Contacts of the helix formed by residues 386 - 409 (chain B) in PDB entry 1ZDT
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 ASN 386 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU 5.7 0.4 + - - -
289B LEU* 5.3 7.0 - - + +
293B ASP* 3.2 15.0 + - - +
384B LEU* 4.7 1.8 - - - -
385B ASN* 1.3 76.5 - - + +
387B HIS* 1.3 59.9 + - - +
388B ILE* 2.8 33.2 - - - +
389B LEU* 2.9 40.6 + - + +
390B VAL* 3.4 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 2.8 49.7 + - + +
382B LYS* 4.5 8.3 - - - -
384B LEU* 2.8 30.4 + - - +
385B ASN 3.2 9.4 + - - -
386B ASN* 1.3 71.8 - - - +
388B ILE* 1.3 58.0 + - - +
390B VAL* 4.0 2.2 - - - -
391B LYS* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ASN* 2.8 26.5 - - - +
387B HIS* 1.3 76.9 - - - +
389B LEU* 1.3 72.4 + - + +
391B LYS* 3.9 8.5 - - - +
392B ASP* 3.1 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 3.2 23.3 - - + +
288B GLU* 3.9 30.3 - - + +
289B LEU* 3.6 31.2 - - + -
386B ASN* 2.9 34.4 + - - +
388B ILE* 1.3 83.8 - - + +
390B VAL* 1.3 57.0 + - - +
392B ASP* 3.6 9.9 - - + +
393B ALA 3.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 4.2 18.2 - - + -
293B ASP* 5.6 0.2 - - - +
297B LEU* 5.0 1.8 - - + -
377B PHE* 4.2 24.5 - - + +
381B LEU* 3.6 22.4 - - + -
384B LEU* 3.9 29.8 - - + -
386B ASN* 3.4 19.2 + - + +
387B HIS* 3.9 2.9 - - - +
388B ILE 3.2 0.4 - - - -
389B LEU* 1.3 76.0 - - - +
391B LYS* 1.3 54.7 + - - +
393B ALA* 3.2 6.9 + - - +
394B GLN* 2.8 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 3.8 21.1 - - + +
387B HIS* 2.9 19.6 + - + +
388B ILE* 3.9 8.5 - - - +
390B VAL* 1.3 76.6 - - - +
392B ASP* 1.3 53.2 + - - +
394B GLN* 3.2 12.0 + - + +
395B GLU* 2.8 72.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.0 13.7 - - - +
388B ILE* 3.1 16.1 + - + +
389B LEU* 3.6 7.2 - - + +
391B LYS* 1.3 80.0 - - - +
393B ALA* 1.3 57.2 + - - +
395B GLU* 3.9 10.5 + - - +
396B LYS* 2.9 67.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 3.6 26.5 - - + -
373B PHE* 3.8 10.3 - - + -
377B PHE* 3.8 24.0 - - + +
389B LEU 3.0 19.1 + - - +
390B VAL 3.2 5.4 + - - +
392B ASP* 1.3 76.0 - - - +
394B GLN* 1.3 65.0 + - - +
396B LYS* 3.9 4.3 - - - +
397B ALA* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 5.6 0.9 - - - +
377B PHE* 2.6 38.2 + - + +
378B SER* 4.5 1.9 - - - +
379B LEU 3.0 26.9 + - - +
380B ASP* 5.1 0.4 - - - +
381B LEU* 3.0 27.1 - - - +
390B VAL* 2.8 24.1 + - + +
391B LYS* 3.2 8.1 + - - +
393B ALA* 1.3 72.3 - - - +
395B GLU* 1.3 64.9 + - + +
397B ALA* 4.0 3.0 - - - +
398B ASN* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LYS* 2.8 63.2 + - + +
392B ASP* 3.9 7.4 - - - +
394B GLN* 1.3 78.0 - - + +
396B LYS* 1.3 57.2 + - + +
398B ASN* 3.9 4.4 - - - +
399B ALA* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 4.1 24.1 - - + +
229B GLN* 6.1 1.1 - - - -
285B VAL* 5.3 7.3 - - + +
373B PHE* 6.0 0.4 - - + -
392B ASP* 2.9 54.4 + - - +
393B ALA* 3.9 5.8 - - - +
395B GLU* 1.3 73.8 - - + +
397B ALA* 1.3 53.7 + - - +
399B ALA* 3.4 5.8 + - - +
400B ALA* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.6 13.0 - - + +
370B CYS* 3.4 13.4 - - - -
373B PHE* 3.5 26.2 - - + -
374B ILE* 3.6 23.1 - - + +
377B PHE* 6.5 0.4 - - + -
393B ALA 3.2 16.4 + - - +
394B GLN* 4.0 2.9 - - - +
396B LYS* 1.3 75.6 - - - +
398B ASN* 1.3 64.9 + - - +
400B ALA* 4.3 0.2 - - - -
401B LEU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 4.4 9.7 - - + +
394B GLN 3.1 18.7 + - - +
