Contacts of the helix formed by residues 392 - 423 (chain B) in PDB entry 5DSG
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 ALA 392 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B GLN 3.6 4.0 + - - -
391B MET* 1.3 79.2 - - - +
393B ALA* 1.3 65.3 + - - +
394B ARG* 3.1 9.4 - - + +
395B GLU* 3.1 28.6 + - + +
396B ARG* 3.3 10.3 + - - +
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B MET 3.6 1.4 + - - -
392B ALA* 1.3 73.7 - - - +
394B ARG* 1.3 57.7 + - - +
396B ARG* 3.2 20.9 + - - +
397B LYS* 2.9 27.2 + - - +
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA* 3.1 8.2 - - + +
393B ALA* 1.3 79.3 - - - +
395B GLU* 1.3 62.0 + - + +
397B LYS* 3.1 10.3 + - - +
398B VAL* 2.9 31.5 + - + +
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASN* 5.1 4.5 + - - -
130B ARG* 2.9 48.3 + - - +
391B MET* 3.7 17.0 - - + -
392B ALA* 3.1 23.4 + - + +
394B ARG* 1.3 77.1 - - + +
396B ARG* 1.3 61.4 + - - +
398B VAL* 3.0 12.0 + - - +
399B THR 2.9 18.5 + - - -
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B SER* 4.6 5.5 + - - +
223B ARG 4.1 6.3 + - - -
224B SER* 3.9 32.7 + - - +
390B GLN* 4.2 15.0 + - - -
391B MET* 3.6 44.6 + - + +
392B ALA 3.5 9.4 - - - +
393B ALA* 3.2 19.5 + - + +
395B GLU* 1.3 75.7 - - - +
397B LYS* 1.3 56.4 + - - +
399B THR* 3.3 9.4 + - - -
400B ARG* 2.9 35.9 + - + +
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Residues in contact with LYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA 2.9 12.6 + - - +
394B ARG* 3.1 12.1 + - - +
396B ARG* 1.3 75.0 - - - +
398B VAL* 1.3 55.4 + - - +
400B ARG* 3.7 17.1 - - - +
401B THR* 2.6 37.1 + - - -
456B CYS* 4.1 17.5 - - - +
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASN* 4.3 23.6 - - + +
130B ARG* 4.1 15.3 - - - +
394B ARG* 2.9 20.2 + - + +
395B GLU* 3.0 19.9 + - - +
397B LYS* 1.3 75.9 - - - +
399B THR* 1.3 59.1 + - - +
401B THR* 3.2 7.8 + - - -
402B ILE* 2.9 45.8 + - + +
457B ASN* 6.3 1.1 - - - +
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Residues in contact with THR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 2.9 32.9 + - + +
134B VAL* 5.1 0.3 - - - +
215B TYR* 4.5 15.9 - - + -
218B ILE* 3.9 25.4 - - + +
219B SER* 5.1 7.2 - - - -
391B MET* 5.2 2.8 - - - +
395B GLU 2.9 4.6 + - - -
396B ARG* 3.5 11.2 - - - -
398B VAL* 1.3 76.9 - - - +
400B ARG* 1.3 56.7 + - + +
402B ILE* 3.4 8.4 + - + +
403B PHE* 2.9 27.9 + - - +
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ARG* 2.9 22.6 + - + +
397B LYS* 3.7 16.0 - - - +
398B VAL 3.2 0.2 - - - -
399B THR* 1.3 75.6 - - + +
401B THR* 1.3 59.1 + - - +
403B PHE* 3.3 12.0 + - + +
404B ALA* 2.9 28.8 + - - +
455B LEU* 6.0 4.4 - - - +
456B CYS* 4.7 22.5 + - - +
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Residues in contact with THR 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 5.3 7.2 - - + -
