Contacts of the strand formed by residues 290 - 297 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PHE* 4.3 6.5 - + - -
221A LEU* 4.8 5.4 - - + -
275A ILE* 3.8 12.3 - - + -
276A LYS* 3.8 37.9 - - + +
287A GLU 3.7 13.2 - - - +
288A LEU* 3.4 20.9 - - - -
289A SER* 1.3 73.3 - - - +
291A THR* 1.3 67.5 + - - +
292A SER* 3.7 28.5 - - - -
358A ILE* 4.1 8.3 - - + -
359A SER* 3.1 5.9 - - - -
360A MET* 3.1 67.1 + - + +
361A LYS* 5.7 0.2 - - - +
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Residues in contact with THR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PHE* 1.3 74.2 + - - +
292A SER* 1.3 66.9 + - - +
357A THR* 4.1 24.5 - - + +
358A ILE 3.9 0.9 - - - -
359A SER* 3.0 27.5 + - - +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ILE* 2.6 41.3 + - - +
290A PHE* 3.7 11.4 - - - -
291A THR* 1.3 83.7 - - - +
293A ALA* 1.3 66.0 + - - +
357A THR* 4.2 2.9 - - - -
358A ILE* 3.0 37.4 + - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A CYS* 4.6 0.9 - - - -
274A LEU 4.5 4.9 - - - +
275A ILE* 4.2 4.7 - - - +
292A SER* 1.3 82.6 + - - +
294A PHE* 1.3 62.9 + - - +
356A GLY 3.3 11.7 - - - +
357A THR* 4.1 9.6 - - + +
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Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A VAL* 4.1 7.9 - - + -
273A CYS* 3.7 16.4 - - - -
275A ILE* 3.9 11.9 - - + -
293A ALA* 1.3 77.0 - - - +
295A CYS* 1.3 64.2 + - - +
296A LEU* 4.2 23.6 - - + -
307A LEU* 4.1 21.8 - - + -
354A ILE* 4.1 19.1 - - + -
355A TYR* 3.4 7.6 - - - +
356A GLY* 2.8 75.5 + - - +
357A THR 3.4 14.6 - - - -
358A ILE* 3.5 22.2 - - + -
374A VAL* 4.3 6.5 - - + -
375A ASP 3.8 5.4 - - - -
376A LEU* 4.6 4.9 - - + -
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Residues in contact with CYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ASN* 4.6 3.5 + - - +
272A ALA 5.2 0.2 - - - +
273A CYS* 3.3 26.7 - - - +
294A PHE* 1.3 75.3 - - - +
296A LEU* 1.3 68.7 + - - +
297A GLN* 4.3 1.3 + - - -
353A GLU* 4.1 20.6 - - - -
354A ILE 3.3 8.7 - - - -
355A TYR* 3.7 39.0 - - + -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A VAL* 3.5 22.2 - - + +
224A VAL* 3.9 7.6 - - - +
225A ALA* 3.8 28.7 - - + +
270A THR* 3.9 13.0 - - + +
271A ASN* 3.4 24.5 - - - +
273A CYS* 3.7 11.7 - - + -
294A PHE* 4.2 18.4 - - + -
295A CYS* 1.3 86.3 - - - +
297A GLN* 1.3 62.3 + - - +
298A ILE* 3.7 2.3 + - - +
307A LEU* 4.2 13.7 - - + -
353A GLU* 3.4 5.2 - - - -
354A ILE* 2.9 43.6 + - + +
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A THR* 3.0 24.4 - - - -
271A ASN* 2.7 29.8 + - - +
295A CYS* 4.3 1.3 - - - -
296A LEU* 1.3 72.3 - - - +
298A ILE* 1.3 64.1 + - - +
299A GLN* 3.1 26.9 + - - +
351A GLY* 5.1 8.7 - - - +
352A GLU 4.1 8.3 - - - +
353A GLU* 3.5 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