Contacts of the helix formed by residues 401 - 429 (chain B) in PDB entry 6A5T
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 LEU 401 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 3.9 32.3 - - + +
34B GLN* 4.7 7.0 - - - +
37B SER* 3.6 35.0 - - - +
203B LEU* 5.2 0.4 - - - -
205B ALA* 3.8 15.9 - - + -
399B LEU* 4.0 11.7 - - + +
400B ASP* 1.3 74.2 - - - +
402B ALA* 1.3 68.0 + - - +
403B GLY 3.1 0.4 + - - -
404B PRO* 4.2 12.1 - - + +
405B LEU* 3.1 29.2 + - - +
538B ILE* 3.9 32.5 - - + -
539B SER 5.2 2.0 - - - +
623B VAL* 5.1 9.6 - - + -
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Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 4.3 13.5 + - - +
38B PHE* 4.4 12.8 - - + +
164B MET* 3.6 28.0 - - + -
194B PHE* 4.5 0.4 - - + -
203B LEU* 3.5 31.3 - - + +
205B ALA* 5.2 0.2 - - - +
401B LEU* 1.3 76.7 - - + +
403B GLY* 1.3 66.7 + - - +
405B LEU* 4.5 0.2 - - - -
406B LEU* 3.0 26.9 + - + +
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Residues in contact with GLY 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 3.1 31.9 + - - -
41B PHE* 3.9 14.8 - - - -
45B SER* 5.8 1.1 - - - -
401B LEU 3.1 2.2 - - - -
402B ALA* 1.3 83.3 - - - +
404B PRO* 1.3 68.6 - - - +
405B LEU 2.9 0.2 + - - -
406B LEU* 3.1 2.8 + - - +
407B ALA* 2.9 19.2 + - - +
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Residues in contact with PRO 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 3.9 7.9 - - - +
238B GLY 5.2 7.6 - - - +
239B SER* 5.3 10.5 - - - +
399B LEU 5.7 0.4 - - - +
400B ASP* 4.6 21.5 - - + +
401B LEU* 4.2 17.0 - - + +
403B GLY* 1.3 86.2 - - - +
405B LEU* 1.3 57.6 + - - +
407B ALA* 3.3 11.8 - - + +
408B ASN* 2.9 35.9 + - - +
623B VAL* 4.7 24.0 - - + +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 5.1 9.2 - - + -
204B ILE 5.1 0.4 - - - +
205B ALA* 4.8 3.4 - - - -
206B GLN* 4.5 12.3 - - + +
400B ASP* 3.8 21.3 - - + +
401B LEU 3.1 24.1 + - - +
402B ALA* 3.7 5.4 - - - +
403B GLY 2.9 2.8 + - - -
404B PRO* 1.3 75.3 - - - +
406B LEU* 1.3 65.7 + - - +
408B ASN* 3.2 7.8 + - + +
409B LEU 3.0 18.9 + - - -
459B TRP* 3.1 48.0 - - + +
469B ARG* 4.3 16.4 - - - +
472B VAL* 4.4 19.5 - - + -
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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
----------------------------------------------------------
38B PHE* 3.8 25.6 - - + -
41B PHE* 3.4 37.9 - - + -
161B VAL* 5.2 5.2 - - + -
162B PRO* 5.4 6.3 - - + +
194B PHE* 4.5 17.0 - - + -
203B LEU* 5.0 5.6 - - + -
402B ALA 3.0 19.7 + - - +
403B GLY 3.9 0.2 - - - +
405B LEU* 1.3 76.1 - - - +
407B ALA* 1.3 65.5 + - - +
409B LEU* 4.5 1.6 - - + +
410B PHE* 2.9 28.3 + - + +
450B LEU* 4.5 22.7 - - + -
454B LEU* 5.4 5.2 - - + -
459B TRP* 4.2 18.4 - - + -
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.6 15.6 - - + -
45B SER* 4.6 12.1 - - - +
49B LEU* 3.4 16.8 - - + +
238B GLY* 4.9 13.0 - - - +
403B GLY 2.9 13.5 + - - +
