Contacts of the helix formed by residues 407 - 421 (chain B) in PDB entry 1Z6T
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 GLU 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LYS* 5.3 2.9 - - + +
308A GLU 5.2 0.3 - - - +
311A HIS* 3.0 39.4 - - - +
312A SER* 2.7 31.7 + - - -
315A LYS* 3.7 24.0 - - + +
47B PRO 5.2 3.6 - - - +
401B CYS* 4.1 0.7 - - - -
406B MET* 1.3 77.0 - - - +
408B THR* 1.3 66.9 - - - +
409B GLU* 3.3 13.8 - - + +
410B GLU* 3.2 22.9 + - + +
411B VAL* 3.1 18.9 + - - +
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Residues in contact with THR 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 3.0 32.1 + - - +
21B LYS* 4.6 7.4 - - - +
49B GLN* 5.6 1.8 - - - +
397B THR* 3.7 11.6 - - + +
401B CYS* 3.6 21.3 - - - -
407B GLU* 1.3 72.2 - - - +
409B GLU* 1.3 60.5 + - - +
411B VAL* 3.3 1.0 + - - +
412B GLU* 2.9 58.3 + - - +
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Residues in contact with GLU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 2.5 38.6 + - - +
47B PRO 3.7 22.2 - - - +
48B THR* 3.2 12.4 - - - +
49B GLN* 2.9 39.0 + - + +
52B ARG* 4.4 21.8 + - - +
407B GLU* 3.3 12.3 - - + +
408B THR* 1.3 78.4 + - + +
410B GLU* 1.3 57.7 + - - +
412B GLU* 3.9 7.2 - - - +
413B ASP* 3.1 36.0 + - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B MET* 3.8 29.6 - - + +
407B GLU* 3.2 25.8 + - + +
409B GLU* 1.3 76.7 - - - +
411B VAL* 1.3 64.3 + - - +
413B ASP* 3.4 8.5 + - + +
414B ILE* 3.2 31.8 + - + +
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B THR* 4.2 12.6 - - + +
400B LEU* 4.0 11.9 - - + -
401B CYS* 3.7 25.8 - - - +
404B TRP* 4.0 15.0 - - + -
406B MET* 3.2 34.3 - - + -
407B GLU 3.1 12.4 + - - +
408B THR* 3.7 6.1 - - - +
410B GLU* 1.3 74.8 - - - +
412B GLU* 1.3 58.2 + - - +
414B ILE* 3.3 3.9 + - - +
415B LEU* 2.9 48.8 + - + +
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Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 2.5 43.1 + - - +
23B SER* 6.1 0.9 - - - +
49B GLN* 5.1 0.3 - - - +
52B ARG* 6.1 1.3 - - - +
397B THR* 3.2 24.4 + - + -
408B THR* 2.9 35.8 + - - +
409B GLU* 4.0 6.8 - - - +
411B VAL* 1.3 77.7 - - - +
413B ASP* 1.3 60.2 + - - +
415B LEU* 3.9 2.4 - - - +
416B GLN* 3.0 29.3 + - - +
433B PHE* 3.7 16.0 - - + -
435B TYR* 3.3 23.8 + - + +
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Residues in contact with ASP 413 (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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23B SER* 5.9 3.6 - - - -
44B ARG* 3.7 37.7 + - - +
52B ARG* 2.8 38.5 + - - -
409B GLU 3.1 20.4 + - - +
410B GLU* 3.6 8.5 - - + +
412B GLU* 1.3 75.9 - - - +
414B ILE* 1.3 66.3 + - + +
416B GLN* 3.4 7.8 + - - +
417B GLU* 3.4 22.8 + - - +
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Residues in contact with ILE 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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376B ARG* 5.4 3.1 - - - +
379B ILE* 4.3 16.6 - - + -
382B TYR* 3.9 34.8 - - + -
404B TRP* 4.3 6.7 - - + -
406B MET* 3.5 30.1 - - + -
410B GLU* 3.2 21.2 + - + +
411B VAL* 3.7 5.6 - - - +
413B ASP* 1.3 75.8 - - + +
415B LEU* 1.3 63.2 + - - +
417B GLU* 3.1 28.8 + - - +
418B PHE* 3.4 32.2 + - + -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 4.3 5.2 - - + -
