Contacts of the helix formed by residues 409 - 435 (chain B) in PDB entry 2HD1
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 PRO 409 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO 3.9 13.2 - - - +
200B THR* 3.6 33.7 - - - +
407B VAL 4.6 0.9 - - - +
408B ARG* 1.3 86.4 - - + +
410B MET* 1.3 57.4 + - - +
411B GLU* 4.7 7.4 - - - +
412B VAL* 2.7 40.3 + - + +
413B ALA 2.8 10.2 + - - -
482B PRO* 6.0 2.0 - - + -
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Residues in contact with MET 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ARG 3.4 3.6 + - - -
409B PRO* 1.3 68.8 - - - +
411B GLU* 1.3 75.2 + - + +
413B ALA* 4.5 4.0 - - - -
414B GLU* 2.9 49.2 + - + +
489B ARG* 2.7 61.0 - - - +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TRP* 4.7 1.7 + - - -
409B PRO* 3.2 6.3 - - + +
410B MET* 1.3 91.2 - - + +
412B VAL* 1.3 61.7 + - + +
414B GLU* 4.9 1.6 - - - -
415B PRO* 3.1 22.2 - - - +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR 4.8 1.6 - - - +
201B PHE 4.5 3.1 - - - +
202B ASP* 3.8 30.5 - - + +
203B VAL* 3.7 32.3 - - + +
204B TRP* 2.8 30.6 + - + +
408B ARG* 4.0 22.9 - - + -
409B PRO* 2.7 31.4 + - + +
411B GLU* 1.3 75.1 - - + +
413B ALA* 1.3 61.9 + - - +
415B PRO* 3.4 2.1 - - - +
416B TRP* 3.4 7.0 - - - +
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Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ASN* 3.2 30.7 - - - +
406B GLU* 4.2 17.6 - - - +
408B ARG* 3.7 9.8 - - - +
409B PRO 2.8 14.5 + - - +
410B MET* 3.9 4.5 - - - +
412B VAL* 1.3 77.0 - - - +
414B GLU* 1.3 65.7 + - - +
416B TRP* 2.9 26.1 + - - +
417B VAL* 3.7 8.0 + - - +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET* 2.9 43.1 + - + +
411B GLU* 4.6 1.1 - - - +
413B ALA* 1.3 72.6 - - - +
415B PRO* 1.3 70.0 - - + +
417B VAL* 3.0 21.0 + - - +
418B ASP* 3.7 7.5 - - - +
449B LYS* 2.6 39.0 + - - -
489B ARG* 3.3 24.9 + - - +
490B TYR* 3.5 23.4 + - - +
493B LEU* 5.3 2.1 - - - +
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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
----------------------------------------------------------
204B TRP* 3.3 41.7 - - + +
411B GLU 3.1 24.2 - - - +
412B VAL 3.4 2.2 - - - +
414B GLU* 1.3 89.1 - - + +
416B TRP* 1.3 58.3 + - - -
418B ASP* 3.4 15.7 + - + +
419B CYS* 3.3 24.5 + - - -
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Residues in contact with TRP 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 3.8 12.3 - - + +
204B TRP* 3.2 32.0 - + - +
250B PRO 4.6 2.2 - - - -
251B PHE* 3.6 50.4 - + - -
253B ASN* 3.8 10.5 - - - -
255B ARG* 3.8 23.6 - - + -
256B HIS* 3.5 27.8 - - + -
259B CYS* 3.5 25.4 - - - -
405B ASN* 3.5 31.8 + - + +
408B ARG* 5.3 2.0 - - - +
412B VAL* 3.4 19.7 - - + -
413B ALA* 2.9 12.9 + - - +
415B PRO* 1.3 76.5 - - - +
417B VAL* 1.3 65.4 + - + +
419B CYS* 3.4 8.1 + - + +
420B LEU* 3.0 23.4 + - - +
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Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 3.5 19.3 - - - +
413B ALA 4.1 5.4 - - - +
414B GLU 3.0 11.6 + - - +
416B TRP* 1.3 79.2 - - + +
418B ASP* 1.3 62.2 + - - +
420B LEU* 3.3 8.7 + - + +
421B LEU* 3.0 29.2 + - + +
449B LYS* 3.9 32.5 - - + -
452B ALA* 5.2 2.2 - - + -
453B GLN* 3.8 30.1 - - + +
