PDB entry 4WFH
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 ALA 256 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER 3.5 0.6 - - - -
255A PRO* 1.3 81.5 - - + +
257A TYR* 1.3 67.9 + - - +
259A PRO* 3.4 9.0 - - - +
260A LEU* 3.1 28.1 + - + +
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Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.8 8.1 - - + -
217A PHE* 3.7 16.7 - + - -
220A MET* 3.5 42.0 - - + -
221A GLU* 2.5 38.6 + - - +
246A ALA* 3.9 12.6 - - - +
247A GLY* 5.0 0.9 - - - -
249A ASP 5.0 7.6 - - - -
251A ARG* 4.3 21.8 - - + -
254A SER* 3.3 25.6 + - - +
255A PRO 3.1 0.8 + - - -
256A ALA* 1.3 79.2 - - - +
258A GLN* 1.3 73.1 + - + +
260A LEU* 3.5 6.3 - - - +
261A VAL* 3.0 43.3 + - + +
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Residues in contact with GLN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY* 5.3 5.6 + - - -
247A GLY* 2.6 28.8 + - - +
248A ALA 3.4 4.4 + - - -
249A ASP* 3.1 25.4 + - - +
250A PRO* 3.0 44.6 - - + +
251A ARG 5.1 0.6 - - - +
254A SER 4.7 0.2 + - - -
255A PRO 3.7 3.2 + - - +
257A TYR* 1.3 85.5 - - + +
259A PRO* 1.3 71.8 - - + +
261A VAL* 3.5 6.0 + - - +
262A TRP* 3.4 50.8 + - + -
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Residues in contact with PRO 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO 3.2 18.8 - - - +
256A ALA* 3.4 13.2 - - - +
258A GLN* 1.3 95.2 - - + +
260A LEU* 1.3 63.6 + - - +
262A TRP* 2.8 24.1 + - + +
263A PHE* 2.8 23.9 + - - +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 6.1 6.3 - - + -
256A ALA* 3.1 25.3 + - + +
257A TYR* 3.5 5.2 - - - +
259A PRO* 1.3 75.7 - - - +
261A VAL* 1.3 52.7 + - + +
263A PHE* 3.4 21.2 - - + +
264A TRP* 2.6 38.7 + - + +
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 5.6 0.9 - - + -
216A VAL* 6.5 0.2 - - + -
217A PHE* 4.1 21.1 - - + -
231A PHE* 5.9 0.4 - - + -
246A ALA* 4.4 8.1 - - + -
247A GLY* 4.2 22.7 - - - +
257A TYR* 3.0 41.1 + - + +
258A GLN* 3.6 8.7 - - - +
259A PRO 3.1 0.2 - - - -
260A LEU* 1.3 73.9 - - + +
262A TRP* 1.3 62.9 + - + +
264A TRP* 3.2 22.1 + - + +
265A ILE* 2.9 37.1 + - + +
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Residues in contact with TRP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY* 4.5 14.1 - - - -
120A PHE* 3.8 39.9 - + + -
121A PHE* 3.5 33.7 - + + -
247A GLY 3.5 9.4 + - - -
258A GLN* 3.4 41.1 + - + -
259A PRO* 2.8 26.5 + - + +
261A VAL* 1.3 74.5 - - + +
263A PHE* 1.3 68.4 + - - +
265A ILE* 3.1 10.9 + - + +
266A LEU* 3.0 23.3 + - - +
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Residues in contact with PHE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO 2.8 14.9 + - - +
260A LEU* 3.4 25.6 - - + +
262A TRP* 1.3 72.7 - - - +
264A TRP* 1.3 62.3 + - - +
266A LEU* 3.4 18.7 + - + +
267A LEU* 3.0 62.9 + - + +
36B LEU* 6.4 1.6 - - + -
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Residues in contact with TRP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU 4.8 0.9 - - - -
209A PHE* 3.1 45.8 + + - +
213A PRO* 3.2 21.4 - - + +
217A PHE* 3.8 31.2 - + - -
231A PHE* 4.2 11.0 - + - -
232A VAL* 4.0 28.5 - - + -
235A THR* 4.4 7.0 - - + -
236A LEU* 3.9 24.5 - - + +
260A LEU* 2.6 23.9 + - + +
261A VAL* 3.2 13.2 - - + +
263A PHE* 1.3 71.7 - - - +
265A ILE* 1.3 84.5 + - + +
267A LEU* 3.3 5.1 + - - +
268A GLY* 2.7 33.3 + - - -
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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