397B THR* 5.3 0.2 - - + -
400B LEU* 3.7 15.3 - - + -
404B TRP* 3.5 28.3 - - + -
411B VAL* 2.9 37.2 + - + +
412B GLU* 4.0 3.1 - - + +
414B ILE* 1.3 76.2 - - - +
416B GLN* 1.3 57.9 + - - +
418B PHE* 3.1 13.8 + - + +
419B VAL* 2.9 32.8 + - - +
424B LEU* 3.6 20.9 - - + +
435B TYR* 3.5 48.5 - - + +
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Residues in contact with GLN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 4.4 16.7 + - - -
24B TYR* 2.4 54.6 + - - -
27B ASP* 4.5 5.5 + - - -
44B ARG* 5.9 5.6 - - - +
412B GLU 3.0 18.3 + - - +
413B ASP* 3.6 9.2 - - - +
414B ILE 3.2 0.2 - - - -
415B LEU* 1.3 72.7 - - - +
417B GLU* 1.3 62.7 + - + +
419B VAL* 4.2 7.9 - - - +
420B ASN* 2.8 68.4 + - - +
435B TYR* 5.3 0.6 - - - -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 4.8 13.6 + - - +
376B ARG* 2.7 49.2 + - - +
379B ILE* 3.9 23.8 - - + +
413B ASP 3.4 13.5 + - - +
414B ILE* 3.1 13.6 + - - +
416B GLN* 1.3 78.0 - - + +
418B PHE* 1.3 61.6 + - - +
420B ASN* 3.6 7.2 + - - +
421B LYS* 3.4 37.4 + - + +
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Residues in contact with PHE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LEU* 4.1 15.7 - - + -
379B ILE* 3.6 39.3 - - + -
382B TYR* 4.3 3.4 - - + -
383B TYR* 3.7 45.8 - + + -
386B LEU* 4.1 10.1 - - + -
404B TRP* 4.6 0.4 - + - -
414B ILE* 3.4 33.4 + - + -
415B LEU* 3.1 24.1 + - + +
417B GLU* 1.3 75.6 - - - +
419B VAL* 1.3 65.6 + - - +
421B LYS* 3.1 7.6 + - - -
423B LEU* 3.0 35.0 + - + +
424B LEU* 3.6 16.8 - - + -
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Residues in contact with VAL 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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24B TYR* 3.8 24.5 - - + +
124B VAL* 3.5 23.3 - - + +
415B LEU 2.9 21.7 + - - +
416B GLN* 3.2 11.2 + - - +
418B PHE* 1.3 75.4 - - - +
420B ASN* 1.3 58.7 + - - +
422B SER* 3.1 18.2 + - - -
424B LEU* 3.3 37.5 - - + +
425B PHE* 4.8 1.1 - - + -
426B CYS* 4.0 27.1 - - + +
428B ARG* 5.5 2.5 - - - +
435B TYR* 4.4 2.5 - - + -
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Residues in contact with ASN 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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27B ASP* 4.6 6.4 - - - +
124B VAL* 4.4 19.6 - - - +
329B ALA* 4.1 2.1 - - - +
332B ARG* 3.0 38.6 + - - +
416B GLN* 2.8 55.5 + - - +
417B GLU* 4.0 8.4 - - - +
419B VAL* 1.3 71.3 - - - +
421B LYS* 1.3 57.7 + - + +
422B SER 3.4 1.1 + - - -
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Residues in contact with LYS 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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326B LEU* 3.7 12.6 - - - +
329B ALA* 3.8 18.9 - - + +
330B LEU* 4.9 5.5 - - - +
332B ARG* 4.2 2.0 - - - +
333B ASP* 3.2 32.1 + - - +
334B PHE* 3.9 24.4 - - - -
371B SER* 4.4 9.0 + - - +
374B MET* 4.1 12.7 + - - +
375B LEU* 3.8 28.5 - - + +
376B ARG 6.1 0.2 - - - +
379B ILE* 6.0 1.3 - - + -
417B GLU* 3.4 27.1 + - + +
418B PHE 3.1 6.4 + - - +
420B ASN* 1.3 77.4 - - + +
422B SER* 1.3 67.9 + - - +
423B LEU* 3.2 14.5 + - + +
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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