Contacts of the helix formed by residues 358 - 390 (chain E) in PDB entry 6M04
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 MET 358 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E MET* 3.3 51.4 - - - +
46E GLN* 3.6 17.7 - - + +
49E LYS* 3.2 32.8 - - + +
50E ASP* 3.7 17.7 - - - +
356E HIS* 3.2 28.0 - - + +
357E ASN* 1.3 80.7 - - - +
359E ALA* 1.3 54.3 + - - +
360E TYR 3.3 1.7 + - - -
361E MET* 3.4 6.6 + - - +
362E LEU* 2.8 50.6 + - + +
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Residues in contact with ALA 359 (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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155D HIS* 5.2 0.6 - - - -
333E ILE* 4.2 13.0 - - + +
334E SER 3.4 26.5 - - - +
335E PHE* 3.9 25.8 - - + -
356E HIS* 3.7 11.3 + - + +
357E ASN 3.5 3.0 - - - -
358E MET* 1.3 76.7 - - - +
360E TYR* 1.3 61.1 + - + +
362E LEU* 3.9 2.7 - - - +
363E LYS* 2.9 32.4 + - - +
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Residues in contact with TYR 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D HIS* 3.7 44.0 + + + +
156D LEU* 5.0 6.6 - - - +
164D TYR* 3.5 17.9 - - - +
335E PHE* 3.5 48.4 - + + +
357E ASN 5.3 0.4 + - - -
358E MET 3.4 0.2 - - - -
359E ALA* 1.3 77.7 - - + +
361E MET* 1.3 62.8 + - - +
363E LYS* 3.3 21.8 + - - +
364E LYS* 3.0 38.1 + - - +
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Residues in contact with MET 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLN* 6.2 0.4 - - - +
155D HIS* 6.1 0.8 - - - -
163D LYS* 4.7 2.2 - - + +
164D TYR* 3.6 34.6 + - + +
167D TYR* 3.6 38.4 - - + -
41E PHE* 5.0 7.2 - - - -
45E MET* 3.6 35.0 - - + -
49E LYS* 5.7 9.2 - - - +
357E ASN 5.6 1.8 - - - +
358E MET* 3.4 8.3 + - - +
360E TYR* 1.3 77.7 - - - +
362E LEU* 1.3 58.3 + - - +
364E LYS* 3.4 5.4 + - - +
365E LEU* 2.9 36.0 + - + +
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Residues in contact with LEU 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E MET* 4.9 6.3 - - + +
46E GLN* 5.6 3.8 - - + -
162E SER* 4.0 27.1 - - - +
163E LYS* 5.8 0.7 - - - -
165E PHE* 4.8 20.2 - - + -
166E PRO* 4.9 14.4 - - + -
329E PHE* 4.7 11.7 - - + -
333E ILE* 4.0 24.0 - - + -
356E HIS* 5.7 1.1 - - - +
358E MET* 2.8 42.4 + - + +
359E ALA* 4.1 2.2 - - - +
361E MET* 1.3 74.4 - - - +
363E LYS* 1.3 57.6 + - - +
365E LEU* 3.7 11.5 - - + +
366E LEU* 2.9 30.5 + - + +
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Residues in contact with LYS 363 (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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330E VAL* 5.0 9.4 - - + +
333E ILE* 4.3 30.3 - - + +
359E ALA 2.9 19.4 + - - +
360E TYR* 3.9 23.9 - - - +
362E LEU* 1.3 78.6 - - - +
364E LYS* 1.3 77.5 + - + +
366E LEU* 3.3 8.6 + - + +
367E ILE* 3.0 41.7 + - + +
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Residues in contact with LYS 364 (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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164D TYR* 3.6 40.2 - - + +
360E TYR* 3.0 22.1 + - - +
361E MET* 4.0 6.5 - - - +
363E LYS* 1.3 95.0 - - + +
365E LEU* 1.3 65.4 + - - +
367E ILE* 3.2 18.1 - - + +
368E SER* 3.1 23.0 + - - -
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Residues in contact with LEU 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E VAL* 3.8 29.5 - - + +
