Contacts of the helix formed by residues 269 - 292 (chain A) in PDB entry 3SAJ
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 LYS 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.1 29.6 + - - +
20A GLU* 3.0 31.9 + - - +
188A SER* 6.2 0.2 - - - +
189A GLU* 6.3 2.7 - - + -
219A ASP* 3.6 28.3 - - + +
240A TYR* 5.2 0.2 - - - -
267A ARG 3.4 4.2 + - - +
268A PRO* 1.3 75.2 - - - +
270A TYR* 1.3 68.9 + - + +
271A THR* 4.0 10.8 - - - +
272A SER* 3.0 13.3 + - - +
273A ALA* 3.0 11.2 + - - +
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.1 41.7 + - - -
188A SER* 3.8 27.4 + - - -
214A ASN* 3.9 4.9 + - - -
215A LEU* 3.9 32.3 - - + -
216A GLY* 3.8 22.2 - - - +
219A ASP* 3.4 18.4 + - - +
236A GLN* 6.4 0.4 - - - +
237A LEU* 4.9 17.3 - - + +
238A VAL* 5.2 4.9 - - + -
267A ARG* 5.1 1.6 - - - +
268A PRO 3.8 1.0 + - - -
269A LYS* 1.3 74.0 - - + +
271A THR* 1.3 78.3 + - + +
273A ALA* 3.3 10.1 + - - +
274A LEU* 3.0 43.5 + - + +
332A THR* 5.1 0.3 - - - +
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 2.5 32.1 + - - -
70A PHE* 5.4 4.7 - - + -
93A PRO* 4.4 9.1 - - + +
108A ARG* 3.7 15.3 - - - +
188A SER* 5.3 2.7 - - - +
269A LYS* 4.0 8.8 + - - +
270A TYR* 1.3 107.6 - - + +
272A SER* 1.3 56.2 + - - +
274A LEU* 3.6 5.8 + - - +
275A THR* 2.7 36.8 + - - -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 2.8 47.4 + - - +
20A GLU* 3.5 10.6 + - - +
23A ALA* 3.5 22.3 - - - +
252A TRP* 4.8 2.2 - - - -
268A PRO* 4.3 7.6 - - - -
269A LYS 3.0 11.1 + - - -
271A THR* 1.3 81.4 + - - +
273A ALA* 1.3 61.8 + - - -
275A THR* 3.1 4.3 + - - -
276A TYR* 3.0 21.0 + - - +
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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
----------------------------------------------------------
238A VAL* 3.7 30.1 - - + -
240A TYR* 4.1 8.5 - - - +
252A TRP* 5.8 0.4 - - - -
268A PRO* 5.0 1.5 - - - +
269A LYS 3.0 11.7 + - - +
270A TYR* 3.3 9.4 + - - +
272A SER* 1.3 75.0 - - - +
274A LEU* 1.3 57.5 + - - +
276A TYR* 3.5 4.5 + - - +
277A ASP* 3.1 30.5 + - - +
331A LEU* 4.0 21.6 - - + +
332A THR* 4.0 7.4 - - + -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 3.8 23.8 - - + +
107A LEU* 3.2 40.8 - - + +
108A ARG* 3.9 31.0 - - + -
237A LEU* 4.1 11.4 - - + -
270A TYR* 3.0 33.7 + - + +
271A THR* 4.0 2.7 - - - +
272A SER 3.2 0.2 - - - -
273A ALA* 1.3 74.5 - - - +
275A THR* 1.3 61.4 + - - +
276A TYR 3.2 0.2 - - - -
277A ASP* 3.7 5.9 - - + +
278A GLY 2.8 23.7 + - - -
332A THR* 4.0 15.7 - - + +
343A ARG* 3.7 13.9 - - - +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 5.2 0.7 - - + -
20A GLU* 3.3 30.9 - - + +
23A ALA* 4.5 0.2 - - - -
24A PHE* 3.9 19.1 - - + +
68A PHE* 3.6 25.6 - - + -
70A PHE* 3.7 20.2 - - + -
93A PRO* 3.8 5.0 - - - +
271A THR 2.7 23.5 + - - -
272A SER* 3.4 6.1 - - - -
274A LEU* 1.3 77.9 - - - +
276A TYR* 1.3 56.3 + - - +
278A GLY* 3.2 1.0 + - - -
279A VAL* 3.0 30.5 + - - +
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Residues in contact with TYR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.1 11.6 - - + +
26A PHE* 3.5 25.4 - + - -
27A ALA* 3.4 32.8 - - + +
