Contacts of the helix formed by residues 387 - 409 (chain B) in PDB entry 6MZL
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 GLY 387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382B MET 4.3 0.4 - - - -
383B LYS 4.6 0.4 + - - -
386B PHE* 1.3 76.9 - - - +
388B VAL* 1.3 56.4 + - - +
389B ASN* 3.1 3.1 - - - -
390B GLU* 2.9 20.1 + - - -
391B TYR* 2.4 34.9 + - - +
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Residues in contact with VAL 388 (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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383B LYS* 3.5 28.9 - - + +
384B LYS* 5.7 6.7 - - + +
387B GLY* 1.3 72.5 - - - +
389B ASN* 1.3 63.2 + - - +
391B TYR* 3.2 18.8 - - + +
392B ARG* 3.0 32.6 + - + +
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Residues in contact with ASN 389 (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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387B GLY* 3.1 1.7 - - - -
388B VAL* 1.3 83.4 - - - +
390B GLU* 1.3 57.9 + - - +
392B ARG* 3.2 8.1 + - - +
393B HIS* 2.9 26.3 + - - +
659B VAL* 3.7 22.6 - - + +
690B CYS 5.1 6.1 + - - -
691B PHE* 3.7 25.3 - - + -
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Residues in contact with GLU 390 (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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340B PRO* 5.8 2.3 - - - +
382B MET* 4.7 6.2 - - + +
386B PHE* 4.4 20.4 - - + +
387B GLY* 2.9 19.2 + - - +
389B ASN* 1.3 73.6 - - - +
391B TYR* 1.3 60.5 + - - +
393B HIS* 3.4 11.1 - - + +
394B TRP* 2.9 27.7 + - - +
691B PHE* 3.5 21.1 - - + -
692B TYR* 3.6 26.3 - - + -
693B ARG* 3.3 33.6 + - - +
748B PHE* 4.7 1.6 - - - -
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Residues in contact with TYR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TYR* 4.8 4.0 - - - -
379B GLY* 3.3 31.6 - - - -
382B MET* 4.3 15.9 - - + +
383B LYS* 3.3 41.9 - - + -
387B GLY 2.4 26.8 + - - +
388B VAL* 3.2 21.8 - - + +
390B GLU* 1.3 69.0 - - - +
392B ARG* 1.3 86.2 + - - +
394B TRP* 3.0 12.8 + + - +
395B ILE* 3.0 36.2 + - + +
458B ARG* 2.3 43.8 + - - -
461B GLU* 4.5 5.2 + - - -
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Residues in contact with ARG 392 (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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383B LYS* 5.2 5.5 - - - +
388B VAL* 3.0 20.1 + - + +
389B ASN* 3.2 11.2 + - - +
391B TYR* 1.3 96.3 + - + +
393B HIS* 1.3 56.6 + - - +
395B ILE* 3.1 25.7 + - - +
396B LYS* 3.0 32.3 + - - +
458B ARG* 4.5 5.3 - - - +
461B GLU* 5.7 2.8 + - - -
632B PRO 5.8 1.6 - - - -
633B ASP* 3.9 40.9 + - - +
634B MET* 4.4 9.2 - - - +
658B ASP* 5.9 3.1 - - - +
659B VAL* 5.2 6.7 - - + -
660B VAL* 4.7 14.1 - - + -
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Residues in contact with HIS 393 (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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389B ASN 2.9 14.5 + - - +
390B GLU* 3.4 17.3 - - + +
392B ARG* 1.3 76.4 - - - +
394B TRP* 1.3 65.6 + - + +
396B LYS* 3.1 12.7 + - - +
397B GLU* 2.7 54.2 + - + +
659B VAL* 4.5 11.1 - - + +
663B GLN* 4.4 21.3 + - - -
691B PHE* 4.4 8.8 - + + -
693B ARG* 3.6 42.9 + - + +
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Residues in contact with TRP 394 (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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344B ARG* 3.0 44.9 - - - +
375B GLY 4.7 4.3 - - - -
376B TYR* 6.3 0.2 - - - -
378B TYR* 3.9 6.7 - + - -
379B GLY* 4.4 13.2 - - - -
