Contacts of the helix formed by residues 384 - 398 (chain A) in PDB entry 4AY6
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 PHE 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A ALA* 4.5 11.9 - - + -
352A ALA* 4.6 9.9 - - + -
355A SER* 3.4 36.1 - - - -
377A ALA* 4.4 9.9 - - + +
378A ILE* 4.1 2.6 - - + +
381A SER* 3.0 31.5 + - - +
382A PRO 3.3 1.0 - - - -
383A THR* 1.3 72.5 + - - +
385A ALA* 1.3 64.8 + - - +
386A ASP* 3.2 31.6 - - + -
387A ALA* 3.2 23.0 + - + +
388A TYR* 3.4 18.6 + - - -
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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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383A THR 2.7 13.6 + - - +
384A PHE* 1.3 73.1 - - - +
386A ASP* 1.3 62.4 + - - +
387A ALA 3.3 1.0 + - - -
388A TYR* 3.3 19.5 + - - +
389A SER 3.3 9.4 + - - -
411A ALA* 3.9 12.0 - - - +
414A ILE* 4.6 6.1 - - + -
415A ASN* 4.0 26.2 - - + +
418A PHE* 3.5 26.3 - - + -
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Residues in contact with ASP 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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355A SER* 4.9 3.3 + - - -
384A PHE* 3.2 24.7 - - + -
385A ALA* 1.3 80.2 - - - +
387A ALA* 1.3 55.5 + - - +
389A SER* 3.7 2.9 + - - -
390A ASN* 2.8 51.9 + - - -
418A PHE* 3.3 28.7 - - + -
420A ASP* 4.4 6.2 - - - +
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Residues in contact with ALA 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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355A SER* 4.5 3.8 - - - +
374A TYR* 4.1 17.6 - - + -
377A ALA* 4.5 6.3 - - + -
378A ILE* 3.2 25.7 - - + +
384A PHE* 3.2 30.0 + - + +
385A ALA 3.2 1.0 - - - -
386A ASP* 1.3 75.9 - - - +
388A TYR* 1.3 68.2 + - - +
390A ASN* 3.4 5.0 + - - +
391A MET* 3.0 24.8 + - - +
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Residues in contact with TYR 388 (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 ILE* 3.2 39.3 - - + +
382A PRO* 3.8 14.8 + - - +
384A PHE 3.4 22.3 + - - -
385A ALA* 3.3 9.5 + - - +
387A ALA* 1.3 78.9 - - - +
389A SER* 1.3 62.2 + - - +
391A MET* 3.1 20.8 + - + +
392A GLY 2.9 19.4 + - - -
407A CYS* 3.4 27.7 - - - +
410A ARG* 3.9 28.5 - - + -
411A ALA* 3.7 15.5 - - + -
414A ILE* 3.7 27.3 - - + +
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Residues in contact with SER 389 (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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385A ALA 3.3 1.6 + - - -
386A ASP* 3.7 5.8 - - - -
387A ALA 3.3 0.4 - - - -
388A TYR* 1.3 78.2 - - - +
390A ASN* 1.3 65.7 + - - +
392A GLY 3.2 1.0 + - - -
393A ASN* 3.3 4.0 + - - -
408A TYR* 3.2 32.6 - - - -
411A ALA* 4.3 5.3 - - - +
418A PHE* 3.7 28.9 - - - -
420A ASP* 4.1 11.8 - - - +
421A ALA* 4.2 6.2 + - - -
424A ASN* 2.6 30.7 + - - +
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Residues in contact with ASN 390 (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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355A SER* 5.1 2.6 + - - -
359A SER* 5.7 3.3 - - - -
362A GLN* 4.1 3.4 - - - +
374A TYR* 3.3 33.1 + - + +
386A ASP* 2.8 40.5 + - - +
387A ALA* 3.4 2.2 + - - +
388A TYR 3.3 0.6 - - - -
389A SER* 1.3 76.4 + - - +
391A MET* 1.3 61.8 + - - +
393A ASN* 2.9 37.3 + - - +
394A THR* 3.0 16.0 + - - -
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Residues in contact with MET 391 (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 LEU* 3.8 29.4 - - + -
374A TYR* 4.1 22.6 - - + -
375A LYS* 4.1 22.4 - - + -