41E PHE* 4.3 22.9 - - + -
42E ALA* 3.6 33.0 - - + -
45E MET* 4.1 19.3 - - + -
165E PHE* 5.5 8.1 - - + -
166E PRO* 6.0 0.7 - - + -
361E MET* 2.9 20.0 + - + +
362E LEU* 3.7 9.2 - - + +
364E LYS* 1.3 76.0 - - - +
366E LEU* 1.3 56.5 + - - +
368E SER* 3.4 7.8 + - - -
369E TYR* 2.9 29.7 + - + +
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Residues in contact with LEU 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E PHE* 3.6 25.0 - - + -
326E THR* 4.5 3.1 - - + -
329E PHE* 3.6 44.4 - - + -
330E VAL* 3.7 29.8 - - + -
333E ILE* 3.8 19.1 - - + -
362E LEU* 2.9 19.9 + - + +
363E LYS* 3.4 7.6 - - + +
364E LYS 3.2 0.2 - - - -
365E LEU* 1.3 77.2 - - - +
367E ILE* 1.3 57.9 + - - +
369E TYR* 3.3 5.1 + - + +
370E ILE* 2.9 47.4 + - + +
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Residues in contact with ILE 367 (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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330E VAL* 4.5 22.7 - - + -
363E LYS* 3.0 24.7 + - + +
364E LYS* 3.2 26.0 - - + +
366E LEU* 1.3 77.4 - - + +
368E SER* 1.3 58.5 + - - +
370E ILE* 3.8 5.7 - - - +
371E SER* 3.0 29.5 + - - -
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Residues in contact with SER 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ILE* 5.9 3.1 - - - +
38E VAL* 4.9 7.3 - - - +
364E LYS 3.1 16.6 + - - -
365E LEU* 3.7 10.8 - - - -
367E ILE* 1.3 79.3 - - - +
369E TYR* 1.3 61.1 + - - +
371E SER* 2.6 23.3 + - - -
372E ILE* 3.0 23.5 + - - +
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Residues in contact with TYR 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E MET* 3.5 39.6 - - + -
38E VAL* 4.4 18.1 - - + +
39E ALA* 5.8 1.1 - - + -
165E PHE* 3.8 27.4 - + + -
168E LEU* 5.7 3.0 - - + +
169E ALA* 4.0 30.3 + - + -
172E HIS* 4.0 13.3 - - - +
322E ILE* 3.9 21.4 - - + +
326E THR* 5.2 2.9 - - + -
365E LEU 2.9 17.7 + - - +
366E LEU* 3.3 5.6 + - - +
368E SER* 1.3 75.1 - - - +
370E ILE* 1.3 79.2 + - + +
372E ILE* 3.3 9.5 + - - +
373E ILE* 3.0 43.2 + - + +
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Residues in contact with ILE 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E ILE* 5.1 2.7 - - + +
323E LEU* 5.5 12.3 - - + -
326E THR* 3.3 36.8 - - + +
330E VAL* 4.9 9.2 - - + -
366E LEU* 2.9 33.0 + - + +
367E ILE* 4.0 6.3 - - - +
369E TYR* 1.3 93.4 - - + +
371E SER* 1.3 60.7 + - - +
373E ILE* 4.1 8.7 - - + +
374E CYS* 2.9 32.5 + - + +
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Residues in contact with SER 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367E ILE 3.0 13.4 + - - -
368E SER* 2.6 27.7 + - - -
370E ILE* 1.3 77.3 - - - +
372E ILE* 1.3 63.2 + - - +
374E CYS* 3.4 5.8 + - - +
375E VAL* 3.0 31.3 + - - +
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Residues in contact with ILE 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.6 26.9 - - + +
34E VAL* 4.2 19.3 - - + -
35E MET* 3.9 26.2 - - + -
38E VAL* 4.1 26.0 - - + -
368E SER* 3.0 20.7 + - - +
369E TYR* 3.5 9.2 - - - +
371E SER* 1.3 83.3 + - - +
373E ILE* 1.3 58.3 + - + +
375E VAL* 3.3 7.6 + - - +
376E TYR* 3.0 25.8 + - - +
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Residues in contact with ILE 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 5.4 0.4 - - + -
35E MET* 3.8 35.0 - - + -
