Contacts of the strand formed by residues 337 - 348 (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 GLN 337 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260J VAL* 3.4 7.1 - - - +
261J ASP 3.0 30.7 + - - +
262J ILE* 3.4 8.8 - - - +
263J VAL* 2.9 32.7 + - + +
308J VAL* 3.6 17.9 - - + -
309J THR 4.0 4.5 - - - +
310J TYR* 4.4 5.4 - - + -
326J THR 2.5 28.2 + - - +
327J ALA 3.1 14.8 + - - -
328J PRO* 3.5 29.0 - - + +
335J TRP 4.1 0.7 - - - -
336J LYS* 1.3 86.1 + - - +
338J THR* 1.3 65.4 + - - +
339J VAL* 4.9 0.2 - - - -
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Residues in contact with THR 338 (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* 4.3 0.7 - - - +
190J CYS* 3.3 36.3 + - + -
258J PRO* 3.9 16.6 - - + -
259J LEU 3.4 4.7 - - - +
260J VAL* 4.6 10.3 - - + +
308J VAL* 3.2 5.4 - - - -
309J THR* 3.0 42.4 + - - -
335J TRP 4.8 2.4 + - - -
337J GLN* 1.3 80.3 + - - +
339J VAL* 1.3 62.8 + - - +
340J PHE* 3.7 22.2 - - + -
393J MET* 4.3 9.4 - - - -
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Residues in contact with VAL 339 (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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226J ILE* 4.7 5.4 - - + -
228J ASP* 4.7 2.7 - - - +
258J PRO* 3.2 7.8 - - - +
259J LEU* 2.9 45.7 + - + +
261J ASP* 4.6 8.7 - - + +
263J VAL* 3.9 28.0 - - + -
306J ALA* 3.7 23.3 - - + -
307J LEU 3.5 4.3 - - - +
308J VAL* 4.0 7.2 - - + -
338J THR* 1.3 77.1 - - - +
340J PHE* 1.3 62.6 + - - +
341J TYR* 3.9 28.0 + - + +
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Residues in contact with PHE 340 (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* 4.2 2.7 - - - -
223J VAL* 6.2 0.4 - - + -
258J PRO* 3.6 17.3 - - + -
306J ALA* 3.4 3.1 - - - +
307J LEU* 2.8 44.6 + - + +
309J THR* 3.8 23.3 - - + -
338J THR* 3.7 35.9 - - + -
339J VAL* 1.3 76.1 - - - +
341J TYR* 1.3 65.7 + - - +
342J LEU* 4.3 3.3 - - - +
358J ILE* 5.3 3.6 - - + -
372J PHE* 3.9 44.9 - + - -
374J VAL* 4.8 9.0 - - + -
391J TYR* 3.8 40.4 + + + +
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Residues in contact with TYR 341 (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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228J ASP* 2.9 30.7 + - + -
231J TYR* 3.5 20.3 - - - -
232J LYS* 3.6 37.1 + - + -
235J LYS* 4.8 1.1 - - + -
236J ILE* 4.0 19.3 - - + -
254J ALA 6.1 0.7 - - - -
255J MET* 3.7 32.0 + - + +
257J GLU 5.6 2.5 - - - -
258J PRO* 5.8 0.6 - - - +
259J LEU* 3.9 32.0 - - + +
305J HIS* 3.9 14.6 - - + -
306J ALA* 3.9 6.5 - - + -
339J VAL* 3.9 20.5 + - + +
340J PHE* 1.3 70.8 - - - +
342J LEU* 1.3 57.2 + - - +
389J ASN* 4.5 0.7 + - - -
391J TYR* 2.6 35.2 + - - -
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Residues in contact with LEU 342 (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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232J LYS* 2.8 27.9 + - - -
255J MET* 3.6 3.4 - - - +
304J VAL* 4.1 30.1 - - + +
305J HIS 3.0 22.7 + - - +
306J ALA* 4.1 5.6 - - - +
307J LEU* 4.6 10.3 - - + -
340J PHE 4.3 4.3 - - - +
341J TYR* 1.3 77.6 - - - +
343J GLU* 1.3 62.0 + - - +