----------------------------------------------------------
121A PHE* 4.9 16.2 - - + -
128A THR* 4.8 5.4 - - + -
130A ILE* 3.9 17.9 - - + -
132A TYR* 4.6 7.6 - - + +
231A PHE* 6.0 0.7 - - + -
235A THR* 4.3 17.3 - - + -
236A LEU* 4.5 5.6 - - + +
261A VAL* 2.9 30.0 + - + +
262A TRP* 3.1 10.5 + - + +
264A TRP* 1.3 94.7 - - + +
266A LEU* 1.3 58.8 + - - +
269A LEU* 2.9 53.7 + - + +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 4.1 22.2 - - + -
160A LEU* 3.7 25.6 - - + -
161A LEU* 4.0 6.4 - - + +
164A VAL* 4.6 10.8 - - + -
262A TRP 3.0 12.0 + - - +
263A PHE* 3.5 25.8 - - + +
265A ILE* 1.3 82.4 - - - +
267A LEU* 1.3 70.2 + - + +
269A LEU* 3.7 5.8 - - - +
270A ALA* 3.3 18.2 + - - +
36B LEU* 4.2 24.7 - - + -
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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
----------------------------------------------------------
164A VAL* 4.2 20.4 - - + -
168A LEU* 3.8 16.9 - - + +
209A PHE* 4.1 27.1 - - + -
263A PHE* 3.0 56.4 + - + +
264A TRP* 3.9 3.8 - - - +
266A LEU* 1.3 83.9 - - + +
268A GLY* 1.3 62.9 + - - +
270A ALA* 3.3 6.9 + - - +
271A TYR* 3.0 22.5 + - - +
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 4.2 24.6 - - - -
236A LEU* 4.1 15.7 - - - -
264A TRP* 2.7 22.7 + - - -
265A ILE 3.9 0.7 - - - -
267A LEU* 1.3 73.0 - - - +
269A LEU* 1.3 56.2 + - - +
271A TYR* 3.3 2.3 + - - +
272A PHE* 2.8 33.6 + - - +
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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
----------------------------------------------------------
128A THR* 4.0 26.0 - - + +
130A ILE* 4.3 2.7 - - + -
157A PHE* 4.5 12.1 - - + -
161A LEU* 4.0 17.1 - - + +
235A THR 4.4 2.7 - - - +
236A LEU* 3.5 33.3 - - + +
238A THR* 3.6 21.8 - - + -
265A ILE* 2.9 43.2 + - + +
266A LEU 3.7 3.6 - - - +
268A GLY* 1.3 76.3 - - - +
270A ALA* 1.3 57.7 + - - +
272A PHE* 3.3 5.3 + - + +
273A ALA* 2.8 30.0 + - - +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.8 17.0 - - + +
164A VAL* 4.1 12.8 - - + +
165A GLY* 3.8 29.1 - - - +
168A LEU* 4.6 4.3 - - + -
266A LEU 3.3 9.4 + - - +
267A LEU 3.3 8.2 + - - +
268A GLY 3.2 0.6 - - - -
269A LEU* 1.3 75.9 - - - +
271A TYR* 1.3 63.9 + - - +
273A ALA* 3.4 5.4 + - - +
274A SER* 2.9 30.9 + - - -
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.0 7.9 - - + +
172A LEU* 4.4 11.4 - - + -
201A PHE* 3.7 22.2 - + - -
202A LEU* 2.2 43.6 + - - +
205A GLY* 3.4 17.0 - - - -
206A CYS* 3.0 21.2 + - - +
209A PHE* 3.4 40.4 - + + -
210A VAL* 5.2 3.8 - - + -
267A LEU 3.0 6.5 + - - +
268A GLY 3.5 6.5 - - - +
270A ALA* 1.3 75.7 - - - +
272A PHE* 1.3 80.4 + + - +
274A SER* 3.5 5.2 + - - -
275A VAL* 3.2 39.2 + - + +
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Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL* 4.3 17.5 - - + -
233A ILE* 4.7 14.8 - - + -
236A LEU* 3.5 57.9 - - + +
237A THR* 4.2 20.0 - - + -
268A GLY 2.8 13.4 + - - +
269A LEU 3.7 4.0 - - - +
271A TYR* 1.3 88.9 - + - +
273A ALA* 1.3 63.0 + - - +
275A VAL* 3.3 8.0 + - + +
276A LEU* 3.0 52.0 + - + +
151B LEU* 4.3 21.3 - - + -
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.6 14.1 - - + +
165A GLY* 6.4 0.2 - - - -
269A LEU 2.8 21.1 + - - +
270A ALA* 3.6 9.2 - - - +
271A TYR 3.3 0.2 - - - -
272A PHE* 1.3 73.6 - - - +
274A SER* 1.3 58.5 + - - +
276A LEU* 3.0 7.8 + - - +
277A THR* 2.9 39.1 + - + +
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY* 3.9 22.2 + - - -
169A GLY* 5.7 1.5 - - - -
