Contacts of the helix formed by residues 389 - 398 (chain A) in PDB entry 3S3J
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 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ARG* 3.0 21.8 + - - -
370A CYS 4.0 3.8 - - - +
371A CYS* 3.3 14.4 - - - -
372A GLY 2.8 28.4 + - - +
374A VAL* 4.8 0.4 - - - -
386A THR 4.4 1.4 + - - -
387A LYS* 4.5 0.4 - - - +
388A TYR* 1.3 73.9 - - - +
390A ALA* 1.3 65.8 + - - +
391A PRO* 3.2 7.9 - - - -
392A PHE* 3.2 44.4 + - + +
393A VAL* 3.7 7.0 + - + +
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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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374A VAL* 3.8 20.4 - - + -
379A ILE* 3.3 10.7 - - + +
383A ASP 4.3 2.9 - - - +
384A LEU* 3.3 41.3 + - + +
386A THR 3.7 15.3 + - - +
388A TYR 3.4 2.4 - - - -
389A ASP* 1.3 74.8 - - - +
391A PRO* 1.3 63.0 - - + +
393A VAL 3.1 3.1 + - - -
394A PHE* 2.9 25.6 + - - +
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Residues in contact with PRO 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 3.7 25.8 - - + +
389A ASP* 3.2 8.7 - - - -
390A ALA* 1.3 95.9 - - + +
392A PHE* 1.3 65.5 + - + +
394A PHE* 3.6 7.7 - - + +
395A ALA* 2.8 33.0 + - - +
571A VAL* 4.1 29.9 - - + +
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Residues in contact with PHE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A CYS* 4.0 23.8 - - - -
389A ASP* 3.2 43.2 + - + +
391A PRO* 1.3 85.4 - - + +
393A VAL* 1.3 63.1 + - + +
395A ALA* 3.4 6.3 + - - +
396A GLU* 3.3 26.7 + - - +
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TRP* 4.7 12.8 - - + +
356A ALA* 4.1 26.2 - - + +
358A ASP* 5.3 9.4 - - + +
371A CYS* 5.0 10.8 - - - +
372A GLY* 6.0 1.3 - - - -
374A VAL* 3.6 20.6 - - + -
379A ILE* 4.0 19.7 - - + -
388A TYR 5.6 0.2 - - - +
389A ASP* 4.2 6.1 - - + +
390A ALA 3.1 6.0 + - - +
392A PHE* 1.3 75.7 - - + +
394A PHE* 1.3 67.5 + - - +
396A GLU* 2.9 23.4 + - + +
397A VAL* 3.5 6.9 + - - +
443A TYR* 4.2 15.3 - - + -
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Residues in contact with PHE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 3.5 35.2 - - + +
382A GLY* 4.2 12.8 - - - -
384A LEU* 3.6 27.6 - - + -
390A ALA 2.9 17.5 + - - +
391A PRO* 3.6 5.8 - - + +
393A VAL* 1.3 77.5 - - - +
395A ALA* 1.3 59.9 + - + +
397A VAL 3.1 2.3 + - - -
398A ASN* 2.9 68.1 + - + -
455A ALA* 5.4 4.0 - - + -
456A PHE* 5.5 5.4 - - - -
459A ALA* 4.1 18.8 - - + -
460A ASN* 5.8 1.1 - - - -
571A VAL 5.9 0.4 - - - -
572A ILE* 4.6 22.4 - - + -
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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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331A ILE* 6.0 0.2 - - - +
391A PRO 2.8 21.0 + - - +
392A PHE* 3.7 7.4 - - - +
393A VAL 3.1 0.4 - - - -
394A PHE* 1.3 77.2 - - - +
396A GLU* 1.3 64.3 + - - +
398A ASN 3.2 10.6 + - - +
422A VAL* 4.2 1.9 - - - +
570A PRO 4.5 4.7 - - - +
571A VAL 3.7 17.7 - - - +
572A ILE 4.9 0.2 - - - -
573A ASN* 2.9 37.8 + - + +
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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
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300A ASN* 3.2 17.0 + - - -
302A ASN* 4.8 4.7 + - - -
329A GLU* 5.3 8.5 - - - +
330A MET 4.7 12.6 - - - +
331A ILE* 6.1 0.3 - - - -
332A TRP* 5.7 1.4 - - - -
335A HIS* 3.3 36.8 + - + +
337A TRP* 4.1 20.2 - - + -
358A ASP* 4.7 7.4 - - - +
392A PHE 3.3 15.8 + - - +
393A VAL* 2.9 14.6 + - - +
395A ALA* 1.3 82.1 - - - +
397A VAL* 1.3 56.6 + - - +
422A VAL* 3.1 15.8 - - - +
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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
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300A ASN* 4.1 4.3 - - - +
337A TRP* 3.8 24.7 - - + -
379A ILE* 4.1 17.0 - - + -
393A VAL 4.0 7.9 - - - +
394A PHE 3.7 4.0 - - - +
396A GLU* 1.3 80.7 - - - +
398A ASN* 1.3 75.5 + - - +
422A VAL* 3.5 8.9 - - - +
423A GLY* 4.0 4.5 - - - -
426A ILE* 4.0 19.3 - - + -
443A TYR* 4.2 18.6 - - + +
444A LYS* 3.1 42.0 + - + -
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Residues in contact with ASN 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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379A ILE* 5.0 1.2 + - - +
394A PHE* 2.9 63.7 + - + +
395A ALA* 3.2 5.2 - - - +
396A GLU 3.7 0.8 - - - -
397A VAL* 1.3 100.4 - - - +
399A ALA* 1.3 61.9 + - - +
422A VAL* 3.8 2.7 - - - +
443A TYR 5.2 1.2 + - - -
444A LYS* 3.8 17.4 - - - +
572A ILE 4.3 1.9 - - - +
573A ASN* 3.0 26.8 + - - +
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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