382B MET* 4.1 18.4 - - + -
390B GLU 2.9 14.9 + - - +
391B TYR* 3.0 13.2 + + - +
393B HIS* 1.3 81.4 - - + +
395B ILE* 1.3 64.8 + - + +
397B GLU* 3.2 16.7 + - + +
398B GLU* 3.0 51.3 + - + +
454B HIS* 3.6 40.6 - + + -
458B ARG* 3.7 27.8 - - - -
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Residues in contact with ILE 395 (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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391B TYR* 3.0 25.3 + - + +
392B ARG* 3.1 35.9 + - - +
394B TRP* 1.3 79.5 - - + +
396B LYS* 1.3 61.0 + - - +
398B GLU* 3.1 10.4 + - - +
399B LEU* 3.0 19.9 + - + +
455B LEU* 4.0 13.5 - - + -
458B ARG* 3.3 54.5 - - - +
634B MET* 3.7 27.2 - - + +
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Residues in contact with LYS 396 (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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392B ARG 3.0 13.8 + - - +
393B HIS* 3.1 16.3 + - - +
395B ILE* 1.3 77.6 - - - +
397B GLU* 1.3 57.3 + - + +
399B LEU* 3.2 5.7 + - + +
400B ASP* 2.9 37.4 + - - +
634B MET* 3.6 20.9 - - + -
659B VAL* 3.8 3.6 + - + +
660B VAL* 2.9 54.1 + - + +
663B GLN* 3.3 28.0 - - + +
664B GLU* 3.3 29.3 + - - +
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Residues in contact with GLU 397 (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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393B HIS* 2.7 51.2 + - + +
394B TRP* 3.2 20.6 + - + +
396B LYS* 1.3 73.2 - - + +
398B GLU* 1.3 68.2 + - - +
400B ASP* 3.1 17.5 + - + +
401B LYS* 2.9 29.7 + - + +
693B ARG* 5.4 1.4 + - - -
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Residues in contact with GLU 398 (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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344B ARG* 4.8 0.9 + - - -
394B TRP* 3.0 62.4 + - + +
395B ILE* 3.1 13.0 + - - +
397B GLU* 1.3 77.3 - - - +
399B LEU* 1.3 59.0 + - - +
401B LYS* 3.1 15.8 + - - +
402B ILE* 2.9 30.3 + - - +
451B CYS* 3.2 36.3 - - + +
454B HIS* 3.5 9.5 + - - -
455B LEU* 4.0 25.6 - - + -
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Residues in contact with LEU 399 (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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395B ILE* 3.0 12.7 + - + +
396B LYS* 3.6 8.1 - - - +
398B GLU* 1.3 76.6 - - - +
400B ASP* 1.3 58.3 + - - +
402B ILE* 4.4 6.1 - - + +
403B VAL* 2.9 43.1 + - + +
455B LEU* 3.8 22.0 - - + -
634B MET* 3.6 30.5 - - + +
636B VAL 4.9 2.7 - - - +
637B LEU* 4.0 27.6 - - + -
638B ARG* 4.3 31.2 - - + +
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Residues in contact with ASP 400 (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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396B LYS* 2.9 27.3 + - - +
397B GLU* 3.2 23.3 - - + +
398B GLU 3.1 0.2 - - - -
399B LEU* 1.3 77.1 - - - +
401B LYS* 1.3 64.5 + - + +
403B VAL* 4.3 1.7 - - - +
404B ALA* 3.0 29.4 + - - +
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Residues in contact with LYS 401 (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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397B GLU* 2.9 17.8 + - + +
398B GLU* 3.5 17.3 + - - +
400B ASP* 1.3 76.5 - - + +
402B ILE* 1.3 57.3 + - - +
404B ALA* 3.8 3.5 - - - +
405B TYR* 2.9 32.1 + - - +
447B SER* 5.6 4.4 - - - -
448B MET* 3.4 30.8 - - + +
451B CYS* 4.1 17.2 - - - -
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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
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398B GLU 2.9 13.0 + - - +
