Contacts of the helix formed by residues 329 - 355 (chain G) in PDB entry 1SMK
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 ASN 329 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G LEU* 5.3 2.2 - - - +
230G SER* 3.7 17.9 + - - +
243G ILE* 4.9 14.5 - - - +
328G LEU* 1.3 70.0 - - - +
330G GLU* 1.3 65.7 + - - +
331G TYR* 3.0 13.5 + - - +
332G GLU* 2.8 49.8 + - - +
333G ARG* 2.9 29.2 + - - +
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Residues in contact with GLU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G ASN* 1.3 73.0 - - - +
331G TYR* 1.3 55.9 + - - +
332G GLU 2.7 2.1 + - - -
333G ARG* 2.7 54.2 + - - +
334G ILE* 2.8 41.7 + - + +
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Residues in contact with TYR 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G LEU* 5.0 1.5 - - + +
240G GLN* 5.1 15.3 - - + -
243G ILE* 3.2 32.1 - - + -
244G SER* 3.1 38.7 + - - -
247G THR* 3.1 37.2 - - + +
248G ASP 5.2 0.2 + - - -
329G ASN* 3.0 11.5 + - - +
330G GLU* 1.3 78.2 - - - +
332G GLU* 1.3 60.6 + - + +
334G ILE* 4.2 10.7 - - + +
335G GLY* 3.1 21.2 + - - -
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Residues in contact with GLU 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G LEU* 3.6 11.8 - - + +
227G PRO 3.7 4.9 - - - +
228G LEU* 2.9 18.9 - - + -
229G LEU* 2.7 34.6 + - + +
230G SER* 2.8 24.2 + - - -
243G ILE* 6.2 0.4 - - + -
328G LEU* 3.5 20.3 - - + +
329G ASN* 2.8 41.7 + - - +
330G GLU 2.7 0.4 + - - -
331G TYR* 1.3 84.7 - - + +
333G ARG* 1.3 59.5 + - - +
334G ILE 3.2 1.1 - - - -
335G GLY 3.6 1.1 - - - +
336G LEU* 2.8 29.6 + - - +
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Residues in contact with ARG 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G LEU* 3.3 30.9 + - + -
329G ASN* 2.9 18.1 + - - +
330G GLU* 2.7 61.3 + - - +
332G GLU* 1.3 72.8 - - - +
334G ILE* 1.3 61.2 + - + +
336G LEU* 3.7 7.0 - - - +
337G GLU* 3.1 29.1 + - - +
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Residues in contact with ILE 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G GLU* 2.8 48.1 + - + +
331G TYR* 4.2 9.9 - - + +
333G ARG* 1.3 77.2 - - + +
335G GLY* 1.3 63.3 + - - +
336G LEU 3.1 0.7 + - - -
337G GLU* 3.6 5.2 + - - +
338G LYS* 3.4 34.1 + - + +
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Residues in contact with GLY 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G VAL 4.1 5.5 - - - +
226G LEU* 4.0 16.1 - - - +
331G TYR* 3.1 21.1 + - - -
332G GLU 3.5 1.8 + - - -
334G ILE* 1.3 80.2 - - - +
336G LEU* 1.3 54.9 + - - +
338G LYS* 3.8 5.2 + - - +
339G ALA* 3.2 25.6 + - - +
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Residues in contact with LEU 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G LEU* 3.4 18.8 - - + +
308G PHE* 3.6 31.9 - - + -
325G LEU* 3.8 17.7 - - + -
328G LEU* 3.7 25.8 - - + -
332G GLU 2.8 18.3 + - - +
333G ARG* 3.7 6.1 - - - +
335G GLY* 1.3 74.2 - - - +
337G GLU* 1.3 68.6 + - - +
338G LYS 3.0 1.8 - - - -
339G ALA* 2.9 14.9 + - + +
340G LYS* 3.1 36.3 + - + +
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Residues in contact with GLU 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G ARG 3.1 14.7 + - - +
334G ILE* 3.6 6.0 + - - +
336G LEU* 1.3 81.1 - - - +
338G LYS* 1.3 59.9 + - + +
340G LYS* 3.8 23.5 + - - +
341G LYS* 3.0 49.4 + - - +
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Residues in contact with LYS 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G VAL* 4.8 20.4 - - + +