397B LYS 2.6 20.7 + - - -
398B VAL* 3.2 12.5 + - - -
400B ARG* 1.3 76.3 - - - +
402B ILE* 1.3 59.0 + - + +
404B ALA* 3.1 4.0 + - - +
405B ILE* 2.9 49.1 + - + +
452B CYS 4.6 3.6 - - - +
453B TYR* 4.4 18.6 - - + -
456B CYS* 3.2 33.7 + - + +
457B ASN* 5.6 1.6 - - + +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 6.3 1.8 - - + -
126B ILE* 3.9 29.2 - - + -
127B SER* 4.8 15.3 - - - +
130B ARG* 3.6 37.9 - - + -
215B TYR* 5.6 7.6 - - + -
218B ILE* 5.8 4.3 - - + -
398B VAL* 2.9 32.0 + - + +
399B THR* 3.7 7.6 - - + +
401B THR* 1.3 77.0 - - + +
403B PHE* 1.3 59.3 + - - +
405B ILE* 3.3 10.3 + - + +
406B LEU* 2.9 33.3 + - + +
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TYR* 3.3 53.6 - + + +
399B THR 2.9 14.7 + - - +
400B ARG* 3.5 13.7 - - + +
402B ILE* 1.3 76.2 - - - +
404B ALA* 1.3 61.2 + - + +
406B LEU* 3.5 9.5 + - + +
407B LEU* 2.9 57.3 + - + +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG 2.9 13.3 + - - +
401B THR 3.1 9.4 + - - +
403B PHE* 1.3 78.3 - - + +
405B ILE* 1.3 59.6 + - - +
407B LEU* 3.3 8.3 + - - +
408B ALA* 2.9 29.6 + - - +
452B CYS* 3.9 21.2 - - + -
456B CYS* 4.3 15.0 - - - -
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.1 11.9 - - + -
74B LEU* 4.1 7.0 - - + -
123B LEU* 3.6 29.8 - - + -
126B ILE* 5.3 4.3 - - + -
401B THR* 2.9 22.0 + - + +
402B ILE* 3.7 11.0 - - + +
404B ALA* 1.3 75.0 - - - +
406B LEU* 1.3 57.4 + - - +
408B ALA* 3.3 5.2 + - - +
409B PHE* 2.9 27.9 + - - +
445B ASN* 4.1 1.4 + - - +
449B ASN* 3.5 23.6 - - - +
452B CYS* 4.4 11.7 - - + -
453B TYR* 3.5 38.1 - - + +
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 5.4 3.8 - - + +
127B SER* 5.4 3.1 - - - +
208B VAL 5.3 0.2 - - - +
211B MET* 3.7 61.0 - - + +
212B THR* 4.9 4.9 - - - +
215B TYR* 4.1 24.7 - - + -
402B ILE* 2.9 21.7 + - + +
403B PHE* 3.8 8.5 - - + +
405B ILE* 1.3 76.0 - - - +
407B LEU* 1.3 59.5 + - - +
409B PHE* 3.3 7.4 + - + +
410B ILE* 2.9 55.5 + - + +
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PHE* 2.9 46.4 + - + +
404B ALA* 3.6 7.2 - - - +
406B LEU* 1.3 76.3 - - - +
408B ALA* 1.3 59.0 + - - +
410B ILE* 3.4 9.8 + - + +
411B LEU* 2.9 66.0 + - + +
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ALA 2.9 17.6 + - - +
405B ILE* 3.6 4.5 - - - +
407B LEU* 1.3 77.2 - - - +
409B PHE* 1.3 52.0 + - - +
411B LEU* 4.0 5.3 - - - -
412B THR* 2.5 41.5 + - - +
445B ASN* 3.5 15.9 - - - +
448B ILE* 3.7 35.7 - - + -
449B ASN* 4.5 3.1 - - - +
452B CYS* 4.9 0.4 - - - -
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Residues in contact with PHE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B SER* 6.2 1.3 - - - -
120B VAL* 3.8 26.0 - - + -
123B LEU* 3.6 28.5 - - + -
204B PHE* 3.8 21.1 - + - -
207B PRO* 6.0 0.2 - - + -
208B VAL* 3.6 24.2 - - + -
211B MET* 3.7 19.3 - - + -
405B ILE 2.9 13.7 + - - +
