Contacts of the helix formed by residues 401 - 413 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A VAL* 3.9 3.3 - - - +
400A ALA* 1.3 77.5 - - - +
402A ALA* 1.3 64.7 + - - +
403A GLU* 3.5 10.0 + - - +
404A GLU* 2.9 40.5 + - - +
405A LEU* 3.1 21.1 + - - +
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A LEU* 3.9 21.7 - - + +
391A PHE* 4.2 12.1 - - + -
395A VAL* 3.8 18.3 - - + +
401A THR* 1.3 73.1 - - - +
403A GLU* 1.3 59.1 + - - +
405A LEU* 3.2 2.3 + - - +
406A LEU* 2.9 29.7 + - - +
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A THR* 3.1 9.5 + - - +
402A ALA* 1.3 79.6 - - - +
404A GLU* 1.3 62.5 + - + +
406A LEU* 3.3 10.2 + - - +
407A THR* 2.9 30.4 + - - +
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A TRP* 4.2 3.1 - - + -
293A HIS* 6.1 0.2 - - - +
399A LYS 4.5 1.4 - - - +
400A ALA* 3.3 17.3 - - + +
401A THR* 2.9 44.5 + - - +
403A GLU* 1.3 76.5 - - + +
405A LEU* 1.3 64.7 + - - +
407A THR* 3.5 3.8 + - - -
408A ASN* 2.8 39.7 + - - +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A TRP* 3.7 33.1 - - + -
379A LEU* 4.1 19.1 - - + -
387A VAL* 4.2 7.9 - - + +
390A PHE* 3.8 21.3 - - + +
391A PHE* 3.9 29.2 - - + +
394A TYR* 5.8 0.2 - - + -
395A VAL* 3.9 23.3 - - + -
400A ALA* 5.5 0.2 - - + -
401A THR 3.1 12.0 + - - +
402A ALA 3.2 6.7 + - - +
404A GLU* 1.3 78.0 - - - +
406A LEU* 1.3 56.7 + - - +
409A VAL* 2.7 50.9 + - + +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A PHE* 4.3 11.2 - - + +
377A LYS* 3.3 25.8 - - - +
378A THR* 3.8 22.2 - - - +
379A LEU* 3.9 13.4 - - + +
382A PHE* 3.7 26.0 - - + -
402A ALA 2.9 17.1 + - - +
403A GLU* 3.3 9.2 + - - +
405A LEU* 1.3 77.7 - - - +
407A THR* 1.3 65.0 - - - +
409A VAL* 4.0 1.7 - - - +
410A ALA* 3.0 31.0 + - + +
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Residues in contact with THR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A GLU* 2.9 19.6 + - - +
404A GLU* 3.8 5.8 - - - -
406A LEU* 1.3 81.2 - - - +
408A ASN* 1.3 72.1 + - - +
410A ALA* 3.9 6.7 - - - +
411A LEU* 3.8 19.0 - - + +
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Residues in contact with ASN 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A TRP* 3.4 28.8 - - + +
293A HIS* 3.4 30.7 + - - -
294A THR* 5.2 3.5 + - - +
404A GLU* 2.8 33.6 + - - +
407A THR* 1.3 86.1 - - - +
409A VAL* 1.3 66.0 + - - +
410A ALA 3.1 1.8 - - - -
411A LEU* 3.1 24.7 + - - +
412A THR* 3.7 7.6 + - - +
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A TRP* 4.0 4.0 + - + -
379A LEU* 4.5 0.7 - - + -
382A PHE* 3.6 26.0 - - + -
387A VAL* 4.0 20.2 - - + -
390A PHE* 3.9 30.7 - - + -
405A LEU* 2.7 44.8 + - + +
406A LEU* 4.0 2.9 - - - +
408A ASN* 1.3 74.8 - - - +
410A ALA* 1.3 59.8 + - - +
412A THR* 3.6 14.1 - - - +
413A SER* 2.8 41.1 + - - +
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Residues in contact with ALA 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ASN* 4.3 3.5 + - - +
374A TYR 4.9 2.7 - - - +
376A PHE* 4.2 24.0 - - + +
382A PHE* 4.0 12.6 - - + -
406A LEU* 3.0 23.1 + - + +
407A THR* 3.9 8.1 - - - +
408A ASN 3.1 0.4 - - - -
409A VAL* 1.3 77.6 - - - +
411A LEU* 1.3 63.8 + - + +
416A ASN* 3.0 24.5 + - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A THR* 4.5 22.6 - - + +
329A PRO* 3.4 21.3 - - - +
373A ASN* 3.9 12.3 + - - +
407A THR* 3.8 18.8 - - + +
408A ASN* 3.1 13.4 + - - +
409A VAL 3.0 1.0 - - - -
410A ALA* 1.3 83.9 - - + +
412A THR* 1.3 61.2 + - + +
416A ASN* 4.1 2.7 - - - -
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ARG* 3.8 39.2 + - - +
291A ARG 3.9 1.6 + - - -
292A TRP* 3.7 19.3 - - - -
294A THR* 3.4 33.4 - - + -
327A ASP 4.7 1.4 - - - +
328A ASN* 4.5 1.6 - - - -
329A PRO* 3.5 21.8 - - + +
390A PHE* 5.4 0.2 - - - -
408A ASN 3.9 7.2 - - - +
409A VAL* 3.5 19.1 + - - +
411A LEU* 1.3 79.3 - - - +
413A SER* 1.3 68.8 + - - +
414A ARG* 3.5 2.3 + - - +
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A PRO 4.2 4.2 - - - -
382A PHE* 3.4 31.8 - - - -
384A ASP* 4.5 1.0 + - - -
386A GLU* 5.7 1.8 - - - -
387A VAL* 3.9 9.3 - - - +
409A VAL* 2.8 31.8 + - - -
412A THR* 1.3 76.1 + - - +
414A ARG* 1.3 66.2 + - - +
415A ASP* 3.0 13.8 + - - +
416A ASN* 3.0 31.0 + - - +
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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