Contacts of the helix formed by residues 252 - 263 (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 ALA 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B THR* 2.9 16.2 + - - +
251B GLY* 1.3 78.4 - - - +
253B GLU* 1.3 66.4 + - - +
254B ALA* 4.5 2.5 - - + +
255B SER* 3.1 6.1 + - - +
256B ILE* 3.0 22.4 + - - +
400B NAD 3.7 33.0 - - - +
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Residues in contact with GLU 253 (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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251B GLY 3.6 3.6 + - - -
252B ALA* 1.3 71.1 - - - +
254B ALA* 1.3 63.5 + - - +
256B ILE* 3.1 5.9 + - - +
257B GLN* 2.9 37.0 + - - +
278B MET 4.7 1.9 - - - +
279B THR* 3.8 23.4 - - + -
280B THR* 3.1 47.6 + - - +
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Residues in contact with ALA 254 (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* 3.5 25.8 - - + +
252B ALA* 3.3 1.7 - - + +
253B GLU* 1.3 80.0 - - - +
255B SER* 1.3 58.1 + - - +
257B GLN* 3.4 5.6 + - - +
258B ALA* 2.9 27.1 + - - +
400B NAD 4.6 11.4 - - - +
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Residues in contact with SER 255 (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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178B CYS* 3.1 24.4 - - - +
202B THR* 5.1 0.3 + - - -
248B GLU* 2.6 31.0 + - - +
250B THR* 3.5 9.1 + - - +
252B ALA 3.1 8.1 + - - -
254B ALA* 1.3 76.4 - - - +
256B ILE* 1.3 61.2 + - - +
258B ALA* 3.1 8.8 + - - +
259B GLY* 2.8 26.3 + - - -
400B NAD 4.1 21.4 + - - -
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Residues in contact with ILE 256 (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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248B GLU* 3.8 24.2 - - + +
251B GLY* 4.4 11.2 - - - +
252B ALA 3.0 19.4 + - - +
253B GLU* 3.4 6.7 - - - +
255B SER* 1.3 76.7 - - - +
257B GLN* 1.3 63.3 + - - +
259B GLY* 3.1 3.6 + - - +
260B ILE* 3.0 25.7 + - + +
269B LEU* 3.9 9.0 - - + +
271B LEU* 4.2 30.1 - - + -
273B GLY 5.9 1.6 - - - +
275B GLY* 6.3 0.7 - - - +
279B THR* 4.1 22.2 - - + +
281B VAL* 3.8 20.6 - - + -
293B ILE* 6.3 0.7 - - + -
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Residues in contact with GLN 257 (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* 3.4 25.4 - - + +
253B GLU* 2.9 33.0 + - - +
254B ALA* 3.6 8.1 - - - +
256B ILE* 1.3 75.0 - - - +
258B ALA* 1.3 64.3 + - - +
260B ILE* 3.1 6.4 + - - +
261B TYR* 3.0 32.6 + - + -
280B THR* 2.8 35.8 + - - +
281B VAL* 4.0 6.5 - - + +
282B PRO* 4.0 22.8 - - + +
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Residues in contact with ALA 258 (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* 5.5 2.9 - - + -
178B CYS* 5.7 3.1 - - - -
228B PRO* 3.7 28.7 - - + +
231B ILE* 4.0 22.2 - - + -
232B ALA* 4.0 1.4 - - - +
254B ALA 2.9 14.5 + - - +
255B SER* 3.3 13.7 - - - +
257B GLN* 1.3 76.9 - - - +
259B GLY* 1.3 56.6 + - - +
261B TYR* 3.3 2.2 + - - +
262B ALA* 2.8 33.0 + - - +
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Residues in contact with GLY 259 (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* 4.9 2.5 - - - -
178B CYS* 5.1 0.6 - - - -
246B THR* 3.9 25.4 - - - -
248B GLU* 6.1 0.2 - - - -
255B SER 2.8 14.0 + - - -
256B ILE 3.1 4.4 + - - -
258B ALA* 1.3 77.4 - - - +
260B ILE* 1.3 60.2 + - - +
262B ALA* 4.6 1.8 - - - -
263B THR* 2.7 32.3 + - - -
269B LEU* 4.2 9.9 - - - -
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Residues in contact with ILE 260 (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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256B ILE* 3.0 22.3 + - + +
257B GLN 3.1 6.7 + - - +
259B GLY* 1.3 79.3 - - - +
261B TYR* 1.3 53.5 + - - +
262B ALA 3.4 0.2 + - - -
263B THR* 3.8 3.4 + - - -
269B LEU* 3.6 16.8 - - + -
281B VAL* 3.8 35.0 - - + -
282B PRO* 3.6 32.3 - - + +
283B LEU 4.7 0.2 - - - +
285B HIS* 3.9 5.4 - - + -
286B ALA* 3.5 33.0 - - + +
289B ARG* 2.7 31.4 + - - -
291B VAL* 4.8 3.7 - - - +
293B ILE* 4.5 12.6 - - + -
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Residues in contact with TYR 261 (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* 4.0 9.2 - - + -
229B GLN* 3.5 54.9 + - + -
232B ALA* 3.6 20.1 - - + +
242B LYS* 3.3 21.8 - - - -
257B GLN* 3.0 27.1 + - + +
258B ALA 3.8 1.1 - - - +
260B ILE* 1.3 77.1 - - - +
262B ALA* 1.3 58.1 + - - +
282B PRO* 3.6 33.3 - - + +
285B HIS* 3.5 36.5 + + + -
289B ARG* 3.9 3.3 + - - -
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Residues in contact with ALA 262 (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* 4.1 23.3 - - + -
231B ILE* 6.4 0.2 - - + -
232B ALA* 3.6 25.5 - - + +
235B VAL* 4.8 4.3 - - + -
236B GLU* 6.4 0.2 - - + -
242B LYS* 3.1 22.6 - - - +
243B PRO* 3.3 16.7 - - + +
258B ALA 2.8 18.4 + - - +
259B GLY 4.1 0.9 - - - +
261B TYR* 1.3 78.9 - - - +
263B THR* 1.3 64.4 + - - +
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Residues in contact with THR 263 (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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242B LYS* 3.7 1.1 - - - +
243B PRO* 3.5 13.5 - - - +
244B GLU 3.8 5.4 - - - +
246B THR* 2.8 22.8 + - - +
259B GLY 2.7 21.7 + - - -
260B ILE 3.8 0.6 + - - -
261B TYR 3.6 0.6 - - - -
262B ALA* 1.3 77.4 - - - +
264B ARG* 1.3 73.9 + - - +
268B THR 3.7 30.1 + - - +
269B LEU* 4.5 2.9 - - - +
289B ARG* 2.8 32.6 + - - -
291B VAL* 3.8 18.6 - - + +
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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