Contacts of the helix formed by residues 224 - 235 (chain E) in PDB entry 1QRP
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 PRO 224 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223E GLY* 1.3 85.5 - - - +
225E THR* 1.3 65.8 + - - +
226E SER 3.3 0.7 - - - +
227E PRO* 3.2 26.4 - - + +
228E ILE* 3.2 11.6 + - - +
289E MET 3.6 5.1 - - - +
290E ASN* 3.4 14.1 - - - +
297E GLU* 3.7 39.9 - - + +
298E LEU 4.0 3.4 - - - +
299E TRP* 3.4 33.0 - - + +
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Residues in contact with THR 225 (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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223E GLY 3.5 0.8 + - - -
224E PRO* 1.3 69.8 - - - +
226E SER* 1.3 62.3 + - - +
228E ILE* 3.5 2.3 + - - +
229E ALA* 3.0 29.7 + - - +
288E GLY* 3.9 29.8 - - - +
289E MET* 4.0 3.4 - - - +
290E ASN* 3.0 35.3 + - - +
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Residues in contact with SER 226 (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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224E PRO* 4.7 0.4 - - - +
225E THR* 1.3 79.0 + - - +
227E PRO* 1.4 70.6 - - - +
229E ALA* 3.3 16.9 + - - +
230E ASN* 3.4 18.1 + - - +
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Residues in contact with PRO 227 (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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204E ILE 4.6 1.0 - - - +
205E ALA* 4.1 11.9 - - + -
206E CYS 5.7 0.9 - - - +
224E PRO* 3.2 32.3 - - + +
226E SER* 1.4 87.9 - - - +
228E ILE* 1.3 60.3 + - - +
230E ASN* 3.2 17.7 + - - +
231E ILE* 3.1 25.8 + - - +
299E TRP* 3.7 27.1 - - + +
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Residues in contact with ILE 228 (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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222E THR 4.6 1.1 - - - -
223E GLY* 3.6 24.7 - - - +
224E PRO 3.2 17.3 + - - +
225E THR 3.8 3.1 - - - +
227E PRO* 1.3 74.6 - - - +
229E ALA* 1.3 59.4 + - - +
231E ILE* 3.0 7.9 + - + +
232E GLN* 2.8 52.6 + - + +
286E PHE* 3.6 31.2 - - + -
287E GLN 3.7 9.9 - - - +
288E GLY* 3.6 25.1 - - - +
299E TRP* 3.8 21.8 - - + -
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Residues in contact with ALA 229 (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 THR 3.0 14.8 + - - +
226E SER* 3.3 12.8 + - - +
228E ILE* 1.3 74.4 - - - +
230E ASN* 1.3 64.0 + - - +
232E GLN* 3.4 10.0 + - - +
233E SER* 3.2 26.1 + - - -
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Residues in contact with ASN 230 (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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204E ILE 4.3 14.8 + - - +
226E SER* 3.4 17.2 + - - +
227E PRO* 3.2 15.3 + - - +
228E ILE 3.2 0.6 - - - -
229E ALA* 1.3 75.0 - - - +
231E ILE* 1.3 64.7 + - - +
233E SER* 3.3 7.6 + - - -
234E ASP* 3.0 33.1 + - - +
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Residues in contact with ILE 231 (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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197E ILE* 4.8 4.7 - - + -
204E ILE* 3.9 29.4 - - + +
205E ALA* 4.1 7.9 - - + -
227E PRO 3.1 11.1 + - - +
228E ILE* 3.0 12.8 + - + +
230E ASN* 1.3 73.0 - - - +
232E GLN* 1.3 62.7 + - - +
234E ASP* 3.2 18.0 + - - +
235E ILE* 3.2 16.3 + - + +
258E ILE* 4.3 11.9 - - + -
286E PHE* 3.9 52.0 - - + -
299E TRP* 3.9 29.4 - - + -
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Residues in contact with GLN 232 (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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228E ILE* 2.8 35.8 + - + +
229E ALA* 3.5 10.5 - - - +
230E ASN 3.3 0.2 - - - -
231E ILE* 1.3 71.5 - - - +
233E SER* 1.3 60.7 + - - +
235E ILE* 3.4 5.9 + - - +
236E GLY 3.2 4.2 + - - -
237E ALA* 3.0 42.5 + - + +
245E MET* 4.2 30.8 - - + +
284E SER* 2.7 29.1 + - - -
286E PHE* 2.9 35.6 + - - +
287E GLN* 4.7 1.0 - - - +
288E GLY 5.2 0.6 - - - +
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Residues in contact with SER 233 (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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229E ALA 3.2 14.1 + - - -
230E ASN* 3.3 8.5 + - - -
232E GLN* 1.3 74.3 - - - +
234E ASP* 1.4 64.4 + - - +
236E GLY* 3.3 13.8 + - - +
237E ALA 5.0 4.3 - - - +
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Residues in contact with ASP 234 (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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199E MET* 3.8 31.3 - - + +
204E ILE* 3.6 31.3 - - + +
230E ASN* 3.0 28.4 + - - +
231E ILE* 3.2 9.3 + - - +
233E SER* 1.4 78.7 - - - +
235E ILE* 1.3 58.8 - - + +
236E GLY 3.5 0.9 - - - -
255E LEU* 4.5 6.6 - - - +
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Residues in contact with ILE 235 (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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199E MET* 4.5 7.9 - - - -
231E ILE* 3.2 16.6 + - + +
232E GLN* 3.5 13.9 - - - +
234E ASP* 1.3 80.3 - - + +
236E GLY* 1.3 59.8 + - - +
237E ALA* 4.4 3.8 - - + +
247E VAL* 3.9 12.3 - - + +
251E ALA* 5.8 0.5 - - - +
255E LEU* 3.8 28.3 - - + +
258E ILE* 4.0 14.4 - - + -
274E TYR* 3.7 33.0 - - + +
275E ILE* 4.0 20.4 - - + -
284E SER* 3.7 25.8 - - - +
286E PHE* 4.3 12.3 - - + -
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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