404B PRO* 3.3 16.2 - - + +
405B LEU 3.1 0.4 - - - -
406B LEU* 1.3 76.8 - - - +
408B ASN* 1.3 58.2 + - - +
411B ARG* 2.9 28.2 + - - +
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Residues in contact with ASN 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLY 3.8 9.9 + - - +
239B SER 3.8 16.3 + - - -
240B ARG* 3.9 9.4 - - - +
404B PRO* 2.9 21.4 + - - +
405B LEU* 4.0 7.2 - - + +
406B LEU 3.2 0.2 - - - -
407B ALA* 1.3 72.7 - - - +
409B LEU* 1.3 67.4 + - - +
410B PHE 3.0 2.7 + - - -
411B ARG* 2.8 29.0 + - - +
412B ILE* 3.0 30.4 + - + +
459B TRP* 5.6 4.5 - - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU 3.0 15.5 + - - +
406B LEU* 4.3 2.5 - - - +
408B ASN* 1.3 78.8 - - - +
410B PHE* 1.3 56.4 + - - +
412B ILE* 3.5 14.7 + - + -
413B LEU* 3.1 39.8 + - + +
450B LEU* 3.7 22.8 - - + +
453B SER* 3.1 38.8 - - - +
459B TRP* 3.8 28.4 - - + +
460B GLY* 4.6 20.4 - - - +
461B GLU* 5.2 1.6 - - + +
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Residues in contact with PHE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 4.9 5.4 - + + -
46B ILE* 3.7 38.4 - - + -
49B LEU* 3.3 26.7 - - + -
50B VAL* 6.0 2.0 - - + -
115B VAL* 5.5 6.1 - - + -
158B ILE* 5.2 6.5 - - + -
161B VAL* 4.3 17.7 - - + -
406B LEU* 2.9 20.1 + - + +
407B ALA 3.9 2.0 - - - +
409B LEU* 1.3 77.0 - - - +
411B ARG* 1.3 66.6 + - - +
413B LEU* 5.1 1.6 - - + -
414B PHE* 2.9 41.9 + + + +
446B ILE* 3.9 41.1 - - + -
450B LEU* 4.4 14.3 - - + +
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Residues in contact with ARG 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.4 27.1 - - + +
52B GLU* 3.4 30.2 + - - +
237B LYS 4.7 0.8 + - - -
238B GLY* 3.3 29.7 + - - -
240B ARG* 3.7 43.9 - - - +
407B ALA* 2.9 13.3 + - - +
408B ASN* 2.8 37.6 + - - +
410B PHE* 1.3 76.8 - - - +
412B ILE* 1.3 68.7 + - + +
414B PHE* 3.3 7.3 + - + +
415B ARG* 3.0 33.1 + - + +
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Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASN* 3.0 23.0 + - + +
409B LEU* 3.9 12.3 - - + +
411B ARG* 1.3 83.6 - - + +
413B LEU* 1.3 71.3 + - + +
415B ARG* 3.0 21.0 + - - +
416B LYS* 3.1 9.9 + - - +
461B GLU* 3.1 32.5 - - + +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU* 3.1 30.8 + - + +
410B PHE* 4.5 2.2 - - - +
412B ILE* 1.3 79.8 - - + +
414B PHE* 1.3 61.5 + - - +
416B LYS* 3.1 27.7 + - + +
417B LEU* 3.0 23.0 + - - +
445B THR* 4.3 12.0 - - + +
446B ILE* 4.6 22.0 - - + +
449B GLY* 3.5 37.2 - - - -
450B LEU* 4.3 5.2 - - + +
453B SER* 5.1 1.3 - - - +
461B GLU* 4.1 25.1 - - + +
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Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.1 24.5 - - + -
50B VAL* 4.1 26.9 - - + -
52B GLU* 5.7 2.7 - - - -
53B GLU* 5.7 7.0 - - + -
79B PHE* 4.4 29.4 - + - -
117B LEU* 4.8 13.9 - - + -
158B ILE* 5.2 3.4 - - + -
410B PHE* 2.9 41.8 + + + +
411B ARG* 3.5 6.5 - - + +
413B LEU* 1.3 79.1 - - - +
