Contacts of the helix formed by residues 329 - 356 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E LEU* 6.2 0.6 - - - +
230E SER* 3.8 17.8 + - - +
243E ILE* 5.4 11.3 - - - +
328E LEU* 1.3 71.4 - - - +
330E GLU* 1.3 53.6 + - - +
331E TYR* 3.0 12.1 + - - +
332E GLU* 2.7 57.1 + - - +
333E ARG* 2.6 46.7 + - - +
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Residues in contact with GLU 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E ASN* 1.3 75.0 - - - +
331E TYR* 1.3 64.1 + - - +
333E ARG* 2.9 24.2 + - - +
334E ILE* 2.8 63.2 + - + +
204G VAL 5.6 0.4 - - - +
239G THR* 5.8 2.3 - - - +
241G GLU* 3.2 14.3 - - - +
242G GLU* 2.9 27.4 - - - +
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Residues in contact with TYR 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E LEU* 5.4 0.5 - - - +
240E GLN* 6.2 4.9 - - + -
243E ILE* 3.2 31.0 - - + -
244E SER* 3.1 39.0 + - - -
247E THR* 3.1 34.4 - - + +
329E ASN* 3.0 11.3 + - - +
330E GLU* 1.3 79.1 - - - +
332E GLU* 1.3 62.1 + - + +
334E ILE* 3.7 12.6 + - + +
335E GLY* 3.0 22.3 + - - -
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Residues in contact with GLU 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E LEU* 3.7 10.3 - - + +
227E PRO 4.8 3.6 - - - +
228E LEU* 2.9 49.1 - - + -
229E LEU* 2.9 4.5 + - + +
230E SER* 2.8 26.0 + - - -
243E ILE* 6.3 0.7 - - + -
328E LEU* 3.4 20.9 - - + +
329E ASN* 2.7 44.9 + - - +
331E TYR* 1.3 78.9 - - + +
333E ARG* 1.3 55.9 + - - +
334E ILE 3.1 2.0 - - - -
335E GLY* 3.6 1.7 - - - +
336E LEU* 2.7 35.0 + - - +
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Residues in contact with ARG 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E LEU* 2.8 46.8 + - + +
329E ASN* 2.6 37.8 + - - +
330E GLU* 3.1 36.9 + - - +
332E GLU* 1.3 73.5 - - - +
334E ILE* 1.3 60.9 + - - +
336E LEU* 3.4 11.0 - - + +
337E GLU* 3.2 19.6 + - - +
204G VAL* 3.3 38.6 + - - +
241G GLU* 3.0 40.9 + - + +
242G GLU* 3.7 8.5 + - - +
245G TYR* 3.3 39.3 - - + -
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Residues in contact with ILE 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E GLU* 2.8 51.2 + - + +
331E TYR* 3.7 10.5 - - + +
333E ARG* 1.3 74.5 - - - +
335E GLY* 1.3 63.9 + - - +
337E GLU* 2.8 25.6 + - + +
338E LYS* 3.0 25.0 + - + +
241G GLU* 3.0 7.5 + - - +
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Residues in contact with GLY 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E VAL 4.6 2.4 - - - +
226E LEU* 3.9 18.7 - - - +
251E GLN* 6.1 1.6 - - - -
331E TYR 3.0 16.0 + - - -
332E GLU 3.2 2.4 + - - -
334E ILE* 1.3 78.3 - - - +
336E LEU* 1.3 50.7 + - - +
338E LYS* 3.1 11.8 + - - +
339E ALA* 2.7 36.6 + - - +
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Residues in contact with LEU 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E LEU* 3.4 17.1 - - + +
308E PHE* 3.7 30.5 - - + -
325E LEU* 3.8 15.3 - - + -
328E LEU* 3.8 24.9 - - + -
332E GLU 2.7 21.4 + - - +
333E ARG* 3.4 9.6 - - + +
335E GLY* 1.3 72.0 - - - +
337E GLU* 1.3 60.2 + - - +
339E ALA* 3.4 2.3 + - + +
340E LYS* 3.0 52.7 + - + +
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Residues in contact with GLU 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333E ARG 3.2 10.4 + - - +
334E ILE* 2.8 16.4 + - + +
336E LEU* 1.3 81.0 - - - +
338E LYS* 1.3 59.8 + - - +
340E LYS* 3.6 26.5 + - - +
341E LYS* 3.0 49.0 + - - +
241G GLU* 5.4 15.0 - - + +
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Residues in contact with LYS 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E VAL* 4.2 39.1 - - + +
