Contacts of the helix formed by residues 313 - 339 (chain R) in PDB entry 6DDE
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 PHE 313 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311R THR* 3.1 4.0 - - - -
312R THR* 1.3 81.2 - - + +
314R GLN* 1.3 64.2 + - - +
315R THR 3.6 1.3 - - - -
316R VAL* 3.3 22.9 - - + +
317R SER* 3.7 8.8 + - - -
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Residues in contact with GLN 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299R TYR* 2.3 38.7 + - + +
308R ILE* 3.3 26.4 - - - +
309R PRO 2.9 23.2 - - - +
310R GLU* 3.4 14.1 + - - +
311R THR* 2.9 27.6 + - - +
313R PHE* 1.3 78.7 - - - +
315R THR* 1.3 61.9 + - - +
317R SER* 3.2 7.7 + - - -
318R TRP* 2.9 27.0 + - + +
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Residues in contact with THR 315 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R TYR* 3.5 22.6 - - + +
310R GLU* 3.6 23.3 - - - +
311R THR 4.8 3.4 - - - +
312R THR* 5.3 6.1 - - - +
314R GLN* 1.3 78.5 - - - +
316R VAL* 1.3 63.5 + - - +
318R TRP* 3.7 16.2 - - - +
319R HIS* 2.9 49.1 + - - -
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Residues in contact with VAL 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R THR* 5.2 9.4 - - - +
71R ILE* 3.8 28.7 - - + -
128R TYR* 3.4 17.7 - - - +
312R THR 4.9 3.8 - - - +
313R PHE* 3.3 24.2 - - + +
315R THR* 1.3 80.9 - - - +
317R SER* 1.3 62.0 + - - +
319R HIS* 3.4 4.3 + - + +
320R PHE* 2.9 26.5 + - - +
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Residues in contact with SER 317 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313R PHE 4.0 8.5 - - - -
314R GLN* 3.2 9.7 + - - -
316R VAL* 1.3 82.5 - - - +
318R TRP* 1.3 57.5 + - - +
320R PHE* 3.3 13.8 + - - +
321R CYS* 2.9 24.1 + - - +
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Residues in contact with TRP 318 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D DAL 3.2 37.8 - - + +
4D MEA 6.3 0.7 - - - -
5D ETA 3.4 24.7 - - - -
296R ILE* 4.4 14.1 - - + +
299R TYR* 3.3 48.6 - + + +
300R VAL* 5.6 3.2 - - + +
303R LYS* 3.7 18.2 - - + -
314R GLN* 2.9 18.5 + - + +
315R THR* 3.9 18.6 - - - +
316R VAL 3.3 0.4 - - - -
317R SER* 1.3 75.0 - - - +
319R HIS* 1.3 72.6 + + - +
321R CYS* 3.0 15.4 + - + -
322R ILE* 2.9 27.9 + - + +
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Residues in contact with HIS 319 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D DAL 5.6 0.7 - - - -
3D GLY* 5.7 4.3 - - - -
4D MEA 5.8 4.7 - - - -
71R ILE* 6.5 0.9 - - + -
75R TYR* 3.7 30.1 - + + -
124R GLN* 5.1 9.4 - - + -
125R SER* 6.3 0.4 - - - -
127R ASN* 5.1 4.3 + - + -
128R TYR* 3.4 39.6 - + + +
315R THR* 2.9 41.2 + - - +
316R VAL* 4.0 5.4 - - + +
318R TRP* 1.3 86.8 - + - +
320R PHE* 1.3 60.2 + - - +
322R ILE* 3.3 26.7 + - + +
323R ALA* 2.9 24.9 + - - +
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Residues in contact with PHE 320 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R LEU* 6.2 3.8 - - + -
316R VAL 2.9 15.3 + - - +
317R SER* 3.4 15.9 - - - +
319R HIS* 1.3 76.4 - - - +
321R CYS* 1.3 58.5 + - - +
323R ALA* 3.3 12.6 - - + +
324R LEU* 2.9 52.7 + - + +
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Residues in contact with CYS 321 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295R PRO* 4.8 20.2 - - + +
296R ILE* 3.9 12.3 - - + +
299R TYR* 5.8 1.3 - - + -
317R SER 2.9 13.7 + - - +
318R TRP* 3.0 26.2 + - + +
320R PHE* 1.3 74.6 - - - +
322R ILE* 1.3 57.3 + - - +
324R LEU* 3.5 16.3 + - + +
325R GLY* 2.9 24.3 + - - -
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Residues in contact with ILE 322 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D TYR 3.4 18.8 - - - +
2D DAL 3.5 26.0 - - - +
3D GLY* 4.1 4.0 - - - +
75R TYR* 3.7 22.2 - - + +
124R GLN* 6.0 0.9 - - + -
296R ILE* 3.7 20.9 - - + -
318R TRP* 2.9 20.9 + - + +
319R HIS* 3.5 37.7 - - + +
