Contacts of the helix formed by residues 285 - 294 (chain E) in PDB entry 2PWZ
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 SER 285 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187E SER* 3.9 17.5 + - - -
199E VAL* 5.9 0.5 - - - +
284E LEU* 1.3 75.9 - - - +
286E ALA* 1.3 59.8 + - - +
287E PHE* 3.5 9.2 + - - +
288E GLU* 3.0 36.7 + - - +
289E GLN* 2.9 28.5 + - - +
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Residues in contact with ALA 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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285E SER* 1.3 72.9 - - - +
287E PHE* 1.3 57.7 + - - +
289E GLN* 3.3 6.0 + - - +
290E ASN* 2.9 33.9 + - - +
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Residues in contact with PHE 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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183E LEU* 5.2 2.7 - - + -
196E GLU* 5.0 5.8 - - + -
199E VAL* 3.6 28.9 - - + -
200E ALA* 4.1 19.5 - - + -
203E THR* 3.7 38.4 - - + -
285E SER* 3.3 7.9 + - - +
286E ALA* 1.3 77.9 - - - +
288E GLU* 1.3 67.2 + - + +
290E ASN* 3.3 7.4 - - + +
291E ALA* 2.9 34.6 + - + +
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Residues in contact with GLU 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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183E LEU* 3.4 19.9 - - + +
184E PRO 4.0 3.0 - - - +
185E LEU* 3.9 25.0 - - + +
186E LEU* 3.2 12.0 + - - +
187E SER* 2.7 46.5 + - - -
199E VAL* 6.0 2.1 - - + +
283E THR 4.2 0.3 - - - +
284E LEU* 3.4 21.0 - - + +
285E SER* 3.0 27.8 + - - +
287E PHE* 1.3 79.1 - - + +
289E GLN* 1.3 61.8 + - - +
292E LEU* 2.9 30.8 + - - +
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Residues in contact with GLN 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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260E TYR* 5.4 5.5 + - - -
284E LEU* 3.8 25.3 - - + +
285E SER 2.9 15.7 + - - +
286E ALA* 3.7 7.0 - - - +
288E GLU* 1.3 75.2 - - - +
290E ASN* 1.3 58.1 + - - +
292E LEU* 3.4 9.8 + - - +
293E GLU* 3.0 73.0 + - - +
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Residues in contact with ASN 290 (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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286E ALA 2.9 18.3 + - - +
287E PHE* 3.3 9.9 - - + +
289E GLN* 1.3 78.3 - - - +
291E ALA* 1.3 57.0 + - - +
293E GLU* 3.6 16.3 + - - +
294E GLY* 3.1 25.5 + - - -
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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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180E VAL 4.7 4.4 - - - +
183E LEU* 3.7 27.8 - - + -
203E THR* 5.8 0.7 - - + -
207E GLN* 5.7 5.4 - - - +
287E PHE* 2.9 28.8 + - + +
288E GLU 3.8 0.7 - - - +
289E GLN 3.4 0.2 - - - -
290E ASN* 1.3 72.7 - - - +
292E LEU* 1.3 67.3 + - - +
294E GLY* 3.3 7.9 + - - -
295E MET* 3.3 20.2 + - - +
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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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174E ILE* 4.6 4.7 - - + -
183E LEU* 3.8 8.4 - - + +
260E TYR* 3.8 34.5 - - + +
264E PHE* 3.6 34.3 - - + -
281E ILE* 4.0 7.2 - - + -
284E LEU* 3.6 25.8 - - + -
288E GLU 2.9 16.8 + - - +
289E GLN* 3.6 12.8 - - - +
290E ASN 3.3 0.2 - - - -
291E ALA* 1.3 74.4 - - - +
293E GLU* 1.3 66.6 + - - +
294E GLY 3.1 0.7 + - - -
295E MET* 3.3 20.1 + - + +
296E LEU* 3.4 25.3 + - + +
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Residues in contact with GLU 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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289E GLN* 3.0 50.8 + - - +
290E ASN* 3.8 20.5 + - - +
292E LEU* 1.3 72.1 - - + +
294E GLY* 1.3 61.9 + - - +
295E MET 3.3 1.4 + - - -
296E LEU* 3.6 22.1 + - + +
297E ASP 5.0 0.7 + - - -
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Residues in contact with GLY 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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180E VAL* 5.1 4.2 - - - +
290E ASN 3.1 17.4 + - - -
291E ALA* 3.3 3.6 + - - -
292E LEU 3.1 1.0 - - - -
293E GLU* 1.3 76.2 - - - +
295E MET* 1.3 58.1 + - - +
296E LEU 3.7 0.2 - - - -
297E ASP* 5.3 1.9 + - - +
298E THR* 5.2 1.9 + - - -
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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