251E GLN* 5.8 0.2 + - - -
334E ILE* 3.0 26.9 + - + +
335E GLY* 3.6 10.1 - - - +
337E GLU* 1.3 74.1 - - + +
339E ALA* 1.3 67.2 + - - +
341E LYS* 3.3 36.6 - - + +
342E GLU* 3.3 9.5 + - - +
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Residues in contact with ALA 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E GLY* 5.1 6.7 - - - -
223E VAL* 3.8 19.9 + - - +
224E THR* 4.0 21.6 + - - +
226E LEU* 4.9 7.9 - - + -
308E PHE* 5.4 1.6 - - + -
335E GLY 2.7 16.7 + - - +
336E LEU* 3.5 12.6 - - + +
338E LYS* 1.3 76.8 - - - +
340E LYS* 1.3 67.3 + - - +
341E LYS 3.2 0.3 + - - -
342E GLU* 3.4 1.4 + - - +
343E LEU* 2.8 28.1 + - + +
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Residues in contact with LYS 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E THR* 4.1 16.7 - - - +
304E GLU* 3.0 38.7 + - - +
305E LEU* 4.1 12.0 - - + +
308E PHE* 4.4 9.8 - - + -
336E LEU* 3.0 50.7 + - + +
337E GLU* 3.8 26.4 + - - +
339E ALA* 1.3 75.5 - - - +
341E LYS* 1.3 67.5 + - - +
343E LEU* 4.1 6.7 - - - -
344E ALA* 2.8 23.6 + - - +
244G SER* 5.9 1.4 + - - -
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Residues in contact with LYS 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E GLU* 3.0 40.9 - - - +
338E LYS* 3.3 29.7 - - + +
340E LYS* 1.3 84.9 - - - +
342E GLU* 1.3 64.7 + - - +
344E ALA* 3.2 14.6 + - - +
345E GLY 3.8 2.8 + - - -
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Residues in contact with GLU 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ASN* 5.1 0.3 + - - -
221E ALA* 4.0 23.0 - - - +
222E GLY* 5.2 1.7 - - - -
223E VAL* 3.7 26.1 + - + +
224E THR* 4.2 9.9 - - - +
338E LYS 3.3 10.3 + - - +
339E ALA* 4.1 1.6 - - - +
341E LYS* 1.3 79.2 - - - +
343E LEU* 1.3 62.2 + - - +
345E GLY* 3.4 3.9 + - - -
346E SER* 3.2 31.2 + - - +
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Residues in contact with LEU 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ASN* 4.0 31.4 - - + +
218E GLY* 3.9 16.8 - - - +
224E THR* 3.8 9.8 + - - +
297E PHE* 4.3 4.7 - - + -
305E LEU* 3.5 24.5 - - + -
307E PHE 4.1 5.6 - - - +
308E PHE* 3.5 26.7 - - + -
339E ALA 2.8 24.6 + - - +
340E LYS 3.6 2.9 - - - +
342E GLU* 1.3 71.0 - - - +
344E ALA* 1.3 66.3 + - - +
346E SER* 2.9 14.1 + - - -
347E ILE* 3.0 32.1 + - + +
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Residues in contact with ALA 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E LEU* 4.3 22.6 - - + +
340E LYS 2.8 14.9 + - - +
341E LYS* 3.2 11.4 + - - +
343E LEU* 1.3 73.8 - - - +
345E GLY* 1.3 62.8 + - - +
347E ILE* 3.5 5.8 + - - +
348E GLU* 3.2 20.3 + - - +
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Residues in contact with GLY 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341E LYS 3.8 3.2 + - - -
342E GLU* 3.4 6.3 + - - -
343E LEU 3.1 0.8 - - - -
344E ALA* 1.3 77.1 - - - +
346E SER* 1.3 55.1 + - - +
348E GLU* 3.0 8.9 + - - +
349E LYS* 2.8 34.8 + - - +
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Residues in contact with SER 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E ASN* 3.7 30.3 + - - +
166E SER* 2.9 25.0 + - - -
221E ALA* 6.1 0.2 - - - +
342E GLU* 3.2 26.0 + - - +
343E LEU* 2.9 11.7 + - - -
345E GLY* 1.3 76.2 - - - +
347E ILE* 1.3 62.9 + - - +
349E LYS* 3.3 12.5 + - - +
350E GLY 3.3 3.5 + - - -
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Residues in contact with ILE 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ASN 3.7 14.4 - - - +
169E PRO* 3.9 15.7 - - + +
297E PHE* 4.4 0.4 - - + -
305E LEU* 4.1 14.1 - - + -
306E PRO* 4.0 13.9 - - + -