344J ASP 3.6 10.5 - - - +
346J LEU* 4.3 23.3 - - + -
374J VAL* 5.8 2.7 - - + -
376J LEU* 4.2 23.6 - - + -
389J ASN* 4.1 18.8 - - - +
391J TYR* 4.1 4.7 - - - +
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Residues in contact with GLU 343 (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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232J LYS* 3.1 16.3 + - - -
237J HIS* 5.1 5.2 - - - -
255J MET* 3.9 20.9 - - + +
256J LYS* 5.7 10.1 - - - -
342J LEU* 1.3 72.4 - - - +
344J ASP* 1.3 70.4 + - - +
387J VAL* 4.1 10.3 - - + +
389J ASN* 3.4 27.3 - - - +
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Residues in contact with ASP 344 (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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232J LYS* 4.7 1.8 - - - +
342J LEU* 3.6 21.0 - - - +
343J GLU* 1.3 86.7 - - - +
345J TYR* 1.3 71.0 + - + +
346J LEU* 3.9 8.4 + - + +
385J THR* 5.9 6.6 - - + +
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Residues in contact with TYR 345 (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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104H TYR 2.9 26.9 + - - -
105H HIS* 3.6 17.3 - + - -
107H LYS* 3.8 15.7 + - + +
232J LYS* 4.9 3.6 - - - +
303J TYR* 3.7 34.3 - + + -
304J VAL 3.1 14.8 - - - +
305J HIS* 3.6 37.9 - + + +
344J ASP* 1.3 82.9 - - + +
346J LEU* 1.3 63.0 + - - +
347J THR* 4.1 9.7 + - - -
383J CYS* 4.8 3.8 - - - -
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Residues in contact with LEU 346 (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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303J TYR* 3.3 7.8 - - - +
304J VAL* 2.7 46.3 + - + +
342J LEU* 4.3 12.6 - - + -
344J ASP* 4.0 9.6 - - + +
345J TYR* 1.3 79.5 - - - +
347J THR* 1.3 61.6 + - - +
348J VAL* 3.8 14.4 + - + -
354J ILE* 4.2 27.8 - - + -
376J LEU* 4.1 23.3 - - + -
378J PHE* 4.3 18.6 - - + -
383J CYS* 4.0 7.6 - - - -
385J THR* 4.0 20.4 - - + +
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Residues in contact with THR 347 (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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105H HIS 5.1 0.5 + - - -
108H HIS* 4.5 12.4 + - + -
319H HIS* 3.4 34.8 - - + +
302J ASP 4.1 1.8 - - - -
303J TYR* 3.6 22.3 - - + -
345J TYR* 4.1 10.6 + - - -
346J LEU* 1.3 73.2 - - - +
348J VAL* 1.3 61.3 + - - +
352J GLU* 4.1 2.1 - - - +
378J PHE* 3.8 12.5 - - - -
382J LEU* 3.9 31.5 - - + +
383J CYS* 3.4 18.7 + - - +
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Residues in contact with VAL 348 (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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319H HIS* 3.1 7.7 - - - -
269J VAL* 4.1 11.2 - - + -
298J ILE* 3.7 36.8 - - + -
301J ASN* 3.4 0.2 - - - -
302J ASP 3.0 48.3 + - - +
303J TYR 4.6 0.2 - - - +
304J VAL* 4.1 11.2 - - + -
346J LEU* 3.8 23.8 - - + +
347J THR* 1.3 79.0 - - - +
349J ARG* 1.3 62.7 + - - +
352J GLU* 3.8 2.7 - - - -
354J ILE* 5.2 0.4 - - + -
378J PHE* 3.6 22.7 - - + -
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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