Contacts of the helix formed by residues 400 - 422 (chain B) in PDB entry 5YD6
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 THR 400 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASP* 1.3 73.6 + - - +
401B GLN* 1.3 79.2 + - - +
403B ILE* 3.4 2.2 + - - -
404B GLN* 3.0 26.6 + - - +
581B LEU* 3.9 31.6 - - + +
582B VAL* 3.4 24.0 - - + +
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASP* 3.3 13.9 + - - +
400B THR* 1.3 103.5 + - - +
402B HIS* 1.3 59.5 + - + +
404B GLN* 3.3 7.8 + - + +
405B GLN* 2.9 46.3 + - + +
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Residues in contact with HIS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASP* 3.0 32.0 + - - +
400B THR 3.3 0.4 - - - -
401B GLN* 1.3 75.5 - - + +
403B ILE* 1.3 64.0 + - - +
405B GLN* 4.0 18.4 + - - +
406B PHE* 3.2 16.6 + - - +
474B GLN* 3.8 23.1 + - + +
477B ARG* 3.6 50.4 - - + -
478B GLY* 3.3 16.9 - - - +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASP 3.4 19.2 + - - +
400B THR 3.4 6.8 + - - +
401B GLN 3.3 0.6 - - - -
402B HIS* 1.3 75.8 - - - +
404B GLN* 1.3 63.5 + - - +
406B PHE* 3.3 4.8 + - - +
407B TYR* 3.1 45.6 + - + +
477B ARG 4.4 12.8 - - - +
478B GLY* 4.3 5.2 - - - -
572B ARG* 5.3 0.4 - - - +
576B LEU* 3.8 29.8 - - + -
579B GLU* 3.7 23.3 - - - +
581B LEU* 4.0 21.8 - - + -
582B VAL* 3.8 15.3 - - + +
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Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ASN* 5.2 12.1 + - - +
554A LYS* 5.9 0.9 + - - -
400B THR 3.0 17.0 + - - +
401B GLN* 3.3 8.7 + - - +
403B ILE* 1.3 76.1 - - - +
405B GLN* 1.3 57.4 + - + +
407B TYR* 3.1 15.9 + - - +
408B ASP* 2.9 62.6 + - - +
582B VAL* 3.4 23.8 - - + +
583B PRO 5.1 0.7 - - - +
585B PRO* 5.3 4.7 - - - +
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Residues in contact with GLN 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 3.1 33.3 + - - +
401B GLN* 2.9 35.6 + - + +
402B HIS* 4.0 19.2 + - - +
403B ILE 3.4 0.2 - - - -
404B GLN* 1.3 69.8 - - + +
406B PHE* 1.3 60.2 + - - +
408B ASP* 3.3 12.9 + - - +
409B LEU* 2.9 43.0 + - + +
470B LEU* 4.8 9.1 - - + +
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B HIS 3.2 15.3 + - - +
403B ILE 3.3 7.9 - - - +
405B GLN* 1.3 77.0 - - - +
407B TYR* 1.3 76.2 + + - +
409B LEU* 3.5 3.8 + - - +
410B LEU* 3.1 48.2 + - + +
478B GLY* 3.6 14.1 - - - -
479B PHE* 3.6 57.4 - + + +
482B TRP* 3.8 17.5 - + - -
572B ARG* 4.0 15.3 - - + -
573B ILE* 4.4 9.6 - - + -
576B LEU* 3.5 31.2 - - + -
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Residues in contact with TYR 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 ILE* 3.1 27.7 + - + -
404B GLN* 3.1 13.7 + - - +
406B PHE* 1.3 95.6 - + - +
408B ASP* 1.3 53.6 + - - +
410B LEU* 3.1 4.3 + - + +
411B THR* 2.8 40.3 + - - +
573B ILE* 5.0 6.9 + - + +
576B LEU* 3.4 28.3 - - + +
577B LYS 4.5 0.9 + - - -
582B VAL* 3.2 40.3 + - + -
583B PRO 3.7 7.9 - - - -
584B PRO* 3.7 25.1 - - + +
585B PRO* 3.6 25.1 - - + -
588B ILE* 3.7 23.7 - - + +
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLN* 2.9 52.5 + - - +
405B GLN* 3.6 13.9 - - - +
407B TYR* 1.3 70.4 - - - +
409B LEU* 1.3 54.9 + - + +
411B THR* 3.1 10.1 + - - +
412B GLY* 2.7 34.8 + - - -
585B PRO* 6.0 0.3 - - - +