321R CYS* 1.3 76.3 - - - +
323R ALA* 1.3 57.0 + - - +
325R GLY* 3.1 2.0 + - - +
326R TYR* 3.0 41.6 + - + -
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Residues in contact with ALA 323 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R LEU 4.9 6.3 - - - +
75R TYR* 4.7 14.1 - - + +
78R VAL* 4.1 25.4 - - + +
121R LEU* 5.6 2.9 - - - -
319R HIS 2.9 13.7 + - - +
320R PHE* 3.1 22.6 + - + +
322R ILE* 1.3 75.9 - - - +
324R LEU* 1.3 59.1 + - - +
326R TYR* 3.3 7.1 + - - +
327R THR* 2.9 25.0 + - - -
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Residues in contact with LEU 324 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291R VAL 4.0 6.7 - - - +
292R CYS* 2.9 57.4 - - - +
295R PRO* 3.7 28.0 - - + -
296R ILE 5.1 0.4 - - - +
320R PHE* 2.9 48.5 + - + +
321R CYS* 3.6 13.7 - - - +
323R ALA* 1.3 72.9 - - - +
325R GLY* 1.3 65.5 + - - +
327R THR* 3.7 15.6 + - - -
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Residues in contact with GLY 325 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292R CYS 3.8 2.9 - - - -
293R TRP* 2.6 44.2 + - - -
296R ILE* 4.3 9.6 - - - -
321R CYS 2.9 15.7 + - - -
322R ILE 3.1 4.9 + - - -
324R LEU* 1.3 79.2 - - - +
326R TYR* 1.3 62.2 + - - +
327R THR 3.3 0.9 + - - -
328R ASN* 3.5 6.4 + - - +
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Residues in contact with TYR 326 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D TYR* 2.4 31.4 + - + -
78R VAL* 4.6 4.0 - - + +
117R ALA* 3.5 36.8 - - + -
118R THR* 5.2 3.5 - - - -
120R THR* 5.4 0.7 - - - -
121R LEU* 3.6 40.2 - - + -
124R GLN* 4.2 9.1 + - - -
147R ASP* 2.3 32.3 + - - -
151R MET* 6.2 2.6 - - + +
293R TRP* 5.7 3.8 - + - -
322R ILE* 3.0 36.5 + - + +
323R ALA 3.6 3.4 - - - +
325R GLY* 1.3 72.4 - - - +
327R THR* 1.3 59.3 + - - +
328R ASN 3.2 2.0 - - - -
329R SER* 3.1 18.6 + - - +
330R CYS* 3.0 24.3 + - - +
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Residues in contact with THR 327 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R VAL* 4.5 7.4 - - - -
288R VAL* 6.0 0.9 - - - +
292R CYS* 4.8 2.9 - - - -
323R ALA 2.9 16.4 + - - -
324R LEU* 3.7 16.8 - - - -
325R GLY 3.2 1.2 - - - -
326R TYR* 1.3 74.5 - - - +
328R ASN* 1.3 59.7 + - - +
330R CYS* 3.5 9.3 - - - +
331R LEU* 2.9 41.8 + - - +
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Residues in contact with ASN 328 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154R SER* 5.9 0.7 - - - -
158R LEU* 4.4 2.6 - - - +
288R VAL* 5.0 11.0 - - - +
289R PHE* 3.3 38.5 - - - +
292R CYS* 3.7 25.0 - - + +
293R TRP* 3.3 30.6 - - + -
325R GLY 3.5 11.2 + - - +
326R TYR 3.2 0.4 - - - -
327R THR* 1.3 77.2 - - - +
329R SER* 1.3 57.6 + - - +
331R LEU* 5.4 1.3 - - - +
332R ASN* 2.9 54.7 + - - +
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Residues in contact with SER 329 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R GLY* 5.6 0.2 - - - -
86R ASN* 3.5 6.8 - - - +
114R ASP* 3.1 62.4 + - - +
117R ALA* 4.1 7.4 - - - +
118R THR* 4.2 6.7 + - - -
154R SER* 5.4 0.7 - - - -
293R TRP* 5.1 7.4 - - - -
325R GLY 4.4 0.4 + - - -
326R TYR* 3.1 27.6 + - - +
328R ASN* 1.3 80.0 - - - +
330R CYS* 1.3 62.1 + - - +
333R PRO* 3.8 2.4 - - - +
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Residues in contact with CYS 330 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R VAL* 4.3 10.5 - - + +
81R VAL* 3.6 33.0 - - - -
82R GLY* 3.7 25.2 - - - +
85R GLY* 5.9 1.0 - - - -
86R ASN* 4.9 2.4 + - - +
118R THR* 5.8 0.8 - - - -
326R TYR 3.0 12.4 + - - +
327R THR* 3.5 11.7 - - - +
328R ASN 3.2 0.2 - - - -
329R SER* 1.3 81.2 - - - +
331R LEU* 1.3 76.3 + - + +
332R ASN 3.2 5.2 + - - -
333R PRO* 3.5 6.2 - - - +
334R VAL* 3.5 19.7 - - - +
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Residues in contact with LEU 331 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288R VAL* 5.1 20.0 - - + +
327R THR* 2.9 30.4 + - - +