490B TYR* 3.4 22.0 - - - +
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU 3.7 5.5 - - - +
415B PRO* 3.4 13.6 + - + +
417B VAL* 1.3 78.6 - - - +
419B CYS* 1.3 57.9 + - - +
421B LEU* 3.5 6.7 + - - +
422B GLU* 2.9 31.5 + - - +
449B LYS* 3.0 40.7 + - - +
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Residues in contact with CYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TRP* 4.1 22.4 - - - -
250B PRO* 3.0 35.3 - - - +
251B PHE* 3.9 11.7 - - + +
415B PRO 3.3 15.6 + - - -
416B TRP* 3.6 12.3 - - + +
417B VAL 3.3 0.4 - - - -
418B ASP* 1.3 79.2 - - - +
420B LEU* 1.3 63.4 + - - +
422B GLU* 3.1 20.3 + - - +
423B GLU 3.2 9.0 + - - -
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B IBM 3.5 46.9 - - + +
251B PHE* 3.6 38.9 - - + -
252B HIS* 4.8 6.3 - - + -
416B TRP 3.0 18.3 + - - +
417B VAL* 3.6 8.7 - - + +
419B CYS* 1.3 76.5 - - - +
421B LEU* 1.3 66.0 + - + +
423B GLU* 3.0 7.0 + - + +
424B TYR* 3.0 58.9 + - + +
452B ALA* 6.3 0.4 - - + -
453B GLN* 4.6 6.3 - - - +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B VAL* 3.0 22.5 + - + +
418B ASP* 4.0 5.6 - - - +
420B LEU* 1.3 79.4 - - + +
422B GLU* 1.3 56.6 + - - +
424B TYR* 3.0 21.2 + - + -
425B PHE* 2.7 66.2 + - + -
441B PHE 5.2 0.4 - - - +
447B VAL* 3.8 20.6 - - + -
448B THR* 4.2 4.9 - - - -
449B LYS* 4.0 39.7 - - + +
452B ALA* 4.2 11.0 - - + -
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PRO* 3.5 26.5 - - + +
418B ASP 2.9 16.4 + - - +
419B CYS* 3.3 15.0 - - - +
421B LEU* 1.3 75.3 - - - +
423B GLU* 1.3 57.2 + - - +
425B PHE* 4.0 7.0 - - - +
426B MET* 3.1 37.4 + - + +
444B ARG* 5.2 3.9 + - - +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 3.5 9.1 - - - +
250B PRO* 3.7 14.5 - - + +
251B PHE* 2.8 33.1 + - + -
252B HIS* 2.5 40.5 + - - -
296B HIS* 3.9 1.9 - - - -
298B GLY* 3.5 39.5 - - - +
419B CYS 3.2 3.2 + - - +
420B LEU* 3.0 11.0 + - + +
422B GLU* 1.3 78.6 - - - +
424B TYR* 1.3 69.9 + - + +
426B MET* 3.2 9.3 + - + +
427B GLN* 3.0 22.2 + - - +
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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
----------------------------------------------------------
1B IBM 3.2 43.9 + + - -
252B HIS* 5.5 6.3 - + - -
300B ASN* 6.1 3.6 - - + -
420B LEU* 3.0 45.3 + - + +
421B LEU* 3.0 22.4 + - + +
423B GLU* 1.3 80.0 - - + +
425B PHE* 1.3 60.8 + - + +
427B GLN* 3.0 6.7 + - - +
428B SER* 2.9 28.2 + - - -
441B PHE* 3.5 33.4 - + - -
442B MET* 3.5 41.4 - - + +
452B ALA* 6.3 0.4 - - + -
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Residues in contact with PHE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU* 2.7 53.8 + - + +
422B GLU* 4.1 4.5 - - - +
424B TYR* 1.3 75.3 - - + +
426B MET* 1.3 63.4 + - - +
428B SER* 3.2 5.3 + - - -
429B ASP* 2.9 31.8 + - - -
442B MET 3.4 16.4 - - - -
443B ASP 3.9 5.2 - - - -
444B ARG* 3.2 62.1 - - + +
447B VAL* 3.9 31.2 - - + -
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Residues in contact with MET 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PRO* 4.5 23.6 - - + -
298B GLY* 5.4 3.6 - - - +
299B TYR* 3.6 29.7 + - + +
422B GLU* 3.1 30.4 + - + +
423B GLU* 3.3 8.7 - - - +
425B PHE* 1.3 76.1 - - - +
427B GLN* 1.3 62.1 + - - +