30A GLN* 2.3 33.6 + - - -
248A ILE* 3.5 39.0 - - + +
252A TRP* 4.5 8.7 - + + -
272A SER 3.0 12.8 + - - +
273A ALA* 3.6 9.0 - - - +
275A THR* 1.3 73.6 - - - +
277A ASP* 1.3 79.2 + - - +
279A VAL* 3.5 5.7 + - - +
280A LYS* 3.4 26.4 + - + +
330A GLY* 5.8 0.9 - - - -
331A LEU* 4.0 13.0 - - + -
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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
----------------------------------------------------------
107A LEU* 5.1 2.0 - - + -
273A ALA 3.1 12.4 + - - +
274A LEU* 4.0 6.7 - - + +
275A THR 3.4 0.2 - - - -
276A TYR* 1.3 82.4 - - - +
278A GLY* 1.3 64.2 - - - +
280A LYS* 3.0 8.4 + - - +
281A VAL* 2.9 25.8 + - + +
328A PHE* 3.8 3.1 - - + -
330A GLY* 3.5 10.0 - - - -
331A LEU* 2.7 28.4 + - - +
332A THR* 2.6 45.1 + - - +
335A VAL* 4.1 14.6 - - + +
343A ARG* 5.7 1.1 - - - +
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 3.9 8.7 - - - -
91A ILE* 4.3 1.7 - - - +
107A LEU* 3.5 34.9 - - - +
274A LEU 2.8 15.5 + - - -
275A THR 3.2 3.0 + - - -
277A ASP* 1.3 72.3 - - - +
279A VAL* 1.3 62.4 + - - +
281A VAL* 3.2 12.5 + - - +
282A MET* 3.2 18.2 + - - +
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.4 51.8 - - + +
27A ALA* 4.0 9.6 - - + +
28A LEU* 3.5 38.4 - - + +
31A LEU* 4.1 11.7 - - + -
37A LEU* 4.2 2.4 - - + +
275A THR 3.0 13.5 + - - +
276A TYR 3.8 7.2 - - - +
277A ASP 3.2 0.2 - - - -
278A GLY* 1.3 77.7 - - - +
280A LYS* 1.3 57.6 + - - +
282A MET* 3.4 10.3 + - + +
283A ALA* 3.0 24.4 + - - +
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 5.6 0.2 - - - +
31A LEU* 4.8 15.3 - - + -
276A TYR* 3.4 18.9 + - + +
277A ASP* 3.0 10.0 + - - +
279A VAL* 1.3 77.6 - - - +
281A VAL* 1.3 57.4 + - - +
283A ALA* 3.6 5.1 - - + +
284A GLU* 2.8 56.8 + - + +
328A PHE* 3.6 45.5 - - + +
329A GLU 4.6 7.0 + - - +
330A GLY* 5.8 1.6 - - - -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 5.0 6.3 - - + -
105A LEU* 5.2 2.7 - - + -
107A LEU* 4.0 19.1 - - + -
277A ASP* 2.9 17.7 + - + +
278A GLY* 3.2 9.6 + - - +
280A LYS* 1.3 77.2 - - - +
282A MET* 1.3 62.5 + - - +
284A GLU 3.4 0.2 + - - -
285A ALA* 3.0 23.0 + - - +
323A LEU* 3.8 24.9 - - + +
326A VAL* 3.7 8.6 - - + +
328A PHE* 3.8 10.7 - - + -
335A VAL* 3.8 28.0 - - + -
337A PHE* 4.0 22.0 - - + -
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Residues in contact with MET 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.7 34.3 - - + -
24A PHE* 4.3 10.1 - - + -
28A LEU* 5.6 1.8 - - + -
37A LEU* 3.9 16.4 - - + -
66A ALA* 4.9 0.4 - - - -
68A PHE* 3.9 35.0 - - + -
91A ILE* 4.0 30.3 - - + -
278A GLY 3.2 7.7 + - - +
279A VAL* 3.7 19.5 - - + +
280A LYS 3.3 0.2 - - - -
281A VAL* 1.3 74.5 - - - +
283A ALA* 1.3 63.9 + - - +
285A ALA* 3.1 1.9 + - - +
286A PHE* 2.9 38.4 + - + -
323A LEU* 3.9 9.6 - - + -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.8 35.4 - - + -
37A LEU* 3.7 11.1 - - + +
279A VAL 3.0 18.0 + - - +
280A LYS* 3.3 7.6 + - + +
282A MET* 1.3 75.6 - - - +
284A GLU* 1.3 58.7 + - + +
286A PHE* 3.8 0.6 - - - -
287A GLN* 2.8 46.1 + - - +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LYS* 2.8 45.1 + - + +