399B LEU* 4.1 7.9 - - + +
401B LYS* 1.3 75.0 - - - +
403B VAL* 1.3 63.6 + - + +
405B TYR* 3.8 0.7 - - - +
406B GLU* 2.9 35.7 + - + +
448B MET* 3.9 12.1 - - + +
451B CYS* 3.5 24.0 - - + -
452B LYS* 3.4 47.6 - - + +
455B LEU* 3.6 22.9 - - + -
528B VAL* 4.3 16.6 - - + -
637B LEU* 4.9 11.2 - - + -
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Residues in contact with VAL 403 (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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399B LEU* 2.9 30.8 + - + +
400B ASP* 4.3 1.8 - - - +
402B ILE* 1.3 74.5 - - + +
404B ALA* 1.3 64.5 + - - +
406B GLU 3.8 0.2 - - - -
407B LEU* 3.0 37.1 + - + +
528B VAL* 3.7 25.8 - - + -
638B ARG 3.6 23.3 - - - +
639B LYS* 3.8 32.1 - - + +
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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
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400B ASP 3.0 21.1 + - - +
401B LYS* 3.9 4.0 - - - +
403B VAL* 1.3 78.9 - - - +
405B TYR* 1.3 59.0 + - - +
407B LEU* 3.5 2.8 + - - +
408B LYS* 2.9 38.4 + - - +
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Residues in contact with TYR 405 (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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401B LYS 2.9 19.1 + - - +
402B ILE 4.0 1.3 - - - +
404B ALA* 1.3 78.1 - - - +
406B GLU* 1.3 61.7 + - + +
407B LEU 3.1 0.4 - - - -
408B LYS* 3.1 15.8 + - + +
409B THR* 2.7 63.6 + - + +
410B GLY 4.7 2.7 - - - -
412B VAL* 4.2 21.3 - - + -
432B HIS* 5.6 3.3 - - - -
442B SER* 3.8 14.6 + - - -
444B GLU* 3.3 38.3 + - + +
445B TYR* 4.0 19.6 + + - +
448B MET* 3.5 29.2 - - + -
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Residues in contact with GLU 406 (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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402B ILE* 2.9 21.7 + - + +
403B VAL 3.8 0.2 - - - -
405B TYR* 1.3 77.4 - - + +
407B LEU* 1.3 60.0 + - - +
409B THR 2.8 18.1 - - - +
410B GLY 3.3 13.7 - - - +
411B GLY* 3.3 4.4 - - - -
412B VAL* 2.4 47.2 + - + +
448B MET* 6.0 0.7 - - + -
452B LYS* 3.7 15.9 + - - +
526B SER 3.5 18.0 - - - +
527B GLY* 4.0 0.7 + - - -
528B VAL* 3.3 28.1 + - + +
557B THR* 3.6 22.4 + - + +
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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
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403B VAL* 3.0 39.0 + - + +
404B ALA* 4.2 3.4 - - - +
406B GLU* 1.3 84.3 - - - +
408B LYS* 1.3 63.1 + - - +
409B THR 3.3 1.1 - - - -
528B VAL* 5.5 9.9 - - + -
530B LYS* 4.4 14.6 - - + -
557B THR* 4.3 25.6 - - + +
639B LYS* 3.9 24.2 - - + +
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Residues in contact with LYS 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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404B ALA* 2.9 26.0 + - - +
405B TYR* 3.3 19.7 - - + +
407B LEU* 1.3 79.3 - - - +
409B THR* 1.3 67.4 + - - +
444B GLU* 4.6 17.0 + - - +
932B LYS* 5.0 14.5 - - - +
976B PHE* 5.9 2.3 - - - -
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Residues in contact with THR 409 (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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405B TYR* 2.7 52.6 + - + +
406B GLU 2.8 23.2 - - - +
407B LEU 4.2 0.3 - - - -
408B LYS* 1.3 81.6 + - - +
410B GLY* 1.3 71.8 + - - +
430B HIS* 5.0 8.7 - - + -
431B LEU* 5.8 5.4 - - + +
557B THR* 4.0 5.1 + - - -
976B PHE* 4.9 20.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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