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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
----------------------------------------------------------
386B ARG* 5.2 10.5 - - - +
405B GLN* 2.9 26.7 + - + +
406B PHE 3.6 5.4 - - - +
408B ASP* 1.3 75.8 - - + +
410B LEU* 1.3 61.1 + - - +
412B GLY* 4.1 0.6 - - - -
413B SER* 3.1 26.6 + - - -
447B PHE* 4.4 4.9 - - + -
464B PHE* 3.5 65.7 - - + -
465B CYS* 5.2 1.0 - - - -
466B ASN* 4.5 16.2 - - - +
468B VAL* 5.5 0.9 - - + -
470B LEU* 4.4 12.6 - - + -
475B CYS* 5.4 0.2 - - - -
479B PHE* 3.8 18.4 - - + -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PHE* 3.1 48.0 + - + +
407B TYR 3.1 6.9 + - - +
409B LEU* 1.3 76.5 - - - +
411B THR* 1.3 61.2 + - - +
413B SER* 3.6 2.3 + - - -
414B MET* 3.2 19.2 + - - +
443B PHE* 3.3 21.2 - - + -
444B LEU* 4.1 17.7 - - + -
447B PHE* 3.8 40.2 - - + -
479B PHE* 5.7 0.2 - - + -
482B TRP* 4.4 5.2 - - + -
573B ILE* 4.2 20.4 - - + -
588B ILE* 4.1 18.2 - - + -
601B 8SU 5.3 2.0 - - + -
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Residues in contact with THR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR 2.8 22.7 + - - +
408B ASP* 3.1 18.4 + - - +
410B LEU* 1.3 70.8 - - - +
412B GLY* 1.3 61.7 + - - +
414B MET* 3.2 18.8 + - - +
415B GLU* 3.6 7.6 + - - +
585B PRO* 3.8 16.6 - - + -
587B ILE* 3.5 32.9 - - + +
588B ILE* 3.7 17.7 - - + -
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Residues in contact with GLY 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP 2.7 20.9 + - - -
409B LEU* 4.1 0.9 - - - -
411B THR* 1.3 69.7 + - - +
413B SER* 1.3 62.9 + - - +
414B MET 3.4 0.3 + - - -
415B GLU* 3.6 12.3 + - - +
416B ILE* 3.6 20.4 + - - +
465B CYS* 4.1 5.8 - - - -
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Residues in contact with SER 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 19.9 + - - -
410B LEU 3.6 3.6 - - - -
412B GLY* 1.3 75.3 - - - +
414B MET* 1.3 58.6 + - - +
416B ILE* 3.2 1.6 + - - +
417B ILE* 2.9 51.9 + - - +
443B PHE* 3.4 5.5 - - - -
447B PHE* 3.4 25.4 - - - -
465B CYS* 3.4 24.0 - - - -
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Residues in contact with MET 414 (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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410B LEU 3.2 11.4 + - - +
411B THR 3.2 13.6 + - - +
413B SER* 1.3 76.5 - - - +
415B GLU* 1.3 57.6 + - - +
418B ARG* 3.0 36.4 + - - +
439B PHE* 3.4 30.3 - - + -
443B PHE* 3.6 37.9 - - + -
587B ILE* 3.5 33.0 - - + +
588B ILE* 4.4 17.3 - - + -
591B LEU* 3.8 27.1 - - + -
601B 8SU 4.6 1.8 - - + -
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Residues in contact with GLU 415 (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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411B THR 3.6 6.6 + - - +
412B GLY* 4.1 8.3 - - - +
413B SER 3.4 0.2 - - - -
414B MET* 1.3 80.5 - - - +
416B ILE* 1.3 60.6 + - + +
418B ARG* 3.6 30.3 + - - +
419B GLY* 3.1 23.0 + - - -
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Residues in contact with ILE 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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375B SER* 3.2 35.2 - - - +
412B GLY 3.6 9.5 + - - +
413B SER 3.2 7.8 + - - +
415B GLU* 1.3 78.7 - - + +