283A ALA* 1.3 72.1 - - - +
285A ALA* 1.3 63.3 - - - +
287A GLN* 4.0 17.5 + - - +
288A SER* 3.0 25.8 + - - -
291A ARG* 4.9 10.0 + - - +
326A VAL* 3.3 22.0 - - + +
327A ARG 4.7 5.7 + - - +
328A PHE* 4.0 30.8 - - + +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL 3.0 17.0 + - - +
282A MET 3.1 4.2 + - - +
284A GLU* 1.3 77.6 - - - +
286A PHE* 1.3 62.0 + - + +
288A SER* 3.2 5.7 + - - -
289A LEU* 3.0 33.9 + - + +
319A ILE 5.0 0.4 - - - +
322A ALA* 3.7 14.2 - - + +
323A LEU* 3.6 42.2 - - + +
326A VAL* 3.7 1.3 - - + +
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Residues in contact with PHE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 3.9 9.8 - - + +
7A ILE* 3.8 23.8 - - + -
9A ILE* 4.0 17.0 - - + -
35A PRO* 3.4 26.3 - - + +
37A LEU* 4.2 16.4 - - + -
65A TYR* 3.7 31.2 - + + -
66A ALA* 4.4 6.5 - - + -
282A MET* 2.9 34.5 + - + +
283A ALA* 4.4 1.3 - - - +
285A ALA* 1.3 78.4 - - + +
287A GLN* 1.3 66.1 + - - +
288A SER 3.2 0.4 - - - -
289A LEU* 3.5 12.0 + - + -
290A ARG* 3.2 16.6 + - - +
296A ILE* 5.7 1.1 - - + -
319A ILE* 3.9 39.0 - - + -
323A LEU* 5.2 3.1 - - + -
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.8 8.0 - - - +
33A GLU* 3.1 43.6 + - + +
34A PRO 3.3 24.9 - - - +
35A PRO* 3.9 7.4 - - + +
283A ALA* 2.8 35.9 + - - +
284A GLU* 4.0 19.8 + - - +
286A PHE* 1.3 76.9 - - - +
288A SER* 1.3 58.2 + - - +
290A ARG* 3.2 3.8 + - - +
291A ARG* 3.0 46.4 + - - +
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU 3.0 19.3 + - - -
285A ALA* 3.5 7.4 - - - -
287A GLN* 1.3 76.2 - - - +
289A LEU* 1.3 59.5 + - - +
291A ARG* 3.8 25.2 + - - +
292A GLN* 3.0 45.9 + - - +
322A ALA* 5.1 8.3 - - - +
326A VAL* 6.1 1.1 - - - -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 3.6 15.5 - - + -
285A ALA* 3.0 22.5 + - + +
286A PHE* 3.9 22.2 - - + +
287A GLN 3.3 0.2 - - - -
288A SER* 1.3 74.8 - - - +
290A ARG* 1.3 65.1 + - - +
292A GLN* 3.5 4.7 + - - +
293A ARG 3.3 3.1 + - - -
294A ILE* 3.2 54.6 + - + +
296A ILE* 3.7 23.8 - - + -
318A ASP* 4.0 20.6 - - + +
319A ILE* 3.9 15.3 - - + -
322A ALA* 3.9 18.4 - - + -
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 3.8 26.0 + - + +
4A PRO 3.8 16.6 + - - -
5A ASN* 3.3 29.3 + - - +
34A PRO* 3.5 31.2 - - - +
35A PRO* 3.5 26.6 - - + +
286A PHE 3.2 13.1 + - - +
287A GLN 3.2 9.7 + - - +
289A LEU* 1.3 78.0 - - - +
291A ARG* 1.3 64.1 + - + +
293A ARG* 3.4 13.3 + - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 5.0 4.4 + - - -
284A GLU* 4.9 10.7 + - - -
287A GLN* 3.0 50.3 + - - +
288A SER* 3.8 23.9 + - - +
290A ARG* 1.3 75.7 - - + +
292A GLN* 1.3 60.9 + - + +
293A ARG* 3.0 18.9 + - - +
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Residues in contact with GLN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER* 3.0 36.4 + - - +
289A LEU* 3.9 5.6 - - - +
290A ARG 3.3 0.2 - - - -
291A ARG* 1.3 78.1 - - + +
293A ARG* 1.3 69.5 + - - +
294A ILE* 3.5 32.2 + - + +
321A ARG* 5.8 3.2 - - - +
322A ALA* 6.1 0.3 - - - +
325A GLN* 6.0 0.2 + - - -
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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