172E HIS* 5.7 0.9 - - + -
176E LEU* 4.7 8.5 - - + -
319E PHE* 3.3 22.2 - - + -
322E ILE* 3.6 28.0 - - + -
323E LEU* 5.6 3.6 - - + -
369E TYR* 3.0 37.1 + - + +
370E ILE* 4.1 8.3 - - + +
371E SER 3.3 0.2 - - - -
372E ILE* 1.3 77.9 - - + +
374E CYS* 1.3 60.3 + - - +
376E TYR* 4.0 13.2 - - + -
377E GLY 2.9 25.8 + - - -
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Residues in contact with CYS 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E PHE* 4.1 11.1 - - - -
323E LEU* 4.6 14.9 - - + +
370E ILE* 2.9 21.6 + - + +
371E SER* 3.8 6.5 - - - +
373E ILE* 1.3 76.3 - - - +
375E VAL* 1.3 56.2 + - + +
377E GLY* 4.1 0.2 - - - -
378E PHE* 3.0 38.4 + - - +
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Residues in contact with VAL 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.9 20.0 - - + -
371E SER* 3.0 16.3 + - - +
372E ILE* 3.5 9.6 - - - +
374E CYS* 1.3 78.5 - - + +
376E TYR* 1.3 62.7 + - - +
378E PHE* 4.0 3.8 - - - +
379E ILE* 3.0 37.9 + - + +
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Residues in contact with TYR 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E MET* 3.4 62.8 + - + +
31E LEU* 3.5 23.8 - - + +
32E ALA* 4.6 4.1 - - + +
176E LEU* 3.4 53.3 + - + +
180E SER* 4.9 7.1 - - - -
315E LYS* 3.8 23.7 - - + +
319E PHE* 5.5 5.6 - + + -
372E ILE 3.0 14.3 + - - +
373E ILE* 3.4 17.7 - - + +
375E VAL* 1.3 76.4 - - - +
377E GLY* 1.3 62.4 + - - +
380E CYS* 3.0 33.3 + - - +
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Residues in contact with GLY 377 (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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315E LYS* 4.2 3.8 + - - -
319E PHE* 3.5 38.9 - - - -
373E ILE 2.9 13.1 + - - -
376E TYR* 1.3 78.9 - - - +
378E PHE* 1.3 56.6 + - - +
380E CYS* 4.7 1.8 - - - -
381E LEU* 2.8 35.3 + - - +
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Residues in contact with PHE 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E PHE* 4.2 3.8 - - + -
374E CYS* 3.0 24.2 + - - +
375E VAL* 4.0 3.4 - - - +
377E GLY* 1.3 76.1 - - - +
379E ILE* 1.3 76.0 + - + +
381E LEU* 3.9 7.5 - - + +
382E TYR* 3.0 52.2 + + + +
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Residues in contact with ILE 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TRP* 5.5 5.4 - - - +
24E TRP* 5.0 8.1 - - + -
27E PHE* 5.1 9.9 - - + -
28E MET* 3.9 19.7 - - + -
31E LEU* 6.1 0.4 - - + -
375E VAL* 3.0 32.7 + - + +
376E TYR 4.0 2.0 - - - +
378E PHE* 1.3 88.6 - - + +
380E CYS* 1.3 65.5 + - - +
382E TYR* 4.1 1.9 - - - +
383E THR* 3.0 37.1 + - - +
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Residues in contact with CYS 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 4.8 3.8 - - - -
28E MET* 3.6 35.2 - - + -
315E LYS* 3.2 33.9 - - + +
376E TYR 3.0 17.9 + - - +
379E ILE* 1.3 78.2 - - - +
381E LEU* 1.3 57.4 + - - +
383E THR* 5.2 0.4 - - - -
384E LEU* 2.9 58.8 + - - +
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Residues in contact with LEU 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E THR* 6.2 0.2 - - - -
315E LYS* 3.1 12.3 - - - +
316E THR* 3.7 29.2 - - + +
319E PHE* 4.5 14.1 - - + -
320E ILE* 5.0 5.8 - - + -
377E GLY 2.8 21.1 + - - +
378E PHE* 3.9 7.6 - - + +
380E CYS* 1.3 75.3 - - - +
382E TYR* 1.3 68.3 + - + +
384E LEU* 3.8 1.2 - - - +
