Contacts of the strand formed by residues 353 - 362 (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 353 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295J CYS* 4.1 11.0 - - - -
296J LEU 3.4 10.8 - - - +
297J GLN* 3.5 25.7 - - - +
298J ILE* 4.0 1.1 - - - +
351J GLY 4.0 8.3 - - - +
352J GLU* 1.3 83.9 - - - +
354J ILE* 1.3 60.5 + - - +
355J TYR* 2.8 43.4 + - + -
378J PHE* 3.2 22.5 - - - -
379J LYS 4.7 2.6 + - - +
271O ASN* 5.8 0.3 + - - -
273O CYS* 3.5 28.6 - - - +
274O LEU 5.4 0.4 - - - +
293O ALA 5.2 0.7 - - - +
295O CYS* 4.0 8.4 - - - +
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Residues in contact with ILE 354 (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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225J ALA* 4.0 26.9 - - + -
270J THR* 4.7 0.7 - - + -
294J PHE* 3.8 11.7 - - + +
295J CYS* 3.2 5.8 - - - -
296J LEU* 2.8 46.5 + - + +
298J ILE* 3.8 22.9 - - + -
304J VAL* 4.6 7.9 - - + -
307J LEU* 5.1 2.7 - - + -
346J LEU* 4.2 17.7 - - + -
348J VAL* 5.2 0.4 - - + -
353J GLU* 1.3 72.9 - - - +
355J TYR* 1.3 63.6 + - - +
376J LEU* 3.7 38.4 - - + -
377J ASP 3.9 4.0 - - - +
378J PHE* 3.9 12.3 - - + -
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Residues in contact with TYR 355 (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* 3.5 4.0 - - - -
295J CYS* 3.6 17.5 - - - -
353J GLU* 2.8 44.2 + - + -
354J ILE* 1.3 81.9 - - - +
356J GLY* 1.3 58.0 + - - +
376J LEU* 3.6 2.9 - - - -
377J ASP* 2.8 46.7 + - + +
378J PHE* 5.9 0.4 - - - -
379J LYS 6.3 0.4 - - - -
293O ALA* 4.0 19.2 - - + -
294O PHE* 3.2 29.7 + - - -
295O CYS* 3.2 9.5 + - + -
355O TYR* 4.0 22.9 - + - -
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Residues in contact with GLY 356 (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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293J ALA* 3.4 5.9 - - - +
294J PHE* 2.8 42.5 + - - +
355J TYR* 1.3 76.6 - - - +
357J THR* 1.3 64.2 + - - +
375J ASP* 3.1 15.3 - - - -
376J LEU* 4.3 0.2 - - - -
377J ASP* 4.6 1.8 - - - -
355O TYR* 5.9 0.3 - - - -
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Residues in contact with THR 357 (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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291J THR* 4.1 21.6 - - + +
292J SER 3.4 8.5 - - - -
293J ALA* 4.4 12.6 - - + +
294J PHE* 3.5 6.7 - - - -
356J GLY* 1.3 78.8 - - - +
358J ILE* 1.3 61.2 + - - +
359J SER* 4.9 3.3 + - - -
373J THR* 5.0 0.5 + - - +
374J VAL* 3.4 2.9 - - - -
375J ASP* 2.8 52.6 + - + +
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Residues in contact with ILE 358 (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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221J LEU* 5.9 0.9 - - + -
223J VAL* 4.9 11.7 - - + -
275J ILE* 4.0 38.8 - - + -
290J PHE* 4.3 4.0 - - + -
291J THR* 3.7 0.2 - - - -
292J SER* 2.9 35.4 + - - +
294J PHE* 3.6 24.2 - - + -
307J LEU* 6.4 1.3 - - + -
309J THR* 4.9 6.7 - - + -
340J PHE* 5.3 3.4 - - + -
357J THR* 1.3 74.7 - - - +
359J SER* 1.3 70.2 + - - +
360J MET* 5.4 3.1 - - + -
372J PHE* 4.2 23.1 - - + -
373J THR 3.5 5.2 - - - -
374J VAL* 4.3 20.2 - - + -
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Residues in contact with SER 359 (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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290J PHE* 3.1 10.1 - - - -
291J THR* 3.1 31.9 + - - +
357J THR* 4.9 2.9 + - - -
358J ILE* 1.3 75.8 - - - +
360J MET* 1.3 62.5 + - - +
361J LYS* 6.3 1.3 - - - -
372J PHE* 3.2 8.8 - - - +
373J THR* 3.0 46.9 + - - +
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Residues in contact with MET 360 (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 5.2 1.6 - - - +
192J PHE* 3.5 45.1 - - + -
221J LEU* 5.0 6.5 - - - -
288J LEU 3.7 17.4 - - - +
289J SER* 3.3 4.5 - - - -
290J PHE* 3.1 51.3 + - + -
358J ILE* 5.4 2.7 - - + -
359J SER* 1.3 75.8 - - - +
361J LYS* 1.3 66.7 + - - +
362J PRO* 5.9 0.7 - - + -
370J LEU* 3.8 20.4 - - + -
371J ASP 3.1 13.5 - - - +
372J PHE* 3.7 32.3 - - + -
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Residues in contact with LYS 361 (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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289J SER* 3.8 14.6 - - - +
290J PHE 5.7 0.2 - - - +
359J SER* 6.0 1.1 - - - -
360J MET* 1.3 77.6 - - - +
362J PRO* 1.3 82.4 - - + +
364J ALA* 5.6 6.4 - - - +
370J LEU* 3.6 10.2 - - - +
371J ASP* 3.0 49.3 + - + +
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Residues in contact with PRO 362 (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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195J SER* 4.1 14.6 - - - +
198J ASN* 5.1 7.0 - - - +
288J LEU* 4.7 10.1 - - + +
289J SER* 3.3 17.9 - - - +
360J MET* 5.9 0.7 - - + -
361J LYS* 1.3 100.2 - - + +
363J ASN* 1.3 65.6 + - - +
364J ALA* 3.5 1.9 + - - -
367J VAL* 3.6 33.4 - - + +
369J ASP 3.6 7.9 - - - +
370J LEU* 4.6 5.4 - - + -
371J ASP* 4.8 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