Contacts of the strand formed by residues 283 - 289 (chain E) in PDB entry 5U0A
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 LEU 283 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E HIS 5.2 0.9 - - - +
8E ALA* 3.1 7.5 - - - +
9E ILE* 2.9 41.7 + - + +
281E PRO* 3.3 2.2 - - - +
282E ASP* 1.3 80.7 - - - +
284E VAL* 1.3 76.3 + - - +
285E HIS* 4.4 5.8 - - + -
315E CYS* 3.8 29.6 - - + +
318E LEU* 4.4 13.0 - - + -
337E TYR* 5.1 0.2 - - + -
338E ALA 3.7 5.2 - - - +
339E THR* 3.3 24.2 - - + +
346E LEU* 3.6 23.8 - - + -
349E LEU* 4.2 19.3 - - + -
356E TYR* 4.3 2.7 - - - -
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Residues in contact with VAL 284 (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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6E ILE* 3.8 15.0 - - + -
7E HIS 3.3 12.3 - - - +
8E ALA* 4.5 1.6 - - + -
264E LEU* 3.5 33.7 - - + -
281E PRO* 5.3 0.9 - - + -
283E LEU* 1.3 78.0 - - - +
285E HIS* 1.3 65.1 + - - +
286E ILE* 4.6 3.1 - - + -
337E TYR* 3.3 5.0 - - - +
338E ALA 2.9 34.4 + - - +
356E TYR* 3.4 32.1 + - + -
359E LEU* 3.4 23.6 - - + -
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Residues in contact with HIS 285 (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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7E HIS* 2.9 58.0 + + + -
283E LEU* 4.4 10.5 - - + -
284E VAL* 1.3 77.2 - - - +
286E ILE* 1.3 60.2 + - - +
287E ALA* 3.8 27.8 - - + -
296E PHE* 4.3 15.4 - + - -
318E LEU* 4.9 2.7 - - + -
322E ALA* 5.3 1.2 - - + +
335E ARG* 4.2 15.8 - - + +
336E GLY 3.5 7.2 - - - -
337E TYR* 4.2 2.5 - - + -
348E ALA 4.9 0.2 + - - -
349E LEU* 3.3 59.4 + - + +
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Residues in contact with ILE 286 (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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4E VAL* 3.9 24.9 - - + -
5E ASP 3.6 5.6 - - - +
6E ILE* 4.0 22.9 - - + -
260E LEU* 3.6 22.9 - - + -
284E VAL* 4.2 2.4 - - + -
285E HIS* 1.3 75.2 - - - +
287E ALA* 1.3 62.9 + - - +
335E ARG 3.6 2.3 - - - -
336E GLY* 2.9 32.3 + - - +
359E LEU* 3.9 22.1 - - + +
360E ILE* 3.9 24.5 - - + -
363E MET* 3.7 30.9 - - + +
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Residues in contact with ALA 287 (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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4E VAL* 3.6 3.8 - - - +
5E ASP* 2.7 51.7 + - - +
7E HIS* 5.0 0.7 - - - +
285E HIS* 3.8 21.8 + - + +
286E ILE* 1.3 73.5 - - - +
288E VAL* 1.3 62.8 + - - +
289E ARG* 4.5 10.8 - - - +
333E ALA* 5.3 2.5 - - + -
334E ILE 3.6 4.0 - - - -
335E ARG* 4.3 14.4 - - + +
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Residues in contact with VAL 288 (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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2E THR 5.0 3.6 - - - +
3E PHE 3.6 7.4 - - - +
4E VAL* 4.4 13.9 - - + -
287E ALA* 1.3 75.1 - - - +
289E ARG* 1.3 60.2 + - - +
290E PHE* 4.0 23.0 - - + -
333E ALA* 3.2 5.7 - - - +
334E ILE* 2.8 46.1 + - + +
363E MET* 3.7 38.6 - - + +
366E ALA* 4.7 3.8 - - + +
367E ALA* 3.8 24.5 - - + -
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Residues in contact with ARG 289 (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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2E THR 3.2 2.3 + - - -
3E PHE* 2.8 45.8 + - + +
5E ASP* 3.1 38.9 + - - +
287E ALA* 4.5 8.5 - - - +
288E VAL* 1.3 74.5 - - - +
290E PHE* 1.3 60.6 + - - +
291E ASP* 2.9 18.5 + - - +
292E ARG 2.3 39.5 + - - +
293E PRO* 3.4 8.1 - - - -
294E ILE* 3.9 24.1 + - - +
329E TRP* 5.0 1.8 - - - -
331E ASP* 2.7 28.7 + - - -
333E ALA* 3.6 10.3 - - + +
335E ARG* 4.3 5.3 - - - +
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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