328R ASN* 3.8 0.9 - - - -
330R CYS* 1.3 90.2 - - + +
332R ASN* 1.3 59.2 + - - +
333R PRO 3.7 0.4 - - - -
334R VAL* 3.7 19.2 - - + +
335R LEU* 2.9 30.5 + - + +
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Residues in contact with ASN 332 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110R LEU* 3.4 28.0 - - - +
114R ASP* 3.8 5.9 + - - +
154R SER* 4.6 2.4 + - - -
158R LEU* 3.4 29.3 - - - +
285R VAL* 4.8 5.6 - - - +
288R VAL* 6.4 1.6 - - - -
328R ASN* 2.9 30.2 + - - +
330R CYS 3.2 1.8 - - - -
331R LEU* 1.3 75.4 - - - +
333R PRO* 1.4 66.7 - - + +
335R LEU* 3.3 6.6 + - - +
336R TYR* 3.0 48.4 + - - +
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Residues in contact with PRO 333 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R GLY 5.1 1.8 - - - +
86R ASN* 3.3 24.9 - - - +
89R VAL* 3.7 31.7 - - + +
107R ILE* 6.0 1.1 - - + +
110R LEU* 4.8 5.8 - - + +
111R ALA* 4.5 8.3 - - + +
114R ASP* 3.8 11.9 - - - +
329R SER 3.8 4.5 - - - +
330R CYS 3.5 12.6 - - - +
332R ASN* 1.4 89.7 - - + +
334R VAL* 1.3 60.0 + - + +
335R LEU 3.2 0.2 - - - -
336R TYR* 3.7 8.5 - - + +
337R ALA* 2.9 31.9 + - + +
338R PHE* 3.9 2.8 - - - -
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Residues in contact with VAL 334 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R VAL 5.8 0.9 - - - +
85R GLY* 5.1 14.4 - - - -
89R VAL* 6.2 0.2 - - + -
330R CYS* 3.5 24.0 - - - +
331R LEU* 3.7 22.2 - - + +
332R ASN 3.2 0.4 - - - -
333R PRO* 1.3 80.2 - - + +
335R LEU* 1.3 60.3 + - - +
338R PHE* 3.3 44.4 - - + +
339R LEU* 4.5 2.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 335 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281R MET* 4.1 11.3 - - + +
284R VAL* 3.8 23.6 - - + -
285R VAL* 3.7 41.1 - - + -
288R VAL* 3.8 17.9 - - + -
331R LEU 2.9 18.6 + - - +
332R ASN* 3.7 6.1 - - - +
333R PRO 3.2 0.2 - - - -
334R VAL* 1.3 78.7 - - - +
336R TYR* 1.3 65.4 + - + +
339R LEU* 3.4 47.9 - - + +
----------------------------------------------------------
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Residues in contact with TYR 336 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R ILE* 5.5 12.6 - - + -
110R LEU* 3.6 25.8 - - + -
158R LEU* 3.3 16.8 + - + +
161R MET* 3.5 33.5 - - + +
165R ARG* 4.2 18.1 + - - +
252R TYR* 4.4 12.0 + - - -
281R MET* 4.3 14.8 - - + -
285R VAL* 3.3 35.1 - - + +
332R ASN* 3.0 28.7 + - - +
333R PRO* 4.4 3.4 - - + +
335R LEU* 1.3 84.4 - - + +
337R ALA* 1.3 62.8 + - + +
338R PHE 3.2 1.6 + - - -
339R LEU 3.4 6.2 + - - -
340R ASP* 2.7 32.1 - - - +
----------------------------------------------------------
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Residues in contact with ALA 337 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R VAL* 3.8 31.6 - - + -
92R VAL* 5.5 6.1 - - + -
107R ILE* 4.8 12.8 - - + -
333R PRO* 2.9 18.9 + - + +
336R TYR* 1.3 74.7 - - - +
338R PHE* 1.3 61.5 + - + +
340R ASP* 4.2 8.4 + - - +
343R PHE* 3.6 21.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 338 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R GLY* 5.6 3.1 - - - -
88R LEU* 5.0 19.5 - - + -
89R VAL* 4.6 14.6 - - + -
333R PRO 3.9 4.0 - - - -
334R VAL* 3.3 49.9 + - + +
336R TYR 3.2 0.6 - - - -
337R ALA* 1.3 80.1 - - - +
339R LEU* 1.3 65.2 + - + +
340R ASP 3.2 13.1 + - - +
343R PHE* 4.5 11.8 - - + +
----------------------------------------------------------
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Residues in contact with LEU 339 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLY 4.7 0.5 - - - +
277R ARG* 3.9 17.2 + - - +
281R MET* 3.4 26.3 - - + +
334R VAL 4.9 1.8 - - - +
335R LEU* 3.4 41.8 + - + +
336R TYR 3.4 3.5 + - - -
338R PHE* 1.3 83.3 - - + +
340R ASP* 1.3 70.3 + - - +
----------------------------------------------------------
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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