417B ILE* 1.3 58.6 + - - +
419B GLY* 3.2 4.0 + - - +
420B TRP* 2.9 25.1 + - - +
450B ARG* 3.4 10.1 - - - +
465B CYS* 3.6 39.0 - - + +
466B ASN* 4.8 5.6 - - + +
380D THR* 6.3 4.3 - - + -
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Residues in contact with ILE 417 (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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413B SER* 2.9 36.3 + - - +
414B MET 4.2 0.2 - - - +
416B ILE* 1.3 73.2 - - - +
418B ARG* 1.3 54.3 + - - +
420B TRP* 3.0 15.7 + - + +
421B ALA* 2.8 32.7 + - - +
439B PHE* 3.6 20.4 - - + -
443B PHE* 4.0 8.7 - - + -
446B LEU* 3.7 29.2 - - + -
447B PHE* 3.7 29.2 - - - +
450B ARG* 3.4 29.2 - - - +
465B CYS* 6.3 0.9 - - + -
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Residues in contact with ARG 418 (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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414B MET* 3.0 30.8 + - - +
415B GLU* 3.8 30.9 + - - +
417B ILE* 1.3 76.3 - - - +
419B GLY* 1.3 60.6 + - - +
421B ALA* 3.3 6.2 + - + +
422B GLU* 3.1 43.7 + - - +
427B PHE* 6.5 0.9 - - + -
432B LYS* 5.0 8.0 - - - +
436B ASP* 4.6 13.9 + - - +
439B PHE* 3.4 54.1 - - + +
440B GLU* 4.3 13.9 + - - +
591B LEU* 5.9 2.0 - - - +
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Residues in contact with GLY 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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375B SER* 5.2 0.9 - - - -
415B GLU 3.1 15.0 + - - -
416B ILE* 3.4 5.6 - - - -
417B ILE 3.2 0.6 - - - -
418B ARG* 1.3 75.7 - - - +
420B TRP* 1.3 60.9 + - - +
422B GLU* 3.4 17.0 + - - +
423B LYS* 3.4 24.1 + - - +
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Residues in contact with TRP 420 (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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368B LEU* 4.9 2.4 + - + +
371B ALA* 3.3 37.6 - - + +
372B HIS* 3.7 14.6 - - - +
375B SER* 3.4 25.4 - - - +
416B ILE 2.9 9.3 + - - +
417B ILE* 3.0 21.5 + - + +
419B GLY* 1.3 75.5 - - - +
421B ALA* 1.3 77.9 + - + +
423B LYS* 3.0 21.2 + - - +
424B ILE* 3.6 19.8 + - + +
446B LEU* 3.6 24.7 - - + -
450B ARG* 4.0 14.5 - - - +
504B SER 4.8 3.0 + - - -
507B ALA* 3.2 48.1 - - + +
508B ALA* 3.6 14.8 - - + -
511B MET* 3.5 21.8 - - + -
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Residues in contact with ALA 421 (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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417B ILE 2.8 15.4 + - - +
418B ARG* 3.5 13.7 - - + +
420B TRP* 1.3 82.0 - - + +
422B GLU* 1.3 61.4 + - - +
423B LYS 3.2 1.4 + - - -
424B ILE* 3.3 13.3 + - - +
427B PHE* 3.2 34.1 - - + +
439B PHE* 4.7 4.9 - - + -
511B MET* 3.5 34.3 - - + -
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 3.1 41.3 + - - +
419B GLY* 3.9 9.0 - - - +
420B TRP 3.2 0.6 - - - -
421B ALA* 1.3 75.4 - - - +
423B LYS* 1.3 59.8 + - + +
424B ILE 3.5 3.7 + - - +
427B PHE* 4.3 5.7 - - + -
428B ALA* 4.4 20.3 - - + +
432B LYS* 5.5 6.2 + - - -
435B GLN* 4.2 24.1 + - - +
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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) + - + + + + + -
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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