378A ILE* 4.7 9.2 - - + -
387A ALA 3.0 18.8 + - - +
388A TYR* 3.4 22.9 - - + +
390A ASN* 1.3 75.3 - - - +
392A GLY* 1.3 57.0 + - - +
394A THR* 3.2 8.8 + - - -
395A LEU* 2.9 33.8 + - + +
407A CYS* 3.4 25.8 - - - -
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Residues in contact with GLY 392 (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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388A TYR 2.9 10.7 + - - -
390A ASN 3.1 0.6 - - - -
391A MET* 1.3 74.5 - - - +
393A ASN* 1.3 51.1 + - - +
395A LEU 3.0 2.3 + - - -
396A LYS* 2.8 32.7 + - - +
404A ALA* 3.1 13.9 - - - +
407A CYS* 3.8 15.8 - - - -
408A TYR* 3.1 26.0 - - - -
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Residues in contact with ASN 393 (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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362A GLN* 3.8 16.8 + - - +
389A SER* 3.3 8.7 + - - -
390A ASN* 2.9 28.8 + - - +
392A GLY* 1.3 70.3 - - - +
394A THR* 1.3 56.7 + - - +
396A LYS* 3.3 9.9 - - - +
397A GLU* 2.9 28.9 + - - +
408A TYR* 2.8 19.8 + - - -
424A ASN* 3.4 27.5 + - - +
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Residues in contact with THR 394 (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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362A GLN* 3.3 23.6 + - + +
367A LEU* 4.0 37.9 - - + +
370A ALA* 4.9 2.9 - - + -
371A LEU* 4.5 15.9 - - + +
374A TYR* 3.4 12.9 - - - -
390A ASN 3.0 12.7 + - - -
391A MET* 3.4 9.2 - - - -
393A ASN* 1.3 72.8 - - - +
395A LEU* 1.3 67.2 + - - +
397A GLU* 3.0 16.5 + - - +
398A MET* 3.0 24.5 + - - +
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Residues in contact with LEU 395 (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 LEU* 4.1 30.5 - - + -
391A MET* 2.9 22.8 + - + +
394A THR* 1.3 72.4 - - - +
396A LYS* 1.3 61.6 + - - +
398A MET* 3.2 16.4 + - + +
400A ASP* 3.1 48.7 + - + +
403A GLY* 3.5 31.0 - - - +
404A ALA* 3.6 14.4 - - + +
407A CYS* 4.0 17.3 - - - -
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Residues in contact with LYS 396 (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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392A GLY 2.8 12.6 + - - +
393A ASN* 3.3 13.7 - - - +
395A LEU* 1.3 75.6 - - - +
397A GLU* 1.3 54.4 + - - +
399A GLN* 2.8 31.7 + - - +
400A ASP 4.5 3.6 - - - -
401A VAL* 5.1 5.1 + - + +
404A ALA* 3.6 9.4 - - + +
408A TYR* 4.1 9.2 - - - +
424A ASN 4.8 1.0 + - - -
427A SER* 3.6 34.1 + - - -
428A ILE* 3.9 23.5 - - + +
431A ASP* 3.3 27.7 + - - -
1399E SER* 5.0 10.4 - - - -
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Residues in contact with GLU 397 (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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362A GLN* 3.6 24.8 + - - +
367A LEU* 3.8 29.0 - - + +
393A ASN 2.9 12.5 + - - +
394A THR* 3.0 10.5 + - - +
396A LYS* 1.3 74.8 - - - +
398A MET* 1.3 57.1 + - - +
399A GLN* 3.3 12.3 + - - +
524A LYS* 3.4 31.2 + - - -
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Residues in contact with MET 398 (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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367A LEU* 3.6 32.1 - - + -
368A GLN* 4.4 13.5 - - - +
371A LEU* 4.2 26.5 - - + -
394A THR* 3.0 18.8 + - - +
395A LEU* 3.5 17.7 - - + +
396A LYS 2.8 1.8 + - - -
397A GLU* 1.3 76.0 - - - +
399A GLN* 1.3 65.7 + - - +
400A ASP* 2.9 15.6 + - + +
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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