415B ARG* 1.3 66.6 + - + +
417B LEU* 3.4 14.1 + - + +
418B THR* 3.0 35.3 + - - -
446B ILE* 5.0 11.8 - - + +
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 2.5 40.4 + - - +
53B GLU* 3.3 33.8 + - + +
240B ARG* 5.0 5.1 - - - +
411B ARG* 3.0 26.7 + - + +
412B ILE* 3.0 12.1 + - - +
414B PHE* 1.3 82.8 - - + +
416B LYS* 1.3 61.6 + - - +
418B THR* 3.0 8.0 + - - +
419B ARG* 2.9 30.7 + - + +
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Residues in contact with LYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ILE 3.1 11.5 + - - +
413B LEU* 3.1 27.1 + - + +
415B ARG* 1.3 76.4 - - - +
417B LEU* 1.3 64.0 + - - +
419B ARG* 3.2 24.2 + - + +
420B GLU* 3.1 30.7 + - + +
445B THR* 4.7 11.0 - - + -
461B GLU* 4.8 16.1 + - + +
463B LYS* 5.0 14.9 - - - +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 6.2 2.0 - - + -
117B LEU* 5.4 2.0 - - + -
119B MET* 5.4 3.6 - - + -
158B ILE* 4.8 12.1 - - + +
413B LEU 3.0 12.4 + - - +
414B PHE* 3.5 19.5 - - + +
416B LYS* 1.3 76.2 - - - +
418B THR* 1.3 59.0 + - - +
420B GLU* 3.0 11.2 + - + +
421B ILE* 2.9 45.4 + - + +
441B VAL* 4.1 22.2 - - + -
442B LYS* 4.1 11.9 - - + +
445B THR* 3.2 36.4 - - + +
446B ILE* 4.6 17.3 - - + -
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Residues in contact with THR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 6.1 4.7 - - + -
56B LEU* 3.6 35.4 - - + -
79B PHE* 3.9 23.8 - - + -
414B PHE* 3.0 25.9 + - - -
415B ARG* 3.0 11.3 + - - -
417B LEU* 1.3 78.3 - - - +
419B ARG* 1.3 58.3 + - - +
421B ILE* 3.7 6.5 - - + +
422B TYR* 2.8 28.0 + - + +
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B ARG* 2.9 18.7 + - + +
416B LYS* 3.7 23.9 - - + +
418B THR* 1.3 75.6 - - + +
420B GLU* 1.3 66.2 + - + +
422B TYR* 3.3 7.8 + - + +
423B ARG* 3.0 22.2 + - - +
-42N G 3.1 50.3 + - - +
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LYS* 3.1 22.7 + - + +
417B LEU* 3.0 13.4 + - + +
419B ARG* 1.3 77.0 - - - +
421B ILE* 1.3 60.3 + - + +
423B ARG* 3.1 25.4 + - + +
424B TYR* 2.9 27.4 + - - +
440B ALA 5.7 0.2 - - - -
442B LYS* 3.8 28.4 + - - +
445B THR* 4.5 11.0 + - - +
46T A 3.0 34.0 + - - +
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Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.5 14.4 - - + -
77B ILE* 4.7 11.0 - - + -
79B PHE* 5.9 4.0 - - + -
119B MET* 3.4 33.7 - - + -
417B LEU* 2.9 35.8 + - + +
418B THR* 4.0 6.1 - - + +
420B GLU* 1.3 74.8 - - + +
422B TYR* 1.3 61.6 + - - +
424B TYR* 3.3 7.5 + - + +
425B MET* 2.9 32.9 + - + +
437B LEU* 5.7 5.6 - - + -
440B ALA* 3.3 21.8 - - + +
441B VAL* 3.6 18.4 - - + -
442B LYS 5.8 0.2 - - - +
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Residues in contact with TYR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.7 28.2 - - + +
57B ILE 3.0 35.8 + - - -
58B LEU* 3.2 19.8 - - + +
418B THR* 2.8 17.6 + - + +
419B ARG* 3.6 8.5 - - + +
420B GLU 3.2 0.2 - - - -
421B ILE* 1.3 75.7 - - - +
