Contacts of the strand formed by residues 290 - 297 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192M PHE* 4.2 8.1 - + - -
221M LEU* 4.9 5.6 - - + -
275M ILE* 3.9 8.5 - - + -
276M LYS* 3.8 39.3 - - + +
287M GLU 3.5 17.3 - - - +
288M LEU* 3.6 17.3 - - - -
289M SER* 1.3 74.6 - - - +
291M THR* 1.3 69.5 + - - +
292M SER* 3.6 28.3 - - - -
358M ILE* 4.1 11.0 - - + -
359M SER* 3.1 4.9 - - - -
360M MET* 3.1 64.7 + - + +
361M LYS* 5.5 0.8 - - - +
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Residues in contact with THR 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379H LYS* 5.5 5.4 + - - -
290M PHE* 1.3 76.5 - - - +
292M SER* 1.3 67.2 + - - +
357M THR* 3.9 25.8 - - + +
358M ILE 3.9 0.4 - - - -
359M SER* 3.1 27.0 + - - +
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Residues in contact with SER 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274M LEU 5.1 0.2 + - - -
275M ILE* 2.5 40.5 + - - -
276M LYS* 5.9 0.2 - - - -
290M PHE* 3.6 11.9 - - - -
291M THR* 1.3 82.4 - - - +
293M ALA* 1.3 66.3 + - - +
357M THR* 3.3 2.9 - - - -
358M ILE* 2.8 42.0 + - - +
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Residues in contact with ALA 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353H GLU* 4.8 0.2 - - - +
355H TYR* 3.4 32.1 + - + -
273M CYS* 4.4 2.6 - - - -
274M LEU 4.5 2.4 - - - +
275M ILE* 4.1 6.4 - - - +
292M SER* 1.3 81.0 + - - +
294M PHE* 1.3 63.4 + - - +
356M GLY 3.4 10.1 - - - +
357M THR* 4.1 10.2 - - + +
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Residues in contact with PHE 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355H TYR* 3.0 11.9 - - - -
223M VAL* 4.0 9.0 - - + -
273M CYS* 3.5 14.6 - - - -
275M ILE* 3.9 11.0 - - + -
293M ALA* 1.3 76.6 - - - +
295M CYS* 1.3 62.3 + - - +
296M LEU* 4.1 29.4 - - + -
307M LEU* 4.0 22.9 - - + -
354M ILE* 4.2 14.6 - - + -
355M TYR* 3.4 4.9 - - - -
356M GLY* 2.8 73.7 + - - +
357M THR 3.6 10.3 - - - -
358M ILE* 3.6 21.1 - - + -
374M VAL* 4.4 5.8 - - + -
375M ASP 3.8 7.9 - - - -
376M LEU* 4.5 5.6 - - + -
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Residues in contact with CYS 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295H CYS* 3.4 37.5 - - + -
353H GLU* 4.2 3.3 - - - +
355H TYR* 3.2 7.4 + - + -
271M ASN* 4.5 4.2 + - - +
272M ALA 5.2 0.3 - - - +
273M CYS* 3.2 23.5 - - - +
294M PHE* 1.3 77.1 - - - +
296M LEU* 1.3 65.1 + - - +
297M GLN* 4.2 0.7 - - - -
353M GLU* 4.2 14.8 - - - -
354M ILE 3.3 7.0 - - - -
355M TYR* 3.4 38.8 - - - -
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Residues in contact with LEU 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M VAL* 3.4 22.4 - - + +
224M VAL* 3.8 7.2 - - - +
225M ALA* 3.7 30.7 - - + +
270M THR* 3.9 13.5 - - + +
271M ASN* 3.3 24.0 - - - +
273M CYS* 3.8 10.8 - - + +
294M PHE* 4.1 18.8 - - + -
295M CYS* 1.3 83.4 - - - +
297M GLN* 1.3 60.9 + - - +
298M ILE* 3.7 1.9 + - - +
307M LEU* 4.1 13.2 - - + -
353M GLU* 3.3 7.4 - - - +
354M ILE* 2.9 43.8 + - + +
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Residues in contact with GLN 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271H ASN* 4.3 18.5 + - - +
272H ALA 3.2 25.2 + - - +
273H CYS* 4.5 0.7 - - - -
274H LEU 5.3 0.5 + - - -
295H CYS 5.6 0.3 - - - +
270M THR* 3.2 17.5 - - - -
271M ASN* 2.8 25.4 + - - +
295M CYS* 4.2 1.2 - - - -
296M LEU* 1.3 72.3 - - - +
298M ILE* 1.3 65.0 + - - +
299M GLN* 3.0 30.7 + - - +
351M GLY* 5.0 9.4 - - - +
352M GLU 4.0 6.1 - - - +
353M GLU* 3.4 24.1 - - + +
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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