307E PHE* 3.5 48.5 - - + +
343E LEU* 3.0 35.4 + - + +
344E ALA* 3.8 5.8 - - - +
346E SER* 1.3 74.8 - - - +
348E GLU* 1.3 58.4 + - - +
350E GLY* 3.3 2.4 + - - -
351E VAL* 2.9 47.3 + - + +
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Residues in contact with GLU 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E ALA 3.2 11.0 + - - +
345E GLY* 3.0 13.4 + - - +
347E ILE* 1.3 75.7 - - - +
349E LYS* 1.3 68.6 + - - +
350E GLY 2.9 2.3 + - - -
351E VAL* 3.0 14.1 + - - +
352E SER* 2.8 45.5 + - - -
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Residues in contact with LYS 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ARG 4.9 3.6 + - - -
131E ASP* 4.8 12.7 + - - +
134E PHE* 3.4 58.6 - - + +
163E PRO* 6.2 0.2 - - - +
166E SER* 4.3 4.9 - - - +
345E GLY 2.8 15.3 + - - +
346E SER* 3.5 12.8 - - - +
348E GLU* 1.3 72.3 - - - +
350E GLY* 1.3 57.5 + - - +
352E SER* 4.0 4.6 - - - -
353E PHE* 3.3 19.2 + - - +
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Residues in contact with GLY 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E PHE* 4.1 2.7 - - - -
166E SER* 3.8 15.9 - - - -
170E ILE* 3.4 38.8 - - - +
346E SER 3.3 4.6 + - - -
347E ILE 3.3 5.1 + - - -
348E GLU 2.9 1.2 + - - -
349E LYS* 1.3 77.1 - - - +
351E VAL* 1.3 66.2 + - - +
352E SER 3.1 1.6 - - - -
353E PHE* 3.2 10.6 + - - +
354E ILE* 3.6 4.0 + - - +
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Residues in contact with VAL 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E PRO* 4.2 10.5 - - + +
173E GLU* 4.1 21.8 - - + +
306E PRO* 5.9 1.8 - - + -
307E PHE* 5.3 3.8 - - + -
347E ILE* 2.9 47.3 + - + +
348E GLU* 3.7 16.6 - - - +
350E GLY* 1.3 73.5 - - - +
352E SER* 1.3 62.8 + - - +
354E ILE* 3.3 2.6 + - - +
355E ARG* 2.9 55.2 + - + +
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Residues in contact with SER 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E GLU* 2.8 31.8 + - - -
349E LYS* 4.0 5.8 - - - -
351E VAL* 1.3 75.7 - - - +
353E PHE* 1.3 65.6 + - - +
355E ARG* 3.1 4.7 + - - +
356E SER* 2.6 43.6 + - - +
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Residues in contact with PHE 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E PHE* 4.2 17.7 - + + -
135E LYS* 4.5 13.2 - - + -
138E ALA* 3.5 42.8 - - + -
139E GLY* 4.0 13.2 - - - -
142E LYS* 4.6 9.9 - - + -
170E ILE* 3.9 9.2 - - + -
349E LYS 3.3 13.3 + - - +
350E GLY 3.2 10.6 + - - +
352E SER* 1.3 78.1 - - - +
354E ILE* 1.3 74.5 + - + +
356E SER* 4.2 10.7 + - - +
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Residues in contact with ILE 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LYS* 4.1 17.7 - - + -
170E ILE* 3.5 39.5 - - + +
173E GLU* 3.4 29.2 - - + +
174E VAL* 3.4 28.9 - - + +
177E LYS* 6.1 5.4 - - + -
350E GLY 3.6 1.5 + - - +
351E VAL 3.3 4.3 + - - +
352E SER 2.9 0.8 + - - -
353E PHE* 1.3 86.9 - - + +
355E ARG* 1.3 60.1 + - + +
356E SER 3.0 17.9 + - - +
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Residues in contact with ARG 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E GLU* 2.9 33.8 + - + +
176E LYS* 5.2 7.9 - - - +
351E VAL* 2.9 36.8 + - + +
352E SER* 3.6 3.4 - - - +
354E ILE* 1.3 76.4 - - + +
356E SER* 1.3 60.9 + - - +
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Residues in contact with SER 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352E SER* 2.6 38.3 + - - -
353E PHE* 4.2 9.5 - - - +
354E ILE 3.0 10.3 - - - +
355E ARG* 1.3 82.2 - - - +
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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