334G ILE* 3.4 25.4 + - + +
335G GLY* 4.0 5.2 - - - +
336G LEU 3.0 0.8 - - - -
337G GLU* 1.3 76.8 - - + +
339G ALA* 1.3 65.9 + - - +
341G LYS* 3.2 38.3 + - - +
342G GLU* 3.2 14.6 + - - +
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Residues in contact with ALA 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G GLY* 5.1 5.2 - - - -
223G VAL* 3.4 25.5 + - - +
224G THR* 3.9 22.3 - - - +
226G LEU* 4.9 5.2 - - + -
308G PHE* 5.3 0.9 - - + -
335G GLY 3.2 11.6 + - - +
336G LEU* 2.9 18.1 + - + +
338G LYS* 1.3 78.7 - - - +
340G LYS* 1.3 56.7 + - + +
342G GLU* 3.5 1.2 + - - -
343G LEU* 2.9 32.2 + - + +
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Residues in contact with LYS 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G THR* 4.0 21.8 + - + +
304G GLU* 3.7 27.7 + - - +
305G LEU* 4.1 13.0 - - + +
308G PHE* 4.4 10.3 - - + -
325G LEU* 5.8 0.4 - - - -
336G LEU* 3.1 44.8 + - + +
337G GLU* 3.8 25.9 + - - +
339G ALA* 1.3 77.6 - - - +
341G LYS* 1.3 65.3 + - + +
343G LEU* 2.8 17.8 + - - +
344G ALA* 2.8 17.6 + - - +
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Residues in contact with LYS 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G GLU* 3.0 41.3 - - - +
338G LYS* 3.2 35.7 + - + +
340G LYS* 1.3 78.8 - - + +
342G GLU* 1.3 61.6 + - - +
344G ALA* 3.6 11.0 + - - +
345G GLY* 3.8 6.1 + - - -
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Residues in contact with GLU 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G ALA* 3.6 12.5 - - - +
222G GLY* 4.9 0.7 - - - -
223G VAL* 3.2 26.1 + - + +
224G THR* 3.2 21.3 - - + +
338G LYS 3.2 8.4 + - - +
339G ALA 4.0 5.4 - - - +
341G LYS* 1.3 79.9 - - - +
343G LEU* 1.3 62.6 + - - +
345G GLY* 3.3 10.3 + - - -
346G SER* 3.5 15.1 + - - +
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Residues in contact with LEU 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G ASN* 3.5 36.6 - - + +
218G GLY 4.0 13.0 - - - +
219G GLY* 4.1 5.4 - - - +
224G THR* 4.5 6.5 - - + -
297G PHE* 4.0 12.1 - - + -
305G LEU* 3.5 13.5 - - + -
307G PHE 3.9 7.9 - - - +
308G PHE* 3.3 38.4 - - + -
339G ALA 2.9 17.7 + - - +
340G LYS 2.8 6.0 + - - +
342G GLU* 1.3 73.3 - - - +
344G ALA* 1.3 66.2 + - - +
345G GLY 3.0 1.8 - - - -
346G SER* 3.0 5.3 + - - +
347G ILE* 2.9 29.1 + - + +
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Residues in contact with ALA 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G LEU* 4.0 20.1 - - + +
340G LYS 2.8 18.1 + - - +
341G LYS* 3.9 7.0 - - - +
343G LEU* 1.3 73.1 - - - +
345G GLY* 1.3 57.4 + - - +
347G ILE* 3.9 6.6 - - - +
348G GLU* 3.1 27.9 + - - +
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Residues in contact with GLY 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341G LYS 3.8 4.9 + - - -
342G GLU* 3.3 7.9 + - - -
343G LEU 3.0 1.2 - - - -
344G ALA* 1.3 77.6 - - - +
346G SER* 1.3 54.4 + - - +
348G GLU* 3.1 6.4 + - - +
349G LYS* 2.6 36.9 + - - +
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Residues in contact with SER 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G ASN* 3.5 28.2 + - - +
166G SER* 2.9 30.0 + - - -
224G THR* 5.5 1.4 - - - +
342G GLU* 3.5 15.5 + - - +
343G LEU* 3.0 10.7 + - - -
345G GLY* 1.3 74.1 - - - +
347G ILE* 1.3 66.2 + - - +
349G LYS* 3.0 7.5 + - - +
350G GLY 2.9 15.6 + - - -
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Residues in contact with ILE 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ASN 3.7 12.3 + - - +
169G PRO* 4.0 10.7 - - + +