429B ASP* 3.9 6.5 - - - +
430B ARG* 3.3 22.3 + - - +
444B ARG* 4.6 2.2 - - - +
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Residues in contact with GLN 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLY 4.6 1.8 - - - +
299B TYR* 3.6 27.7 - - + -
300B ASN* 3.0 49.2 + - - +
302B THR* 5.1 1.6 - - - +
303B TYR* 3.6 9.1 - - + +
423B GLU 3.0 12.1 + - - +
424B TYR* 3.4 9.0 - - - +
426B MET* 1.3 76.0 - - - +
428B SER* 1.3 60.4 + - - +
430B ARG* 3.1 3.5 + - - +
431B GLU* 2.8 61.0 + - + +
442B MET* 3.6 24.7 - - - +
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR 2.9 9.9 + - - -
425B PHE* 3.2 11.6 + - - -
427B GLN* 1.3 70.8 - - - +
429B ASP* 1.3 64.9 + - - +
431B GLU* 3.2 13.8 + - - +
432B LYS* 2.8 39.4 + - - +
438B VAL* 3.9 21.5 - - - +
442B MET* 2.8 32.6 + - - +
443B ASP* 4.4 2.0 - - - -
444B ARG 4.0 6.6 + - - -
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Residues in contact with ASP 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B PHE 2.9 23.7 + - - +
426B MET* 3.9 6.2 - - - +
428B SER* 1.3 77.0 + - - +
430B ARG* 1.3 59.3 + - - +
432B LYS* 3.3 16.1 + - - +
433B SER* 2.9 29.5 + - - -
444B ARG* 2.4 52.9 + - - +
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Residues in contact with ARG 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B TYR* 3.4 44.7 + - - +
303B TYR* 2.8 38.6 + - + -
426B MET 3.3 11.7 + - - +
427B GLN 3.1 9.7 + - - +
429B ASP* 1.3 80.6 - - - +
431B GLU* 1.3 56.4 + - - +
433B SER* 3.1 6.7 + - - -
434B GLU* 2.8 56.9 + - + +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B THR* 5.1 3.8 - - - +
303B TYR* 3.7 28.7 + - + +
306B ASN* 5.2 2.9 + - - +
427B GLN* 2.8 48.2 + - - +
428B SER* 3.2 20.6 + - - +
430B ARG* 1.3 73.1 - - - +
432B LYS* 1.3 62.1 + - - +
434B GLU* 4.5 2.0 - - - +
435B GLY* 3.0 3.3 + - - -
436B LEU* 2.7 53.9 + - + +
437B PRO 3.4 18.7 - - - +
438B VAL* 3.9 11.3 - - + -
439B ALA* 4.3 4.4 + - - +
442B MET* 5.0 2.9 - - - +
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Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER* 2.8 26.4 + - - +
429B ASP* 3.5 17.9 + - - +
431B GLU* 1.3 78.1 - - - +
433B SER* 1.3 63.9 + - - +
435B GLY* 3.4 9.2 + - - -
436B LEU 4.8 0.4 - - - -
438B VAL* 3.5 22.4 - - + -
443B ASP* 3.0 36.6 + - - -
444B ARG* 4.4 6.5 - - - +
445B ASP* 3.1 19.6 + - - -
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Residues in contact with SER 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ASP 2.9 17.3 + - - -
430B ARG* 3.5 7.0 - - - -
432B LYS* 1.3 80.0 - - - +
434B GLU* 1.3 61.8 + - - +
435B GLY 3.2 0.7 + - - -
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR* 2.7 25.8 + - - -
307B ALA* 4.6 1.0 - - - +
430B ARG* 2.8 53.3 + - + +
431B GLU 4.3 0.4 - - - +
433B SER* 1.3 75.7 - - - +
435B GLY* 1.3 60.9 + - - +
436B LEU* 3.4 28.4 + - + +
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Residues in contact with GLY 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLU 3.0 5.4 + - - -
432B LYS* 3.4 7.5 + - - -
433B SER 3.2 4.2 + - - -
434B GLU* 1.3 80.2 - - - +
436B LEU* 1.3 64.5 + - - +
437B PRO* 4.6 1.6 - - - +
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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