Contacts of the strand formed by residues 290 - 297 (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 PHE 290 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192J PHE* 4.2 7.9 - + - -
221J LEU* 4.9 5.8 - - + -
275J ILE* 3.9 10.1 - - + -
276J LYS* 3.7 40.2 - - + +
287J GLU 3.6 16.2 - - - +
288J LEU* 3.5 16.8 - - - -
289J SER* 1.3 74.2 - - - +
291J THR* 1.3 65.6 + - - +
292J SER* 3.6 28.0 - - - -
358J ILE* 4.3 8.7 - - + -
359J SER* 3.1 5.7 - - - -
360J MET* 3.1 65.3 + - + +
361J LYS* 5.7 0.2 - - - +
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Residues in contact with THR 291 (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* 1.3 75.0 - - - +
292J SER* 1.3 64.6 + - - +
357J THR* 4.1 23.8 - - + +
358J ILE 3.7 0.7 - - - -
359J SER* 3.1 30.0 + - - +
379O LYS* 5.9 0.7 + - - -
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Residues in contact with SER 292 (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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275J ILE* 2.5 42.1 + - - -
290J PHE* 3.6 13.2 - - - -
291J THR* 1.3 80.3 - - - +
293J ALA* 1.3 63.8 + - - +
357J THR* 3.4 3.0 - - - -
358J ILE* 2.9 41.3 + - - +
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Residues in contact with ALA 293 (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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273J CYS* 4.4 3.8 - - - -
274J LEU 4.5 3.3 - - - +
275J ILE* 4.4 4.5 - - - +
292J SER* 1.3 77.5 + - - +
294J PHE* 1.3 63.8 + - - +
356J GLY 3.4 10.5 - - - +
357J THR* 4.2 8.7 - - + +
353O GLU* 4.6 1.2 - - - +
355O TYR* 3.7 25.4 + - + +
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Residues in contact with PHE 294 (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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223J VAL* 4.1 9.6 - - + -
273J CYS* 3.7 15.9 - - - -
275J ILE* 3.9 12.1 - - + -
293J ALA* 1.3 76.8 - - - +
295J CYS* 1.3 60.7 + - - +
296J LEU* 4.1 24.9 - - + -
307J LEU* 4.1 22.9 - - + -
354J ILE* 4.2 17.9 - - + -
355J TYR* 3.5 4.9 - - - +
356J GLY* 2.8 73.0 + - - +
357J THR 3.5 15.0 - - - -
358J ILE* 3.6 20.6 - - + -
374J VAL* 4.4 4.9 - - + -
375J ASP 3.9 4.7 - - - -
376J LEU* 4.7 4.7 - - + -
355O TYR* 3.3 11.0 + - - -
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Residues in contact with CYS 295 (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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271J ASN* 4.6 4.7 + - - +
273J CYS* 3.4 22.4 - - - +
294J PHE* 1.3 76.6 - - - +
296J LEU* 1.3 66.1 + - - +
297J GLN 4.2 0.4 - - - -
353J GLU* 4.1 14.4 - - - -
354J ILE 3.2 9.0 - - - -
355J TYR* 3.6 25.1 - - - -
295O CYS* 3.5 43.7 - - - -
297O GLN* 5.5 0.3 - - - +
353O GLU* 3.9 6.5 - - - +
355O TYR* 3.4 8.2 + - + +
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Residues in contact with LEU 296 (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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223J VAL* 3.4 22.0 - - + +
224J VAL* 3.7 8.3 - - - +
225J ALA* 3.7 31.4 - - + +
270J THR* 3.9 13.5 - - + +
271J ASN* 3.4 24.7 - - - +
273J CYS* 3.8 12.3 - - + +
294J PHE* 4.1 17.9 - - + -
295J CYS* 1.3 80.1 - - - +
297J GLN* 1.3 63.0 + - - +
298J ILE* 3.7 2.9 + - - +
307J LEU* 4.2 12.6 - - + -
353J GLU* 3.4 6.0 - - - -
354J ILE* 2.8 42.6 + - + +
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Residues in contact with GLN 297 (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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270J THR* 3.2 18.3 - - - -
271J ASN* 2.9 24.6 + - - +
295J CYS* 4.2 1.2 - - - -
296J LEU* 1.3 71.8 - - - +
298J ILE* 1.3 70.4 + - - +
299J GLN* 3.2 27.1 + - - +
351J GLY* 4.8 11.2 - - - +
352J GLU 3.9 7.2 - - - +
353J GLU* 3.5 22.9 - - + +
271O ASN* 3.9 23.1 + - - +
272O ALA 3.5 18.0 + - - +
273O CYS* 5.0 0.5 - - - -
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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