Contacts of the helix formed by residues 394 - 411 (chain A) in PDB entry 5JZU
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 SER 394 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ALA* 3.3 7.0 + - - +
392A ARG* 3.2 16.5 - - - +
393A ARG* 1.3 78.7 - - - +
395A ASN* 1.3 62.2 + - - +
396A GLU* 3.2 7.6 + - - +
397A VAL* 3.2 49.9 + - - +
398A LEU* 3.4 11.4 + - - +
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Residues in contact with ASN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG 4.2 1.0 + - - -
394A SER* 1.3 71.0 + - - +
396A GLU* 1.3 55.7 + - - +
397A VAL 3.4 0.2 - - - -
398A LEU* 3.6 6.5 - - - +
399A ARG* 2.6 35.6 + - - +
433A LEU* 4.1 24.3 - - + +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A SER* 3.2 7.1 + - - +
395A ASN* 1.3 77.3 - - - +
397A VAL* 1.3 62.6 + - + +
399A ARG* 3.4 10.0 + - - +
400A GLY* 2.9 23.0 + - - -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 4.3 11.7 - - + +
388A LEU* 4.4 10.1 - - + +
389A ALA* 3.4 26.7 - - + +
392A ARG* 3.6 35.2 - - + +
394A SER* 3.2 31.6 + - - +
396A GLU* 1.3 77.6 - - + +
398A LEU* 1.3 65.2 + - - +
400A GLY* 3.1 3.1 + - - +
401A ALA* 2.8 26.0 + - - +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASP* 4.2 16.4 - - - +
389A ALA* 3.6 20.9 - - + -
394A SER 3.4 14.5 + - - +
395A ASN* 3.4 5.4 + - - +
396A GLU 3.3 0.4 - - - -
397A VAL* 1.3 79.8 - - - +
399A ARG* 1.3 59.3 + - - +
401A ALA* 3.0 11.2 + - + +
402A ILE* 2.8 29.3 + - + +
429A ARG* 3.5 40.2 - - + +
432A PHE* 4.0 17.3 - - + -
433A LEU* 3.8 32.1 - - + -
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASN 2.6 22.9 + - - +
396A GLU* 3.4 13.9 - - - +
397A VAL 3.3 0.2 - - - -
398A LEU* 1.3 71.0 - - - +
400A GLY* 1.3 61.8 + - - +
402A ILE* 3.3 10.0 + - - +
403A GLU* 3.3 19.6 + - - +
433A LEU* 4.4 11.8 - - + +
435A HIS* 5.7 5.2 - - + -
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Residues in contact with GLY 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 4.1 7.9 - - - -
396A GLU 2.9 14.8 + - - -
397A VAL* 3.1 5.6 + - - -
398A LEU 3.0 0.4 - - - -
399A ARG* 1.3 76.2 - - - +
401A ALA* 1.3 59.1 + - - +
403A GLU* 3.2 7.9 + - - +
404A THR* 2.9 31.3 + - - -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ALA 3.8 10.8 - - - +
385A GLU* 3.6 32.0 + - + -
386A ASP* 3.9 11.7 - - - +
397A VAL 2.8 10.4 + - - +
398A LEU* 3.0 15.0 + - + +
400A GLY* 1.3 73.2 - - - +
402A ILE* 1.3 60.2 + - - +
404A THR* 3.1 2.0 + - - -
405A TYR* 2.8 43.5 + - + -
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Residues in contact with ILE 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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398A LEU* 2.8 12.8 + - + +
399A ARG* 3.4 14.1 - - - +
400A GLY 3.2 0.2 - - - -
401A ALA* 1.3 77.3 - - - +
403A GLU* 1.3 62.0 + - - +
405A TYR* 3.4 8.8 + - - +
406A GLN 3.3 9.9 + - - -
426A ARG* 3.1 39.9 + - + +
429A ARG* 5.6 8.1 - - + -
430A GLN* 4.8 13.0 - - + +
433A LEU* 5.7 4.5 - - + -
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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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399A ARG 3.3 8.5 + - - +
400A GLY* 3.2 10.8 + - - +
402A ILE* 1.3 77.8 - - - +
404A THR* 1.3 59.4 + - - +
406A GLN* 3.0 24.8 + - - +
407A GLU* 2.8 47.6 + - - +
426A ARG* 4.6 4.4 + - - +
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Residues in contact with THR 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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378A ARG* 3.6 17.0 - - - +
