Contacts of the strand formed by residues 289 - 295 (chain E) in PDB entry 1PQ3
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 289 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E HIS* 5.4 2.9 - - - -
112E SER* 3.0 16.8 + - - -
246E ILE* 3.6 13.2 - - + +
248E LEU* 4.1 17.9 - - + +
283E ILE* 4.1 22.6 + - + +
284E HIS* 5.6 1.6 - - - -
286E THR* 4.3 2.6 + - - -
287E GLY* 3.7 3.3 - - - +
288E LEU* 1.3 75.9 - - - +
290E SER* 1.3 58.3 + - - +
291E ALA 3.3 28.7 - - - +
292E LEU* 4.2 6.3 - - + -
322E SER* 3.6 37.9 - - - +
323E PHE* 3.9 28.9 - - + -
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Residues in contact with SER 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E VAL* 4.4 4.7 - - - +
111E TYR 4.0 4.4 - - - +
112E SER* 3.3 11.2 - - - +
113E CYS* 2.9 22.1 + - - +
130E HIS* 3.1 30.2 + - - -
134E CYS* 5.0 4.1 - - - -
245E PRO* 3.5 21.4 - - - +
246E ILE 2.9 8.6 + - - -
288E LEU 3.2 6.4 + - - -
289E LEU* 1.3 71.5 + - - +
291E ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 291 (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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103E VAL* 5.5 2.0 - - + -
107E VAL* 5.1 0.4 - - + -
112E SER* 4.9 0.4 - - - -
113E CYS* 3.1 19.5 - - + +
130E HIS* 3.3 16.2 - - + +
246E ILE 3.5 1.8 + - - -
247E HIS* 3.3 30.6 - - + +
248E LEU 2.9 24.3 + - - -
289E LEU* 3.3 9.2 - - - +
290E SER* 1.3 83.3 - - - +
292E LEU* 1.3 61.3 + - - +
293E ASP* 5.7 0.2 - - - +
323E PHE* 6.1 0.9 - - - -
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Residues in contact with LEU 292 (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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113E CYS 2.7 12.3 + - - +
114E VAL* 3.4 17.1 - - + -
115E THR* 2.8 26.0 + - - -
248E LEU* 3.1 25.8 - - + +
250E PHE* 5.3 1.3 - - + -
289E LEU* 4.2 11.0 - - + -
291E ALA* 1.3 76.0 - - - +
293E ASP* 1.3 83.3 + - - +
294E LEU* 4.1 8.1 - - + +
318E VAL* 4.9 2.0 - - + +
319E ILE* 4.2 26.0 - - + -
322E SER* 3.5 36.3 - - - +
323E PHE* 4.3 9.6 - - + -
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Residues in contact with ASP 293 (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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115E THR* 3.5 10.1 + - + +
120E HIS* 5.4 0.2 - - + -
122E LEU 6.0 0.2 - - - -
123E ALA* 4.5 5.9 - - - +
126E THR* 3.1 33.2 + - - +
247E HIS* 2.6 29.5 + - - -
248E LEU 2.7 9.7 + - - +
249E SER* 3.0 25.5 + - - +
250E PHE* 2.7 34.2 + - - +
292E LEU* 1.3 80.7 - - - +
294E LEU* 1.3 60.7 + - - +
295E VAL* 4.2 15.0 - - + -
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Residues in contact with LEU 294 (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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49E ILE* 4.1 5.3 - - + +
115E THR 3.0 10.7 + - - +
116E LEU* 3.7 8.2 - - + -
117E GLY 2.9 23.7 + - - +
250E PHE* 3.4 20.6 - - + +
252E ILE* 4.2 8.5 - - + -
292E LEU* 4.1 5.1 - - + +
293E ASP* 1.3 73.1 - - - +
295E VAL* 1.3 65.1 + - - +
297E VAL* 3.9 17.9 - - + +
315E ALA* 3.7 27.6 - - + +
318E VAL* 3.9 29.6 - - + -
319E ILE* 4.1 30.5 - - + -
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Residues in contact with VAL 295 (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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115E THR* 5.1 2.5 - - + +
117E GLY* 4.1 10.1 - - - +
118E GLY 3.4 13.7 - - - +
119E ASP 4.4 6.5 - - - +
120E HIS* 3.4 50.0 - - + +
122E LEU* 5.1 6.5 - - + -
123E ALA 5.9 0.4 - - - +
250E PHE 3.1 12.4 + - - +
251E ASP* 3.9 2.9 - - - -
252E ILE* 3.2 23.2 + - - +
293E ASP* 4.2 13.2 - - + +
294E LEU* 1.3 88.6 - - - +
296E GLU* 1.3 74.3 + - + +
297E VAL 3.3 4.6 + - - -
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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