Contacts of the helix formed by residues 386 - 395 (chain A) in PDB entry 1A4Y
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 CYS 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A SER 3.9 3.6 - - - -
383A ASP 3.3 12.4 + - - +
385A SER* 1.3 76.4 - - - +
387A SER* 1.3 56.9 + - - +
389A LEU* 3.9 11.4 - - - +
390A ALA* 3.1 26.0 + - - +
409A LEU* 3.6 36.1 - - - -
413A GLY* 3.4 42.8 - - - +
416A GLN* 3.6 9.8 - - - +
417A LEU* 4.2 12.1 - - + +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASP 4.5 0.9 + - - -
384A SER 3.9 12.0 + - - -
385A SER 3.0 0.6 + - - -
386A CYS* 1.3 75.0 - - - +
388A SER* 1.3 63.0 + - - +
390A ALA* 3.3 5.3 + - - +
391A ALA* 3.0 28.1 + - - +
416A GLN* 3.2 25.3 + - - -
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ARG* 4.4 19.5 - - - +
361A CYS* 3.8 19.7 - - - -
384A SER 4.6 3.5 + - - -
385A SER* 3.0 13.4 + - - -
387A SER* 1.3 77.5 - - - +
389A LEU* 1.3 55.8 + - - +
391A ALA* 4.0 4.6 - - - +
392A THR* 2.7 38.0 + - - -
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Residues in contact with LEU 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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357A VAL* 4.3 6.7 - - + -
361A CYS* 3.9 20.6 - - - -
374A LEU* 6.0 2.0 - - + -
376A LEU* 4.6 19.1 - - + -
381A VAL* 4.5 6.5 - - + -
385A SER* 2.9 36.5 + - - +
386A CYS* 4.2 8.7 - - - +
388A SER* 1.3 73.7 - - - +
390A ALA* 1.3 66.1 + - - +
392A THR* 3.7 2.4 - - + -
393A LEU* 3.0 32.1 + - + +
402A LEU* 4.6 20.4 - - + -
404A LEU* 4.3 23.3 - - + -
409A LEU* 5.7 0.2 - - + -
417A LEU* 4.0 13.7 - - + -
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Residues in contact with ALA 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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386A CYS 3.1 21.6 + - - +
387A SER* 3.4 8.5 - - - +
389A LEU* 1.3 78.3 - - - +
391A ALA* 1.3 61.6 + - - +
393A LEU* 3.6 10.1 - - - +
394A LEU* 3.8 4.9 + - - +
416A GLN* 3.6 20.6 - - + +
417A LEU* 4.4 3.1 - - - +
420A SER* 2.8 37.4 + - - +
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Residues in contact with ALA 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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387A SER 3.0 16.1 + - - +
388A SER* 4.0 6.1 - - - +
390A ALA* 1.3 74.0 - - - +
392A THR* 1.3 53.5 + - - +
393A LEU 3.1 1.6 - - - -
394A LEU* 2.8 12.1 + - - +
395A ALA* 2.8 34.9 + - + +
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Residues in contact with THR 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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361A CYS* 3.3 29.0 + - - +
364A LEU* 3.8 41.5 - - + -
365A GLY* 4.0 9.1 - - - +
388A SER 2.7 21.9 + - - -
389A LEU* 3.7 5.8 - - + -
391A ALA* 1.3 76.8 - - - +
393A LEU* 1.3 57.3 + - + +
394A LEU 3.0 0.2 - - - -
395A ALA* 4.2 7.4 - - - -
396A ASN* 2.8 34.6 + - + +
399A LEU* 5.9 1.6 - - + -
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Residues in contact with LEU 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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389A LEU* 3.0 21.1 + - + +
390A ALA* 3.6 9.6 - - - +
391A ALA 3.1 0.2 - - - -
392A THR* 1.3 77.3 - - - +
394A LEU* 1.3 59.7 + - - +
396A ASN* 3.6 13.1 - - - +
399A LEU* 4.7 12.1 - - + -
402A LEU* 4.5 19.3 - - + -
417A LEU* 4.4 20.0 - - + +
420A SER* 4.3 8.7 - - - -
421A VAL* 4.0 21.8 - - + -
425A GLY 5.1 0.5 - - - +
426A CYS* 3.7 31.6 - - - +
427A LEU 5.2 0.5 + - - -
428A LEU* 4.0 33.0 - - + -
431A LEU* 6.0 1.1 - - + -
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Residues in contact with LEU 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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390A ALA 4.1 2.0 - - - +
391A ALA* 2.8 11.4 + - - +
393A LEU* 1.3 81.2 - - - +
395A ALA* 1.3 64.7 + - - +
396A ASN 3.8 1.1 - - - +
397A HIS* 3.8 17.8 + - - -
420A SER* 3.9 26.0 - - - +
423A GLN* 3.8 41.3 - - + +
425A GLY* 4.4 6.0 - - - +
426A CYS* 4.0 17.9 - - + +
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Residues in contact with ALA 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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365A GLY* 3.4 31.5 - - - +
366A GLN 4.9 2.3 - - - +
367A PRO* 6.0 0.7 - - - +
391A ALA* 2.8 20.5 + - + +
392A THR* 3.9 2.9 - - - +
394A LEU* 1.3 75.5 - - - +
396A ASN* 1.3 60.3 + - - +
397A HIS* 3.4 13.5 + - - -
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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