381A LYS* 3.5 18.5 + - + +
382A ALA* 3.6 20.0 - - + +
385A GLU* 2.5 31.9 + - - +
400A GLY 2.9 10.3 + - - -
401A ALA 3.1 5.4 + - - -
403A GLU* 1.3 77.0 - - - +
405A TYR* 1.3 61.7 + - - +
407A GLU* 3.1 32.7 + - - +
408A VAL* 3.1 14.7 + - - +
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Residues in contact with TYR 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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379A TYR* 3.9 20.4 - + - -
382A ALA* 3.6 28.0 - - + -
383A GLN* 3.6 22.7 + - + +
386A ASP* 3.3 22.0 + - - +
401A ALA* 2.8 34.4 + - + +
402A ILE* 3.5 11.2 - - - +
403A GLU 3.2 0.2 - - - -
404A THR* 1.3 78.0 - - - +
406A GLN* 1.3 59.7 + - - +
408A VAL* 3.5 8.4 - - - +
409A ALA 3.9 2.4 + - - -
422A SER* 2.9 52.6 + - - +
423A LEU* 4.4 4.4 - - - +
425A ARG* 3.5 29.4 + - + +
426A ARG* 4.0 12.6 - - + -
429A ARG* 5.7 4.5 - - + -
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Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE 3.3 2.4 + - - +
403A GLU* 3.0 24.1 + - - +
405A TYR* 1.3 75.2 - - - +
407A GLU* 1.3 67.3 + - - +
408A VAL 3.1 1.8 - - - -
409A ALA* 2.9 14.3 + - - +
410A SER* 3.3 10.8 + - - -
423A LEU* 4.6 6.1 - - + -
426A ARG* 2.7 54.3 + - - +
445A ARG* 3.7 25.7 + - - +
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 3.0 42.8 + - + +
381A LYS* 4.1 9.9 + - - -
403A GLU* 2.8 36.1 + - - +
404A THR* 3.2 26.4 + - - +
406A GLN* 1.3 77.1 - - - +
408A VAL* 1.3 62.7 + - - +
410A SER* 2.9 20.6 + - - -
411A LEU* 3.3 15.1 + - - +
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Residues in contact with VAL 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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375A PRO* 4.1 17.2 - - + +
378A ARG* 3.5 20.8 - - + +
379A TYR* 3.6 21.3 - - + +
382A ALA* 4.9 0.4 - - + -
404A THR 3.1 15.3 + - - +
405A TYR* 3.5 9.0 - - - +
406A GLN 3.1 0.4 - - - -
407A GLU* 1.3 76.9 - - - +
409A ALA* 1.3 61.9 + - - +
410A SER 3.4 0.7 + - - -
411A LEU* 3.5 18.4 + - - +
414A VAL* 4.2 13.2 - - + +
418A LEU* 4.4 20.9 - - + +
419A LEU* 5.6 1.8 - - - -
422A SER* 3.5 25.4 - - - +
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Residues in contact with ALA 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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405A TYR 3.9 1.1 + - - +
406A GLN 2.9 11.1 + - - +
408A VAL* 1.3 78.9 - - - +
410A SER* 1.3 60.5 + - - +
411A LEU 3.8 5.1 - - - +
414A VAL* 5.5 1.4 - - - +
419A LEU* 3.8 29.9 - - + +
422A SER* 5.7 0.6 - - - -
423A LEU* 3.9 22.9 - - + -
445A ARG* 3.7 28.2 + - - +
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Residues in contact with SER 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLN* 3.3 9.3 + - - -
407A GLU* 2.9 13.9 + - - -
409A ALA* 1.3 75.4 - - - +
411A LEU* 1.3 69.6 + - - +
412A PRO* 4.5 0.7 - - - +
445A ARG* 4.8 3.3 - - - +
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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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372A PRO 3.6 20.0 - - - +
373A GLN* 3.9 12.1 - - + +
374A SER 3.4 33.2 - - - +
375A PRO* 3.7 8.7 - - + -
378A ARG* 3.7 35.2 - - + +
407A GLU 3.5 13.0 - - - +
408A VAL 3.7 11.1 - - - +
409A ALA 3.4 8.1 - - - +
410A SER* 1.3 85.1 - - - +
412A PRO* 1.3 75.4 - - + +
413A ASP 4.1 0.5 + - - -
414A VAL* 4.5 6.5 + - - +
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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