395B GLU* 3.9 4.7 - - - +
397B ALA* 1.3 76.0 - - - +
399B ALA* 1.3 59.4 + - - +
402B LEU* 3.1 29.6 + - - +
416B PHE* 3.5 30.3 - - - -
420B LEU* 4.3 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLU 2.9 20.1 + - - +
396B LYS* 3.7 5.8 - - - +
398B ASN* 1.3 76.8 + - - +
400B ALA* 1.3 64.2 + - - +
402B LEU* 3.9 6.5 - - - +
403B ASP* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PRO* 3.6 29.3 - - + +
226B LEU* 4.1 22.9 - - + -
227B ILE* 4.1 11.0 - - + -
370B CYS* 4.3 0.4 - - - -
396B LYS 2.7 21.9 + - - +
397B ALA 3.9 3.8 - - - +
399B ALA* 1.3 72.6 - - - +
401B LEU* 1.3 58.5 + - - +
403B ASP* 4.6 0.7 - - - -
404B TYR* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ILE* 4.6 0.9 - - + -
366B GLN 5.1 0.2 - - - +
367B GLU* 4.0 41.7 - - + +
370B CYS* 3.8 19.2 - - + -
371B LEU* 3.9 24.7 - - + -
374B ILE* 4.0 8.3 - - + -
397B ALA 3.1 16.2 + - - +
400B ALA* 1.3 77.3 - - - +
402B LEU* 1.3 65.2 + - - +
404B TYR* 4.4 4.7 - - + -
405B THR* 2.9 36.1 + - + +
416B PHE* 3.6 28.3 - - + -
419B LEU* 4.4 12.1 - - + -
420B LEU* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASN* 3.1 22.1 + - - +
399B ALA* 3.9 6.3 - - - +
400B ALA 3.4 0.2 - - - -
401B LEU* 1.3 75.7 - - - +
403B ASP* 1.3 65.2 + - - +
405B THR* 3.0 14.5 + - - -
406B LEU* 3.0 40.0 + - + +
416B PHE* 3.6 41.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN* 5.0 3.8 - - - +
224B PRO* 3.9 18.3 - - + +
399B ALA 3.0 18.2 + - - +
400B ALA* 3.8 4.0 - - - +
402B LEU* 1.3 77.4 - - - +
404B TYR* 1.3 65.7 + - - +
406B LEU* 3.0 23.8 - - - +
407B CYS* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN 5.3 0.4 - - - -
223B VAL* 4.3 7.0 - - + -
224B PRO* 4.1 17.7 - - + -
227B ILE* 3.6 18.8 - - + -
364B ASP* 2.6 23.6 + - - -
366B GLN* 3.1 38.6 + - + +
367B GLU* 3.6 32.3 - - + -
400B ALA 2.9 19.7 + - - +
401B LEU* 3.8 3.6 - - + +
402B LEU 3.3 0.2 - - - -
403B ASP* 1.3 81.1 - - - +
405B THR* 1.3 61.1 + - + +
407B CYS* 4.8 0.2 - - - -
408B HIS* 2.9 74.5 + + + +
409B TYR* 3.9 6.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLU* 3.8 25.6 - - + +
401B LEU* 2.9 27.1 + - + +
402B LEU* 3.0 9.4 + - - +
404B TYR* 1.3 78.5 - - + +
406B LEU* 1.3 56.8 + - - +
409B TYR* 2.8 39.5 + - - +
412B SER 5.0 0.6 - - - +
415B LYS* 4.0 26.5 - - + -
416B PHE* 3.7 19.4 + - - +
419B LEU* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 3.0 47.1 + - + +
403B ASP* 3.0 37.7 - - - +
405B THR* 1.3 78.0 - - - +
407B CYS* 1.3 67.5 + - - +
408B HIS 3.5 0.2 - - - -
409B TYR 4.3 4.5 - - - -
410B PRO* 3.3 27.9 - - + +
412B SER 5.6 2.7 - - - +
413B GLY* 6.0 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN* 4.8 16.5 - - + +
403B ASP* 3.0 43.9 + - - +
404B TYR* 4.0 2.2 - - - +
406B LEU* 1.3 83.8 - - - +
408B HIS* 1.3 71.4 + - + +
410B PRO* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO 3.2 18.3 + - - -
222B ASN* 2.8 35.2 + - + +
223B VAL* 3.8 6.4 - - + +
404B TYR* 2.9 50.6 + + + +
407B CYS* 1.3 84.6 - - + +
409B TYR* 1.3 83.5 + - + +
410B PRO* 3.4 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLN* 4.2 26.5 + - + -
364B ASP* 2.5 34.7 + - - +
367B GLU* 3.1 27.6 - - - -
404B TYR* 3.9 2.7 - + - -
405B THR* 2.8 22.5 + - - +
406B LEU* 4.3 0.7 - - - -
408B HIS* 1.3 99.7 - - + +
410B PRO* 1.3 62.8 - - - +
411B HIS 3.1 6.7 + - - -
412B SER* 3.1 34.0 + - - +
415B LYS* 3.5 22.2 - - + -
----------------------------------------------------------
Back to top of page
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