406B LEU* 3.5 7.9 - - + +
408B ALA* 1.3 77.4 - - - +
410B ILE* 1.3 72.7 + - + +
412B THR* 3.1 2.9 + - - -
413B TRP* 2.9 69.1 + + - +
445B ASN* 3.2 16.0 - - - +
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Residues in contact with ILE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 5.0 4.5 - - + -
208B VAL* 4.3 26.5 - - + -
212B THR* 4.5 7.2 - - - +
406B LEU* 2.9 48.8 + - + +
407B LEU* 3.9 9.0 - - + +
409B PHE* 1.3 82.2 - - + +
411B LEU* 1.3 64.4 + - + +
414B THR* 2.3 50.7 + - - +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU* 2.9 54.5 + - + +
408B ALA* 4.0 4.5 - - - +
410B ILE* 1.3 78.8 - - + +
412B THR* 1.3 65.3 + - + +
414B THR* 4.5 2.1 - - - -
415B PRO* 3.4 18.9 - - - +
441B LEU* 4.5 2.9 - - - +
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Residues in contact with THR 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ALA* 2.5 25.9 + - - +
409B PHE 3.1 6.6 + - - -
411B LEU* 1.3 80.2 - - + +
413B TRP* 1.3 70.6 + - - +
415B PRO* 3.8 1.9 - - - +
416B TYR 5.3 0.3 + - - -
438B GLY 4.6 0.2 - - - +
441B LEU* 3.4 56.2 - - + +
442B CYS* 3.7 2.8 + - - -
444B VAL* 4.4 5.2 - - + -
445B ASN* 3.3 17.7 - - - +
448B ILE* 3.9 25.1 - - + -
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Residues in contact with TRP 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 5.6 5.2 - - + -
116B SER* 3.6 41.1 - - - -
119B SER* 5.3 5.8 - - - -
120B VAL* 3.8 6.3 - - + -
204B PHE* 3.5 17.9 - + + -
409B PHE* 2.9 45.8 + + - +
412B THR* 1.3 93.0 - - - +
414B THR* 1.3 65.5 + - - +
415B PRO 3.4 1.4 - - - -
416B TYR* 3.5 9.3 + - - +
417B ASN* 2.8 23.3 + - - +
442B CYS* 2.8 38.6 + - + -
445B ASN* 3.8 12.4 - - - +
1201B 0HK 3.7 54.7 - - + -
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Residues in contact with THR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.9 17.1 - - + -
205B TYR* 6.4 0.7 - - + -
410B ILE* 2.3 41.7 + - - +
411B LEU* 4.5 2.0 - - - -
413B TRP* 1.3 76.5 - - - +
415B PRO* 1.4 71.2 - - + +
417B ASN* 3.2 4.3 + - - +
418B VAL* 2.9 41.7 + - + +
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Residues in contact with PRO 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU 3.4 17.0 - - - +
412B THR 3.8 5.8 - - - +
413B TRP 3.5 4.3 - - - -
414B THR* 1.4 91.1 - - + +
416B TYR* 1.3 55.8 + - - +
418B VAL* 3.2 10.2 + - + +
419B MET* 2.9 46.9 + - + +
438B GLY* 5.1 1.3 - - - -
441B LEU* 3.8 23.3 - - + -
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Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 4.1 9.5 + - - -
412B THR 5.3 0.2 + - - -
413B TRP 3.5 2.5 + - - +
414B THR 3.3 0.6 - - - -
415B PRO* 1.3 79.4 - - - +
417B ASN* 1.3 57.9 + - - +
419B MET* 3.1 14.8 + - - +
420B VAL* 2.9 33.3 + - + +
435B TRP* 3.7 28.0 - + - -
438B GLY* 4.1 7.7 + - - -
439B TYR* 3.7 45.8 - + + -
442B CYS* 3.7 22.2 - - - -
