Contacts of the strand formed by residues 370 - 379 (chain J) in PDB entry 5DST
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 LEU 370 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189J TYR 4.8 2.2 - - - +
190J CYS* 5.0 2.0 - - + -
192J PHE* 4.1 14.1 - - + +
193J TYR* 3.7 39.7 - - + +
195J SER* 4.6 10.5 - - - +
360J MET* 3.8 26.5 - - + -
361J LYS 3.6 12.6 - - - +
362J PRO* 4.6 2.7 - - + -
368J ARG 4.6 0.7 - - - +
369J ASP* 1.3 81.1 - - - +
371J ASP* 1.3 63.4 + - - +
372J PHE* 3.7 33.2 - - + -
392J LYS* 3.3 5.4 - - - +
393J MET* 2.8 41.8 + - + +
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Residues in contact with ASP 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360J MET* 3.1 25.6 - - - +
361J LYS* 3.0 34.3 + - + +
363J ASN* 3.2 41.5 + - - +
364J ALA 4.7 0.9 + - - -
369J ASP* 4.3 0.9 + - - +
370J LEU* 1.3 76.6 - - - +
372J PHE* 1.3 62.5 + - - +
391J TYR 3.7 4.3 - - - +
392J LYS* 3.4 23.7 + - - +
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Residues in contact with PHE 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J CYS* 3.8 25.6 - - + -
221J LEU* 6.1 0.7 - - + -
340J PHE* 3.9 30.5 - + + -
358J ILE* 4.2 18.2 - - + -
359J SER 3.2 7.9 - - - -
360J MET* 3.7 28.3 - - + -
370J LEU* 3.7 37.0 - - + -
371J ASP* 1.3 78.5 - - - +
373J THR* 1.3 68.0 + - - +
374J VAL* 4.9 1.6 - - + -
390J ASP* 3.5 4.9 - - - +
391J TYR* 2.9 50.9 + - + +
393J MET* 4.0 18.2 - - + -
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Residues in contact with THR 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J THR* 4.0 1.2 + - - +
358J ILE* 3.5 2.1 - - - -
359J SER* 3.0 41.4 + - - +
372J PHE* 1.3 74.3 + - - +
374J VAL* 1.3 63.4 + - - +
375J ASP* 3.5 24.7 + - - +
388J SER* 3.7 10.3 - - - +
389J ASN 3.2 6.3 - - - +
390J ASP* 3.0 21.5 + - - +
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Residues in contact with VAL 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294J PHE* 4.4 7.0 - - + -
307J LEU* 3.8 29.2 - - + -
340J PHE* 4.8 10.5 - - + -
342J LEU* 5.8 3.4 - - + -
357J THR 3.4 10.1 - - - +
358J ILE* 4.3 22.9 - - + -
372J PHE* 4.9 1.8 - - + -
373J THR* 1.3 76.1 - - - +
375J ASP* 1.3 70.6 + - - +
376J LEU* 4.1 7.6 + - + +
387J VAL 3.9 0.7 - - - +
388J SER* 3.4 0.7 - - - -
389J ASN* 2.8 35.4 + - + +
391J TYR* 3.8 28.5 - - + +
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Residues in contact with ASP 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294J PHE* 3.9 2.6 - - - -
356J GLY* 3.1 5.6 - - - -
357J THR* 2.8 49.9 + - + +
373J THR* 3.5 11.2 - - - +
374J VAL* 1.3 76.1 - - - +
376J LEU* 1.3 60.9 + - - +
377J ASP* 5.1 3.4 - - - +
387J VAL 3.2 5.4 - - - +
388J SER* 2.5 35.0 + - - -
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Residues in contact with LEU 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294J PHE* 4.7 2.5 - - + -
307J LEU* 4.3 24.2 - - + -
342J LEU* 4.2 28.7 - - + -
346J LEU* 4.1 24.2 - - + -
354J ILE* 3.7 27.1 - - + -
355J TYR 3.6 3.4 - - - +
374J VAL* 4.6 6.5 - - + +
375J ASP* 1.3 76.0 - - - +
377J ASP* 1.3 71.8 + - - +
378J PHE* 4.5 3.6 - - + -
385J THR* 4.5 10.1 - - - +
386J SER* 3.2 1.9 - - - -
387J VAL* 2.7 49.1 + - + +
389J ASN* 6.2 1.6 - - - +
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Residues in contact with ASP 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354J ILE* 3.9 0.7 - - - -
355J TYR* 2.8 51.0 + - + +
356J GLY* 4.6 1.3 - - - -
375J ASP* 5.1 3.1 - - - +
376J LEU* 1.3 84.0 + - - +
378J PHE* 1.3 62.5 + - - +
385J THR 3.6 3.1 - - - +
386J SER* 3.4 23.0 + - - -
387J VAL 4.3 1.2 + - - +
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Residues in contact with PHE 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298J ILE* 4.1 3.8 - - + -
346J LEU* 4.3 12.6 - - + -
347J THR 3.8 14.6 - - - -
348J VAL* 3.6 23.6 - - + -
352J GLU* 3.4 34.3 - - + -
353J GLU 3.2 34.3 - - - -
354J ILE* 3.9 9.4 - - + -
355J TYR* 5.9 0.4 - - - -
376J LEU* 4.3 12.5 - - + -
377J ASP* 1.3 77.0 - - - +
379J LYS* 1.3 60.3 + - - +
380J GLY* 3.5 17.3 - - - -
383J CYS* 3.6 27.6 - - - -
384J GLU* 3.3 6.4 - - - +
385J THR* 2.9 34.3 + - - +
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Residues in contact with LYS 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352J GLU* 5.6 1.4 - - - +
353J GLU 4.7 3.1 + - - +
355J TYR* 6.3 0.2 - - - -
378J PHE* 1.3 77.1 - - - +
380J GLY* 1.3 65.2 + - - +
383J CYS 4.1 2.2 - - - -
384J GLU* 3.5 34.5 - - + +
291O THR 6.0 0.4 + - - -
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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