Contacts of the helix formed by residues 373 - 387 (chain A) in PDB entry 2ZB5
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 ASP 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A VAL* 3.3 17.6 - - + +
371A ARG* 3.0 45.0 + - - +
372A THR* 1.3 79.2 + - - +
374A ASP* 1.3 61.4 + - - +
375A LYS 3.3 2.5 - - - -
376A LEU* 3.5 21.4 + - + +
377A ARG* 3.0 50.0 + - - +
431A PHE* 3.9 1.2 - - - -
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Residues in contact with ASP 374 (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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371A ARG 2.9 17.7 + - - +
372A THR 4.0 4.9 - - - +
373A ASP* 1.3 76.0 + - - +
375A LYS* 1.3 89.0 + - - +
378A MET* 2.6 36.2 + - - +
379A GLU 3.3 1.2 + - - -
406A ARG* 2.8 32.5 + - - +
407A ILE* 3.4 43.4 + - + +
431A PHE* 3.4 16.2 - - + -
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Residues in contact with LYS 375 (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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372A THR 4.7 3.3 + - - +
373A ASP 3.3 0.4 - - - -
374A ASP* 1.3 96.1 + - - +
376A LEU* 1.3 65.1 + - - +
378A MET 3.5 0.2 + - - -
379A GLU* 3.1 58.5 + - + +
380A THR* 4.5 1.6 + - - +
382A PHE* 6.0 3.0 - - - -
405A ASN* 2.7 42.9 + - - +
406A ARG* 5.1 2.5 - - - +
407A ILE* 4.4 15.4 - - + +
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Residues in contact with LEU 376 (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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372A THR 5.6 0.2 + - - -
373A ASP* 3.5 22.0 + - + +
374A ASP 3.4 0.2 - - - -
375A LYS* 1.3 79.7 - - - +
377A ARG* 1.3 91.3 + - + +
380A THR* 5.7 2.9 - - - +
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Residues in contact with ARG 377 (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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371A ARG* 4.5 6.7 - - - +
373A ASP* 3.0 37.6 + - - +
376A LEU* 1.3 101.1 - - + +
378A MET* 1.3 66.9 + - - +
379A GLU 4.0 0.2 - - - -
380A THR* 4.6 9.7 - - - +
381A CYS* 5.8 0.2 - - - +
431A PHE* 3.9 21.1 - - + -
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Residues in contact with MET 378 (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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374A ASP 2.6 18.1 + - - +
377A ARG* 1.3 81.1 - - - +
379A GLU* 1.3 65.0 + - - +
380A THR* 3.3 3.1 - - - -
381A CYS* 2.8 18.3 + - - +
382A PHE 3.0 10.2 + - - -
407A ILE* 3.7 22.8 - - + +
408A PRO 5.9 0.2 - - - +
431A PHE* 3.4 46.7 - - + -
432A GLY 3.5 24.7 - - - +
434A LEU* 4.4 15.5 - - + -
493A ASP 6.1 0.9 - - - +
494A CYS* 4.3 23.6 - - - -
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Residues in contact with GLU 379 (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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374A ASP 3.3 3.8 + - - -
375A LYS* 3.1 52.7 + - + +
378A MET* 1.3 75.3 - - - +
380A THR* 1.3 65.3 + - - +
381A CYS 2.9 1.7 + - - -
382A PHE* 3.1 10.5 + - + +
383A GLN* 3.2 40.2 + - + +
407A ILE* 3.5 11.2 - - + +
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Residues in contact with THR 380 (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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375A LYS 4.5 1.2 + - - -
376A LEU 5.7 2.9 - - - +
377A ARG 4.6 10.3 - - - +
378A MET 4.5 5.8 - - - +
379A GLU* 1.3 78.9 - - - +
381A CYS* 1.3 65.3 + - + +
