Contacts of the helix formed by residues 401 - 413 (chain B) in PDB entry 1ZJA
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 401 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B VAL* 4.1 3.7 - - - +
400B ALA* 1.3 76.9 - - - +
402B ALA* 1.3 65.7 + - - +
403B GLU* 3.5 10.4 + - - +
404B GLU* 3.0 35.3 + - - +
405B LEU* 3.1 19.6 + - - +
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Residues in contact with ALA 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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379B LEU* 3.9 22.0 - - + +
391B PHE* 4.2 12.1 - - + -
395B VAL* 3.8 17.7 - - + +
401B THR* 1.3 74.1 - - - +
403B GLU* 1.3 57.7 + - - +
405B LEU* 3.3 3.0 + - - +
406B LEU* 2.9 28.8 + - - +
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Residues in contact with GLU 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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401B THR* 3.1 8.4 + - - +
402B ALA* 1.3 77.5 - - - +
404B GLU* 1.3 65.9 + - + +
406B LEU* 3.3 13.0 + - + +
407B THR* 3.0 35.4 + - - +
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Residues in contact with GLU 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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292B TRP* 4.2 3.4 - - + -
399B LYS 4.6 1.0 - - - +
400B ALA* 3.3 18.2 - - + +
401B THR* 3.0 43.7 + - - +
403B GLU* 1.3 77.3 - - + +
405B LEU* 1.3 62.8 + - - +
407B THR* 4.5 3.1 - - - -
408B ASN* 2.9 37.8 + - - +
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Residues in contact with LEU 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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292B TRP* 3.6 34.0 - - + -
379B LEU* 4.2 15.7 - - + -
387B VAL* 4.2 7.9 - - + +
390B PHE* 3.8 21.8 - - + -
391B PHE* 3.8 39.9 - - + +
394B TYR* 5.8 0.2 - - + -
395B VAL* 3.9 15.0 - - + -
400B ALA* 5.6 0.2 - - + -
401B THR 3.1 12.2 + - - +
402B ALA* 3.6 7.6 - - - +
403B GLU 3.2 0.2 - - - -
404B GLU* 1.3 76.7 - - - +
406B LEU* 1.3 58.4 + - - +
409B VAL* 2.8 47.1 + - + +
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Residues in contact with LEU 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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376B PHE* 4.4 10.3 - - + +
377B LYS* 3.4 23.1 - - - +
378B THR* 3.8 30.7 - - - +
379B LEU* 4.0 13.6 - - + +
382B PHE* 3.8 18.4 - - + -
402B ALA 2.9 16.7 + - - +
403B GLU* 3.6 13.2 - - + +
405B LEU* 1.3 77.1 - - - +
407B THR* 1.3 68.2 + - - +
409B VAL* 4.0 2.4 - - - +
410B ALA* 3.0 30.6 + - + +
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Residues in contact with THR 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 GLU* 3.0 23.8 + - - +
404B GLU* 3.8 6.7 - - - -
406B LEU* 1.3 81.2 - - - +
408B ASN* 1.3 74.6 + - - +
410B ALA* 3.9 10.9 - - - +
411B LEU* 3.9 13.5 - - + +
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Residues in contact with ASN 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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292B TRP* 3.3 28.5 - - + +
293B HIS* 3.5 31.7 + - - -
294B THR* 5.2 2.1 + - - -
404B GLU* 2.9 31.3 + - - +
407B THR* 1.3 90.1 - - - +
409B VAL* 1.3 65.8 + - - +
410B ALA 3.1 2.2 - - - -
411B LEU* 3.1 29.0 + - - +
412B THR* 3.7 4.9 + - - +
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Residues in contact with VAL 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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292B TRP* 3.9 4.4 + - + -
379B LEU* 4.7 0.4 - - + -
382B PHE* 3.7 24.9 - - + -
387B VAL* 4.2 19.3 - - + -
390B PHE* 3.8 32.8 - - + -
405B LEU* 2.8 42.1 + - + +
406B LEU* 4.0 2.9 - - - +
408B ASN* 1.3 73.7 - - - +
410B ALA* 1.3 59.5 + - - +
412B THR* 3.5 15.5 - - - +
413B SER* 2.7 40.0 + - - +
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Residues in contact with ALA 410 (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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373B ASN* 4.3 3.5 + - - +
374B TYR 5.0 2.0 - - - +
376B PHE* 4.2 23.0 - - + +
382B PHE* 4.1 12.3 - - + -
406B LEU* 3.0 22.4 + - + +
407B THR* 3.9 8.5 - - - +
408B ASN 3.1 0.2 - - - -
409B VAL* 1.3 78.8 - - - +
411B LEU* 1.3 61.9 + - + +
416B ASN* 3.0 25.3 + - - +
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Residues in contact with LEU 411 (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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294B THR* 4.3 23.8 + - + +
329B PRO* 3.3 22.9 - - - +
373B ASN* 4.0 11.8 + - - +
407B THR* 3.9 14.8 - - + +
408B ASN* 3.1 19.6 + - - +
410B ALA* 1.3 82.1 - - + +
412B THR* 1.3 60.0 + - - +
416B ASN* 4.2 2.2 - - - -
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Residues in contact with THR 412 (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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287B ARG* 3.5 47.2 + - - +
291B ARG 3.9 1.4 + - - -
292B TRP* 3.7 21.1 - - - -
293B HIS 4.4 0.2 - - - -
294B THR* 3.6 19.3 - - - +
327B ASP 4.8 1.4 - - - +
328B ASN* 4.5 1.0 - - - -
329B PRO* 3.5 21.1 - - + +
386B GLU* 5.6 0.9 - - - +
390B PHE* 5.4 0.2 - - - -
408B ASN 4.1 4.5 - - - +
409B VAL* 3.1 22.5 + - - +
411B LEU* 1.3 84.5 - - - +
413B SER* 1.3 68.4 + - - +
414B ARG* 3.5 1.9 + - - +
416B ASN* 4.1 0.2 - - - -
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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
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328B ASN 4.2 4.4 - - - -
382B PHE* 3.4 33.1 - - - -
384B ASP* 4.5 1.0 + - - -
386B GLU* 5.2 4.7 - - - -
387B VAL* 3.9 8.6 - - - +
409B VAL* 2.7 31.9 + - - -
412B THR* 1.3 74.7 + - - +
414B ARG* 1.3 67.4 + - - +
415B ASP* 3.0 13.3 + - - +
416B ASN* 3.0 31.1 + - - +
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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
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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