1201B 0HK 3.5 50.6 - - + +
1205B P6G 2.9 31.4 + - - -
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Residues in contact with ASN 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA* 3.8 10.9 - - - +
204B PHE* 3.4 38.2 - - + +
205B TYR* 2.8 26.8 + - + +
413B TRP* 2.8 24.9 + - - +
414B THR 3.2 6.7 + - - +
416B TYR* 1.3 74.0 - - - +
418B VAL* 1.3 60.8 + - - +
420B VAL* 3.2 10.1 + - - +
421B LEU 2.9 20.6 + - - -
1201B 0HK 2.7 45.2 + - - +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 3.8 11.0 - - + +
414B THR* 2.9 35.8 + - + +
415B PRO* 3.4 11.2 - - + +
417B ASN* 1.3 74.3 - - - +
419B MET* 1.3 60.6 + - + +
421B LEU* 3.0 13.9 + - + +
422B VAL* 2.9 37.2 + - + +
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Residues in contact with MET 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO* 2.9 36.2 + - + +
416B TYR* 3.2 13.5 - - - +
418B VAL* 1.3 79.0 - - + +
420B VAL* 1.3 57.7 + - - +
422B VAL* 4.5 2.2 - - - -
423B ASN* 2.9 28.4 + - - +
430B ILE* 3.2 26.4 - - + +
434B VAL* 3.5 48.5 - - + +
435B TRP* 3.4 27.3 - - + -
437B ILE* 6.0 1.1 - - + -
438B GLY* 3.8 16.6 - - - +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO 4.9 1.0 - - - +
196B THR* 3.7 24.6 - - + +
197B PHE* 3.7 28.9 - - + +
200B ALA* 3.9 8.5 - - + -
416B TYR* 2.9 41.8 + - + +
417B ASN* 3.2 14.8 - - - +
419B MET* 1.3 77.2 - - - +
421B LEU* 1.3 60.8 + - - +
423B ASN* 3.5 11.2 + - - +
424B THR* 3.4 14.6 - - - +
435B TRP* 4.1 12.3 - - + -
1201B 0HK 4.1 10.5 - - + -
1205B P6G 4.4 0.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 4.6 6.1 - - + -
158A VAL* 3.8 26.5 - - + -
197B PHE* 3.5 35.7 - - + -
205B TYR* 4.0 11.4 - - + +
417B ASN 2.9 13.1 + - - +
418B VAL* 3.0 17.5 + - + +
420B VAL* 1.3 74.5 - - - +
422B VAL* 1.3 64.5 + - + +
424B THR* 2.6 31.1 + - - +
425B PHE* 3.7 5.1 - - + -
1202B OLC 3.8 32.1 - - + -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B VAL* 2.9 30.7 + - + +
419B MET* 4.6 1.3 - - - -
421B LEU* 1.3 74.5 - - + +
423B ASN* 1.3 56.7 + - - +
424B THR 3.0 7.7 + - - -
425B PHE* 3.2 31.4 + - + -
426B CYS* 2.9 39.9 + - + +
429B CYS* 4.5 7.6 - - + -
430B ILE* 3.7 21.8 - - + -
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Residues in contact with ASN 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B SER 5.8 0.2 + - - -
193B PRO* 3.5 29.8 - - - +
196B THR* 5.6 3.4 + - - +
419B MET 2.9 18.6 + - - +
420B VAL* 3.6 8.1 - - - +
421B LEU 3.2 0.4 - - - -
422B VAL* 1.3 75.5 - - - +
424B THR* 1.3 60.9 + - - +
425B PHE 3.3 0.7 - - - -
426B CYS 3.7 8.3 - - - -
427B GLN* 3.3 41.9 - - - +
430B ILE* 4.4 0.7 - - + -
435B TRP* 3.5 28.7 + - + -
1205B P6G 5.1 12.1 - - - +
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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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