173A ARG* 5.0 7.2 - - - -
201A PHE* 4.4 20.6 - - - -
270A ALA 2.9 16.0 + - - -
271A TYR* 3.8 6.4 - - - -
272A PHE 3.4 0.2 - - - -
273A ALA* 1.3 77.7 - - - +
275A VAL* 1.3 60.7 + - - +
277A THR* 2.9 22.3 + - - -
278A THR* 3.1 17.8 + - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 5.1 9.4 - - + -
202A LEU* 4.8 13.9 - - + -
271A TYR* 3.2 41.4 + - + +
272A PHE* 3.4 11.0 - - + +
273A ALA 3.2 0.6 - - - -
274A SER* 1.3 76.7 - - - +
276A LEU* 1.3 66.3 + - + +
278A THR* 3.1 7.4 + - - -
279A ILE* 2.9 41.0 + - + +
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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
----------------------------------------------------------
272A PHE* 3.0 46.1 + - + +
273A ALA* 3.0 9.8 + - - +
275A VAL* 1.3 85.3 - - + +
277A THR* 1.3 58.1 + - + +
279A ILE* 3.2 7.0 - - + +
280A GLY* 2.5 34.7 + - - -
154B ILE* 4.9 9.4 - - + -
155B PRO* 4.0 37.7 - - + -
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 2.9 25.1 + - + +
274A SER* 2.9 18.3 + - - -
276A LEU* 1.3 76.7 - - + +
278A THR* 1.3 60.1 + - - +
280A GLY* 3.4 1.4 - - - -
281A ASN* 2.5 34.9 + - - +
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 4.7 15.7 - - - +
201A PHE* 5.6 4.1 - - + -
274A SER* 3.1 14.6 + - - +
275A VAL* 3.1 11.6 + - - -
277A THR* 1.3 84.6 + - - +
279A ILE* 1.3 56.4 + - - +
281A ASN* 3.0 14.2 - - + +
282A TRP* 2.6 34.3 + - - +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 2.9 36.2 + - + +
276A LEU* 3.2 25.1 - - + +
278A THR* 1.3 74.3 + - - +
280A GLY* 1.3 63.8 + - - +
282A TRP* 3.8 18.9 - - + +
283A LEU* 3.0 47.6 + - + +
151B LEU 5.8 1.1 - - - +
155B PRO* 4.8 13.2 - - + -
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU 2.5 25.1 + - - -
277A THR* 3.4 2.0 - - - -
279A ILE* 1.3 73.8 - - - +
281A ASN* 1.3 61.0 + - - +
283A LEU* 3.1 11.5 + - - +
284A ARG* 3.1 27.9 + - - +
155B PRO* 5.7 2.2 - - - -
159B ILE* 3.9 9.2 - - - +
----------------------------------------------------------
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A THR 2.5 22.6 + - - +
278A THR* 3.0 21.0 - - - +
280A GLY* 1.3 75.9 - - - +
282A TRP* 1.3 59.8 + - - +
284A ARG* 3.7 17.8 - - - +
285A VAL* 3.6 18.0 - - - +
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Residues in contact with TRP 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A THR 2.6 16.9 + - - +
279A ILE* 3.8 18.2 - - + +
280A GLY 3.3 0.2 - - - -
281A ASN* 1.3 73.2 - - - +
283A LEU* 1.3 98.6 + - + +
285A VAL* 3.0 27.5 - - + +
286A VAL* 3.2 33.3 - - + +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 3.0 36.9 + - + +
280A GLY* 3.1 3.3 + - - +
282A TRP* 1.3 106.7 - - + +
284A ARG* 1.3 66.4 + - - +
286A VAL* 3.1 25.9 + - + +
155B PRO* 3.9 28.0 - - + +
156B LEU* 4.9 1.6 - - - +
159B ILE* 3.5 29.6 - - + +
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY 3.1 14.3 + - - +
281A ASN* 3.7 19.7 - - - +
283A LEU* 1.3 77.4 - - - +
285A VAL* 1.3 73.6 + - + +
286A VAL 4.2 4.0 - - - +
159B ILE* 4.2 17.9 - - + -
162B ALA* 6.3 2.7 - - + -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 3.6 18.4 - - - +
282A TRP* 3.0 28.5 - - + +
284A ARG* 1.3 85.2 - - + +
286A VAL* 1.3 70.2 - - + +
----------------------------------------------------------
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TRP* 3.2 51.8 - - + +
283A LEU* 3.1 21.8 + - + +
284A ARG 4.2 4.0 - - - +
285A VAL* 1.3 86.8 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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