383A GLN* 4.1 11.8 - - - +
384A GLN* 3.5 24.6 + - - +
489A GLU 5.5 0.3 + - - -
490A ALA* 5.0 4.4 - - - +
491A GLY* 4.7 18.5 + - - +
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Residues in contact with CYS 381 (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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377A ARG 5.8 0.2 - - - +
378A MET* 2.8 16.9 + - + +
380A THR* 1.3 83.7 - - + +
382A PHE* 1.3 66.2 + - - +
383A GLN 3.1 2.0 - - - -
384A GLN* 3.1 3.5 + - - +
385A ALA* 2.9 22.4 + - - +
434A LEU* 4.0 9.4 - - - -
487A ILE* 4.4 11.0 - - - -
490A ALA* 4.2 11.4 - - + -
491A GLY* 5.0 1.3 - - - +
494A CYS* 2.0 53.6 - - + -
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Residues in contact with PHE 382 (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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375A LYS* 6.0 2.7 - - - -
378A MET* 3.0 6.2 + - - +
379A GLU* 3.1 8.5 + - + +
381A CYS* 1.3 75.7 - - - +
383A GLN* 1.3 62.9 + - + +
385A ALA* 3.5 1.7 + - - +
386A CYS* 3.0 54.4 + - - -
390A ILE* 6.0 1.3 - - + -
394A CYS* 4.5 14.6 - - + -
402A LEU* 4.0 33.0 - - + -
405A ASN* 5.9 2.9 - - - -
406A ARG 5.8 0.2 - - - -
407A ILE* 3.9 36.6 - - + -
434A LEU* 3.6 28.6 - - + +
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Residues in contact with GLN 383 (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 GLU* 3.4 40.5 + - + +
380A THR* 4.1 10.7 - - - +
381A CYS 3.1 0.4 - - - -
382A PHE* 1.3 79.9 - - + +
384A GLN* 1.3 70.8 + - + +
386A CYS* 2.9 17.4 + - - +
387A LYS* 3.3 20.2 + - + +
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Residues in contact with GLN 384 (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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380A THR* 3.5 16.3 + - - +
381A CYS 3.1 6.3 + - - +
383A GLN* 1.3 79.0 - - - +
385A ALA* 1.3 63.1 + - - +
386A CYS 3.1 1.2 + - - -
387A LYS* 3.1 50.0 + - - +
388A GLY 4.0 2.4 + - - -
487A ILE* 3.6 20.1 - - + +
488A LYS 3.5 10.0 - - - +
489A GLU* 3.4 36.5 - - - +
490A ALA* 4.3 5.2 - - + -
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Residues in contact with ALA 385 (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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381A CYS* 2.9 17.1 + - - +
382A PHE 3.7 3.6 - - - +
384A GLN* 1.3 76.1 - - - +
386A CYS* 1.3 60.2 + - - +
387A LYS 3.4 0.4 + - - -
388A GLY* 3.7 10.1 + - - +
389A LYS 4.8 0.3 + - - -
390A ILE* 3.3 22.4 + - + +
434A LEU* 4.3 13.2 - - + -
487A ILE* 3.6 34.7 - - + +
496A ALA* 4.2 14.3 - - + +
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Residues in contact with CYS 386 (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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382A PHE* 3.0 45.7 + - - +
383A GLN* 2.9 10.8 + - - +
385A ALA* 1.3 75.9 - - - +
387A LYS* 1.3 57.5 + - + +
388A GLY 3.0 5.4 - - - -
390A ILE* 5.0 1.8 - - - -
391A GLN* 3.0 35.6 + - - +
394A CYS* 2.0 51.8 - - + -
434A LEU* 6.0 0.2 - - - -
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Residues in contact with LYS 387 (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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383A GLN* 3.6 18.8 - - + +
384A GLN* 3.1 41.1 + - - +
386A CYS* 1.3 77.8 - - + +
388A GLY* 1.3 59.3 + - - +
391A GLN* 4.2 13.6 + - - +
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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