423B ARG* 1.3 67.7 + - - +
425B MET* 3.2 27.5 + - - +
426B GLN* 3.3 28.5 + - - +
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Residues in contact with ARG 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ARG 3.0 14.1 + - - +
420B GLU* 3.2 29.4 - - - +
422B TYR* 1.3 77.3 - - - +
424B TYR* 1.3 60.8 + - - +
426B GLN* 2.8 34.3 + - - +
427B ARG* 3.6 14.4 + - + +
46T A 5.3 5.9 - - - -
47T G 3.2 36.0 + - - -
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Residues in contact with TYR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B GLU 2.9 17.3 + - - +
421B ILE* 3.3 10.7 + - + +
423B ARG* 1.3 76.1 - - + +
425B MET* 1.3 63.7 + - + +
427B ARG* 3.8 7.7 + - + +
428B CYS* 3.6 34.8 + - - +
435B PHE* 3.4 40.2 - + + +
436B ASN 4.6 3.1 + - - -
437B LEU* 5.8 0.4 - - + -
439B LEU* 5.4 7.9 - - + +
440B ALA* 3.5 40.1 + - + +
442B LYS* 5.2 8.5 - - - +
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Residues in contact with MET 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.1 8.7 - - + -
57B ILE 4.7 0.4 - - - -
58B LEU* 3.5 29.2 - - + +
75B TYR* 3.7 30.3 - - + +
77B ILE* 3.5 36.1 - - + -
421B ILE* 2.9 19.5 + - + +
422B TYR* 3.2 34.8 - - - +
423B ARG 3.0 0.2 - - - -
424B TYR* 1.3 80.1 - - + +
426B GLN* 1.3 57.7 + - - +
427B ARG 2.8 7.9 + - - -
428B CYS 3.3 8.8 + - - -
429B ILE* 3.4 26.6 + - + +
435B PHE* 4.8 9.2 - - + -
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Residues in contact with GLN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.2 39.8 - - + +
422B TYR* 3.3 30.7 + - - +
423B ARG* 2.8 18.7 + - - +
425B MET* 1.3 71.4 - - - +
427B ARG* 1.3 63.1 + - - +
429B ILE* 5.0 2.2 - - - +
430B GLU* 4.5 21.9 - - - +
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ARG* 3.6 18.3 + - + +
424B TYR* 3.8 9.4 + - + +
425B MET 2.8 6.7 + - - -
426B GLN* 1.3 80.9 - - - +
428B CYS* 1.3 62.4 + - - +
429B ILE 3.1 8.8 + - - -
430B GLU* 3.3 5.9 + - - +
431B THR* 3.0 32.2 + - + +
47T G 4.0 40.8 + - - +
48T G 4.5 7.7 + - - -
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Residues in contact with CYS 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR* 3.6 39.4 + - - +
425B MET 3.3 2.8 + - - -
427B ARG* 1.3 81.1 - - - +
429B ILE* 1.3 60.4 + - - +
431B THR* 3.7 6.1 - - - -
432B ASP 3.6 0.6 - - - -
433B ARG* 2.7 68.1 + - + +
435B PHE* 3.3 26.1 - - + -
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Residues in contact with ILE 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.5 23.1 - - + -
60B GLN* 3.8 26.8 - - - +
73B LYS* 5.2 5.0 + - + -
75B TYR* 3.3 61.6 + - + -
425B MET* 3.4 26.5 - - + +
426B GLN* 5.3 0.9 - - - -
427B ARG 3.1 0.8 - - - -
428B CYS* 1.3 79.8 - - - +
430B GLU* 1.3 66.9 + - + +
432B ASP* 3.2 20.4 + - - +
435B PHE* 3.6 16.4 - - + -
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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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