297G PHE* 4.5 2.2 - - + -
305G LEU* 3.9 17.7 - - + -
306G PRO* 3.4 40.4 - - + -
307G PHE* 3.5 37.0 - - + +
343G LEU* 2.9 23.3 + - + +
344G ALA* 3.9 5.6 - - - +
346G SER* 1.3 75.1 - - - +
348G GLU* 1.3 58.9 + - - +
350G GLY* 3.3 1.2 + - - -
351G VAL* 3.0 38.7 + - + +
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Residues in contact with GLU 348 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G ALA 3.1 19.8 + - - +
345G GLY* 3.3 7.6 - - - +
346G SER 3.1 0.6 - - - -
347G ILE* 1.3 73.8 - - - +
349G LYS* 1.3 64.8 + - - +
350G GLY 2.9 6.6 + - - -
351G VAL* 4.6 7.3 - - - +
352G SER* 3.0 45.9 + - - -
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Residues in contact with LYS 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG 4.7 4.0 + - - -
131G ASP* 3.3 36.5 + - - +
134G PHE* 3.3 45.3 - - + +
166G SER* 4.3 5.8 - - - +
345G GLY 2.6 20.3 + - - +
346G SER* 3.4 10.3 - - - +
348G GLU* 1.3 74.5 - - - +
350G GLY* 1.3 60.5 + - - +
352G SER* 4.0 4.9 - - - -
353G PHE* 3.7 8.8 + - - +
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Residues in contact with GLY 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G PHE* 4.3 4.0 - - - -
166G SER* 3.9 9.6 - - - -
170G ILE* 3.7 29.7 - - - +
346G SER 2.9 11.4 + - - -
347G ILE 3.7 2.7 - - - -
348G GLU 2.9 1.8 - - - -
349G LYS* 1.3 75.7 - - - +
351G VAL* 1.3 65.1 + - - +
352G SER 2.9 3.4 + - - -
353G PHE* 2.9 19.2 + - - +
354G ILE* 3.5 4.3 + - - +
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Residues in contact with VAL 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G PRO* 4.0 17.0 - - + +
173G GLU* 3.6 28.5 - - + +
306G PRO* 5.9 0.9 - - + -
307G PHE* 5.2 4.5 - - + -
347G ILE* 3.0 28.9 + - + +
348G GLU* 4.3 8.1 - - - +
350G GLY* 1.3 70.9 - - - +
352G SER* 1.3 62.8 + - - +
354G ILE* 3.4 2.1 + - - +
355G ARG* 3.1 49.3 + - + +
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Residues in contact with SER 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348G GLU* 3.0 35.3 + - - -
349G LYS* 4.0 6.7 - - - -
350G GLY 2.9 1.0 + - - -
351G VAL* 1.3 79.6 - - - +
353G PHE* 1.3 65.0 + - - -
354G ILE 2.8 2.3 + - - -
355G ARG* 3.1 9.7 + - - -
356G SER* 3.2 25.6 + - - -
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Residues in contact with PHE 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G PHE* 4.2 15.5 - + + -
135G LYS* 5.0 4.9 - - + -
138G ALA* 3.3 44.0 - - + -
139G GLY* 4.1 12.1 - - - -
142G LYS* 4.5 10.1 - - + -
170G ILE* 4.3 9.0 - - + -
349G LYS 3.7 10.4 + - - +
350G GLY 2.9 9.9 + - - +
352G SER* 1.3 79.2 + - - +
354G ILE* 1.3 77.1 + - + +
356G SER* 4.4 9.3 + - - +
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Residues in contact with ILE 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G LYS* 4.3 15.7 - - + -
170G ILE* 3.4 46.9 - - + +
173G GLU* 3.4 34.8 - - + +
174G VAL* 3.6 16.4 - - + +
177G LYS* 5.0 19.6 + - + -
350G GLY 4.3 2.7 - - - +
351G VAL 3.4 3.7 + - - +
352G SER 2.8 4.6 + - - -
353G PHE* 1.3 83.4 - - + +
355G ARG* 1.3 61.6 + - + +
356G SER 2.8 19.0 + - - +
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Residues in contact with ARG 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G GLU* 2.8 32.9 + - + +
176G LYS* 4.4 12.5 - - - +
177G LYS* 6.1 1.3 - - - +
351G VAL* 3.1 29.3 + - - +
352G SER* 3.6 1.6 - - - +
354G ILE* 1.3 76.4 - - + +
356G SER* 1.3 64.9 + - - +
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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