Contacts of the strand formed by residues 353 - 362 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295E CYS* 4.0 11.5 - - - -
296E LEU 3.3 11.0 - - - +
297E GLN* 3.6 25.3 - - + +
298E ILE* 4.1 1.3 - - - -
351E GLY 4.0 8.5 - - - +
352E GLU* 1.3 85.2 - - - +
354E ILE* 1.3 61.6 + - - +
355E TYR* 2.6 47.1 + - + -
377E ASP 4.3 1.6 - - - +
378E PHE* 3.2 20.5 - - - -
379E LYS 4.8 2.6 + - - +
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Residues in contact with ILE 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E ALA* 4.0 26.2 - - + -
270E THR* 4.7 0.7 - - + -
294E PHE* 4.2 11.9 - - + -
295E CYS* 3.2 6.1 - - - -
296E LEU* 2.9 44.2 + - + +
298E ILE* 3.8 22.2 - - + -
304E VAL* 4.6 7.2 - - + -
307E LEU* 5.2 2.5 - - + -
346E LEU* 4.2 17.5 - - + -
348E VAL* 5.2 0.2 - - + -
353E GLU* 1.3 75.8 - - - +
355E TYR* 1.3 65.1 + - - +
376E LEU* 3.7 36.3 - - + -
377E ASP 3.9 4.9 - - - +
378E PHE* 3.8 12.1 - - + -
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Residues in contact with TYR 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E PHE* 3.5 7.4 - - - -
295E CYS* 3.6 21.8 - - + -
353E GLU* 2.6 44.5 + - + -
354E ILE* 1.3 80.6 - - - +
356E GLY* 1.3 59.5 + - - +
376E LEU* 3.5 3.1 - - - +
377E ASP* 2.8 45.5 + - + +
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Residues in contact with GLY 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E ALA* 3.4 6.8 - - - +
294E PHE* 2.9 41.0 + - - +
355E TYR* 1.3 77.4 - - - +
357E THR* 1.3 64.4 + - - +
375E ASP* 3.0 15.3 - - - -
376E LEU* 4.3 0.2 - - - -
377E ASP* 4.6 1.8 - - - -
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Residues in contact with THR 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E THR* 3.9 22.0 - - + +
292E SER 3.3 9.4 - - - -
293E ALA* 4.3 12.1 - - + +
294E PHE* 3.7 2.7 - - - -
356E GLY* 1.3 78.8 - - - +
358E ILE* 1.3 63.5 + - - +
359E SER* 5.0 1.4 + - - -
373E THR 3.6 1.9 + - - +
374E VAL* 3.5 2.3 - - - -
375E ASP* 2.9 47.0 + - + +
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Residues in contact with ILE 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E LEU* 5.8 1.3 - - + -
223E VAL* 5.0 10.3 - - + -
275E ILE* 3.8 37.9 - - + -
290E PHE* 4.1 4.1 - - + +
291E THR* 3.8 0.6 - - - -
292E SER* 2.9 32.3 + - - +
294E PHE* 3.4 24.7 - - + -
307E LEU* 6.4 0.7 - - + -
309E THR* 5.0 7.4 - - + -
340E PHE* 5.3 3.8 - - + -
357E THR* 1.3 74.9 - - - +
359E SER* 1.3 70.5 + - - +
360E MET* 5.2 4.0 - - + -
372E PHE* 4.3 24.2 - - + -
373E THR 3.4 4.7 - - - +
374E VAL* 4.3 18.8 - - + -
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Residues in contact with SER 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E PHE 3.0 9.0 - - - -
291E THR* 2.9 33.3 + - - +
357E THR* 5.0 1.9 + - - -
358E ILE* 1.3 76.4 - - - +
360E MET* 1.3 64.1 + - - +
361E LYS* 5.9 1.8 - - - -
372E PHE* 3.3 7.1 - - - +
373E THR* 3.0 46.4 + - - +
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Residues in contact with MET 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E CYS 5.1 1.6 - - - +
192E PHE* 3.5 45.3 - - + -
221E LEU* 4.9 7.4 - - - -
288E LEU 3.7 17.3 - - - +
289E SER* 3.3 5.4 - - - -
290E PHE* 3.0 51.1 + - + -
358E ILE* 5.2 3.1 - - + -
359E SER* 1.3 77.0 - - - +
361E LYS* 1.3 65.4 + - - +
362E PRO* 6.1 0.2 - - + -
370E LEU* 3.8 19.3 - - + -
371E ASP 3.1 12.6 - - - +
372E PHE* 3.6 32.5 - - + -
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Residues in contact with LYS 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E LEU 5.4 0.2 - - - -
289E SER* 3.7 15.3 - - - +
290E PHE 5.7 0.2 - - - +
359E SER* 5.9 1.6 - - - -
360E MET* 1.3 78.5 - - - +
362E PRO* 1.3 84.4 - - + +
363E ASN* 5.7 0.2 - - - +
364E ALA* 5.6 5.8 - - - +
370E LEU* 3.6 10.0 - - - +
371E ASP* 3.1 45.4 + - + +
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Residues in contact with PRO 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E SER* 4.0 14.6 - - - +
198E ASN* 5.1 7.0 - - - +
288E LEU* 4.6 10.8 - - + +
289E SER* 3.3 17.7 - - - +
360E MET* 6.1 0.4 - - + -
361E LYS* 1.3 99.2 - - + +
363E ASN* 1.3 67.1 + - - +
364E ALA* 3.6 1.7 + - - -
367E VAL* 3.7 33.2 - - + +
369E ASP 3.7 7.0 - - - +
370E LEU* 4.7 4.0 - - + -
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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