385E PHE* 2.9 37.2 + - + +
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Residues in contact with TYR 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378E PHE* 3.0 41.2 + + + +
379E ILE* 4.1 2.0 - - - +
381E LEU* 1.3 86.5 - - + +
383E THR* 1.3 65.0 + - - +
385E PHE* 3.4 9.7 + + - +
386E TRP* 3.0 81.7 + + - +
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Residues in contact with THR 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TRP* 3.6 36.7 + - + -
24E TRP* 3.6 25.1 - - + -
379E ILE* 3.0 23.0 + - - +
380E CYS* 4.7 0.7 - - - -
382E TYR* 1.3 83.9 - - - +
384E LEU* 1.3 61.5 + - - +
386E TRP* 3.3 10.2 + - + +
387E LEU* 2.9 27.3 + - + +
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Residues in contact with LEU 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 3.4 44.2 - - + +
308E TYR* 3.7 25.1 - - + +
312E THR* 3.3 43.4 - - + +
380E CYS* 2.9 40.1 + - - +
381E LEU* 4.2 1.3 - - - +
383E THR* 1.3 74.9 - - - +
385E PHE* 1.3 61.0 + - - +
387E LEU* 3.6 7.7 - - + +
388E PHE* 2.8 31.5 + - + +
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Residues in contact with PHE 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381E LEU* 2.9 24.1 + - + +
382E TYR* 3.4 11.4 - + + +
384E LEU* 1.3 77.2 - - - +
386E TRP* 1.3 79.2 + + - +
388E PHE* 3.1 12.2 + + - +
389E ARG* 3.0 76.3 + - + +
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Residues in contact with TRP 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E TYR* 3.0 64.2 + + - +
383E THR* 3.3 11.0 + - + +
385E PHE* 1.3 102.7 - + - +
387E LEU* 1.3 60.2 + - - +
388E PHE 3.2 0.2 - - - -
389E ARG* 6.1 0.2 - - + -
390E ILE* 3.4 41.6 + - + +
391E PRO* 4.1 0.5 - - - +
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Residues in contact with LEU 387 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 3.6 36.8 - - + -
305E TYR* 6.0 1.9 - - - -
308E TYR* 5.9 5.2 - - + -
383E THR* 2.9 17.0 + - + +
384E LEU* 3.6 8.2 - - + +
386E TRP* 1.3 76.9 - - - +
388E PHE* 1.3 60.0 + - - +
391E PRO* 3.8 30.5 - - + +
421E HIS* 6.2 5.4 - - + -
422E MET* 5.8 9.6 - - + -
425E GLN* 4.6 25.1 - - + +
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Residues in contact with PHE 388 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E TYR* 4.3 24.3 + + - -
309E VAL* 3.6 45.5 - - + -
312E THR* 6.1 3.6 - - + -
384E LEU 2.8 18.9 + - - +
385E PHE* 3.1 15.2 + + - +
387E LEU* 1.3 82.2 - - - +
389E ARG* 1.3 78.5 + - + +
390E ILE 3.6 0.2 - - - -
391E PRO* 4.7 0.4 - - - +
392E LEU* 4.7 7.8 + - - -
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Residues in contact with ARG 389 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E PHE* 3.0 56.0 + - + +
386E TRP* 5.4 0.7 - - + -
388E PHE* 1.3 92.9 - - + +
390E ILE* 1.3 83.9 + - + +
391E PRO 3.8 0.2 - - - -
392E LEU* 4.0 12.6 + - - +
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Residues in contact with ILE 390 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E TRP* 3.4 32.0 + - + +
389E ARG* 1.3 100.2 - - + +
391E PRO* 1.3 71.0 - - + +
392E LEU* 3.4 8.8 + - - +
----------------------------------------------------------
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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).
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