Contacts of the helix formed by residues 227 - 240 (chain B) in PDB entry 1PL8
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 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B LYS 3.8 0.6 + - - -
226B GLU* 1.3 73.9 - - - +
228B PRO* 1.3 76.4 - - - +
229B GLN* 3.6 11.6 + - - +
230B GLU* 2.7 42.1 + - - +
231B ILE* 2.8 23.6 + - - +
233B ARG* 4.7 0.3 + - - -
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Residues in contact with PRO 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLU 4.6 0.9 - - - +
227B SER* 1.3 87.0 - - - +
229B GLN* 1.3 65.4 + - - +
231B ILE* 3.2 6.3 + - + +
232B ALA* 2.9 28.1 + - - +
254B ALA* 3.5 24.0 - - + +
257B GLN* 3.4 31.2 - - + +
258B ALA* 3.7 32.4 - - + +
261B TYR* 4.0 7.6 - - + -
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B SER* 3.6 10.1 + - - +
228B PRO* 1.3 93.1 - - - +
230B GLU* 1.3 57.8 + - - +
232B ALA* 3.3 5.6 + - - +
233B ARG* 2.9 50.5 + - - +
261B TYR* 3.5 42.2 + - + -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LYS 4.4 0.9 - - - +
226B GLU* 3.0 20.7 - - + +
227B SER* 2.7 48.8 + - - +
229B GLN* 1.3 72.9 - - - +
231B ILE* 1.3 62.1 + - - +
233B ARG* 3.1 30.3 + - - +
234B LYS* 2.9 43.2 + - - +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 5.9 2.2 - - + -
178B CYS* 6.5 0.7 - - - -
202B THR* 4.9 5.4 - - + -
221B LEU* 4.9 4.0 - - + -
223B ILE* 3.3 45.5 - - + -
226B GLU* 3.5 30.5 - - + +
227B SER 2.8 22.1 + - - +
228B PRO* 3.4 9.4 - - + +
230B GLU* 1.3 76.3 - - - +
232B ALA* 1.3 64.9 + - - +
234B LYS* 3.1 7.0 + - + +
235B VAL* 2.9 41.4 + - + +
258B ALA* 4.0 18.2 - - + -
262B ALA* 6.4 0.2 - - + -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B PRO 2.9 13.8 + - - +
229B GLN 3.5 9.2 - - - +
231B ILE* 1.3 76.7 - - - +
233B ARG* 1.3 62.3 + - - +
235B VAL* 3.4 3.1 + - - +
236B GLU* 3.0 25.8 + - - +
258B ALA* 4.0 2.2 - - - +
261B TYR* 3.6 16.6 - - + +
262B ALA* 3.6 42.1 - - + +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B SER* 4.7 0.6 + - - -
229B GLN* 2.9 33.9 + - - +
230B GLU* 3.1 41.0 + - - +
232B ALA* 1.3 77.6 - - + +
234B LYS* 1.3 58.5 + - + +
236B GLU* 3.3 9.0 + - - +
237B GLY* 2.8 26.7 + - - -
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 3.6 31.2 - - + -
226B GLU* 3.6 40.7 - - + +
230B GLU* 2.9 26.9 + - - +
231B ILE* 3.7 4.0 - - + +
233B ARG* 1.3 72.5 - - + +
235B VAL* 1.3 61.2 + - - +
237B GLY* 3.2 2.0 + - - +
238B GLN* 2.9 37.5 + - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 4.2 40.8 - - + -
200B VAL* 4.7 8.5 - - + +
202B THR* 4.7 2.5 - - + -
221B LEU* 4.0 17.7 - - + -
231B ILE* 2.9 31.6 + - + +
232B ALA* 3.7 7.2 - - - +
234B LYS* 1.3 75.5 - - - +
236B GLU* 1.3 59.5 + - - +
238B GLN* 3.2 6.9 + - - +
239B LEU* 3.0 47.1 + - + +
243B PRO* 4.4 10.3 - - + -
262B ALA* 4.8 2.0 - - + -
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ALA 3.0 18.2 + - - +
233B ARG* 3.7 8.1 - - - +
235B VAL* 1.3 74.6 - - - +
237B GLY* 1.3 58.2 + - - +
240B GLY* 2.7 33.3 + - - -
241B CYS* 3.2 26.7 + - - +
242B LYS* 3.2 45.8 + - + +
243B PRO* 5.5 0.9 - - + -
262B ALA* 5.9 0.4 - - + +
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ARG 2.8 17.3 + - - -
234B LYS* 3.2 3.3 + - - -
236B GLU* 1.3 78.4 - - - +
238B GLN* 1.3 60.9 + - - +
240B GLY* 3.5 7.8 + - - -
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Residues in contact with GLN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLN* 5.2 1.6 + - - -
200B VAL* 4.5 4.7 - - + +
219B LEU* 3.7 43.0 - - + +
220B VAL 3.5 17.3 + - - +
221B LEU* 2.8 44.5 - - - +
234B LYS* 2.9 18.3 + - - +
235B VAL* 3.6 6.1 - - - +
237B GLY* 1.3 78.2 - - - +
239B LEU* 1.3 60.7 + - + +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B LYS* 4.2 15.9 + - + -
175B VAL 5.2 0.9 - - - +
198B GLN* 3.9 37.8 + - + +
200B VAL* 3.2 35.9 - - + -
219B LEU* 3.6 11.7 - - + -
235B VAL* 3.0 17.5 + - + +
238B GLN* 1.3 77.4 - - - +
240B GLY* 1.3 60.9 + - - +
241B CYS* 3.0 27.1 + - - +
243B PRO* 3.9 40.2 - - + -
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B GLU* 2.7 16.0 + - - -
237B GLY* 3.5 6.7 + - - -
238B GLN 3.4 3.2 + - - -
239B LEU* 1.3 73.6 - - - +
241B CYS* 1.3 62.7 + - - +
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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