Contacts of the strand formed by residues 384 - 393 (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 GLU 384 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378J PHE 3.3 11.4 - - - +
379J LYS* 3.5 36.4 - - + +
380J GLY 5.0 1.6 - - - +
383J CYS* 1.3 80.1 - - - +
385J THR* 1.3 72.5 + - - +
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Residues in contact with THR 385 (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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344J ASP* 5.9 7.2 - - + +
346J LEU* 4.0 22.1 - - + +
376J LEU* 4.0 6.7 - - - +
377J ASP* 3.6 1.4 - - - -
378J PHE* 2.9 35.1 + - - +
383J CYS* 5.4 5.8 - - + -
384J GLU* 1.3 84.5 - - - +
386J SER* 1.3 61.6 + - - +
387J VAL* 3.8 19.6 - - + +
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Residues in contact with SER 386 (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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376J LEU 3.2 5.4 - - - -
377J ASP* 3.4 25.7 + - - -
385J THR* 1.3 75.1 - - - +
387J VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 387 (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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343J GLU* 4.1 11.0 - - + +
374J VAL 4.5 0.7 - - - -
375J ASP* 3.2 4.9 - - - +
376J LEU* 2.7 47.7 + - + +
377J ASP* 4.3 1.1 + - - +
385J THR* 3.8 26.0 - - + +
386J SER* 1.3 79.1 - - - +
388J SER* 1.3 69.1 + - - +
389J ASN* 3.2 28.7 - - - +
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Residues in contact with SER 388 (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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373J THR* 3.7 12.1 - - - +
374J VAL 3.4 0.4 - - - -
375J ASP* 2.5 27.8 + - - -
387J VAL* 1.3 76.5 - - - +
389J ASN* 1.3 67.7 + - - +
390J ASP* 4.4 2.8 + - - +
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Residues in contact with ASN 389 (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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256J LYS* 5.5 8.3 - - - +
341J TYR 4.5 0.4 + - - -
342J LEU* 4.1 24.9 - - - +
343J GLU* 3.4 21.5 + - - +
373J THR* 3.2 4.2 - - - -
374J VAL* 2.8 38.1 + - + +
376J LEU* 6.2 1.4 - - - +
387J VAL* 3.2 24.8 - - - +
388J SER* 1.3 80.1 + - - +
390J ASP* 1.3 65.7 + - - +
391J TYR* 3.4 34.8 + - + +
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Residues in contact with ASP 390 (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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256J LYS* 2.9 37.7 - - + +
372J PHE 3.5 5.6 - - - +
373J THR* 3.0 26.0 + - - +
388J SER* 4.8 3.0 + - - -
389J ASN* 1.3 76.6 - - - +
391J TYR* 1.3 68.3 + - - +
392J LYS* 6.2 1.6 - - + -
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Residues in contact with TYR 391 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255J MET 3.6 22.9 - - - -
256J LYS* 3.1 13.9 - - + +
258J PRO* 4.2 17.0 - - + -
340J PHE* 3.8 35.4 + + + +
341J TYR 2.6 32.2 + - - -
342J LEU* 4.1 5.0 - - - +
371J ASP* 3.7 0.9 - - - +
372J PHE* 2.9 41.4 + - + +
374J VAL* 3.8 23.7 - - + +
389J ASN* 3.4 43.1 + - + -
390J ASP* 1.3 77.8 - - - +
392J LYS* 1.3 70.0 + - - +
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Residues in contact with LYS 392 (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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256J LYS* 2.7 18.4 + - + +
257J GLU* 3.7 8.5 - - - +
258J PRO* 3.3 15.6 - - - +
363J ASN* 3.3 30.3 - - - +
369J ASP* 6.0 2.5 - - + +
370J LEU 3.3 5.4 - - - +
371J ASP* 3.4 16.6 + - - +
372J PHE* 5.3 0.2 - - - -
390J ASP* 6.2 1.8 - - + -
391J TYR* 1.3 79.0 - - - +
393J MET* 1.3 63.4 + - - +
394J ARG 3.6 4.4 + - - +
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Residues in contact with MET 393 (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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189J TYR* 3.8 21.3 - - + +
190J CYS* 4.0 26.0 - - - -
193J TYR* 3.5 50.6 - - + -
258J PRO* 3.8 26.7 - - + +
260J VAL* 4.5 9.4 - - + -
338J THR* 4.3 11.2 - - - -
369J ASP* 3.6 14.6 - - - +
370J LEU* 2.8 24.5 + - + +
372J PHE* 4.0 9.2 - - + -
392J LYS* 1.3 71.0 - - - +
394J ARG* 1.3 85.4 + - + +
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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