Contacts of the helix formed by residues 227 - 240 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D LYS 3.7 1.2 + - - -
226D GLU* 1.3 74.1 - - - +
228D PRO* 1.3 75.4 - - - +
229D GLN* 3.6 12.0 + - - +
230D GLU* 2.7 39.2 + - - +
231D ILE* 2.9 25.3 + - - +
233D ARG* 4.5 1.0 + - - -
254D ALA* 6.2 0.2 - - - -
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Residues in contact with PRO 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D GLU 4.7 0.4 - - - +
227D SER* 1.3 88.5 - - - +
229D GLN* 1.3 65.4 + - - +
231D ILE* 3.2 5.1 + - + +
232D ALA* 2.9 29.1 + - - +
254D ALA* 3.6 22.7 - - + +
257D GLN* 3.1 42.2 - - + +
258D ALA* 3.6 20.4 - - + +
261D TYR* 3.8 9.2 - - + -
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Residues in contact with GLN 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D SER* 3.6 9.6 + - - +
228D PRO* 1.3 90.2 - - - +
230D GLU* 1.3 58.1 + - - +
232D ALA* 3.4 5.3 + - - +
233D ARG* 2.8 56.5 + - - +
261D TYR* 3.6 42.8 + - + -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A SER* 4.1 24.5 + - - +
225A LYS* 3.5 37.2 - - - +
225D LYS 4.7 0.3 - - - +
226D GLU* 3.2 18.0 - - + +
227D SER* 2.7 46.9 + - - +
229D GLN* 1.3 74.5 - - - +
231D ILE* 1.3 60.3 + - - +
233D ARG* 3.3 26.1 + - - +
234D LYS* 2.9 35.3 + - - +
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Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 6.0 2.2 - - + -
178D CYS* 6.4 1.3 - - - -
202D THR* 4.9 6.7 - - + -
221D LEU* 5.1 1.3 - - + -
223D ILE* 3.2 45.1 - - + -
226D GLU* 3.3 33.9 - - + +
227D SER 2.9 21.4 + - - +
228D PRO* 3.2 8.9 + - + +
230D GLU* 1.3 76.0 - - - +
232D ALA* 1.3 65.1 + - - +
234D LYS* 3.1 8.8 + - + +
235D VAL* 2.9 40.1 + - + +
254D ALA 5.9 0.2 - - - +
258D ALA* 3.9 18.2 - - + -
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D PRO 2.9 16.3 + - - +
229D GLN* 3.5 4.9 - - - +
231D ILE* 1.3 77.6 - - - +
233D ARG* 1.3 62.4 + - + +
235D VAL* 3.4 2.4 + - - +
236D GLU* 3.0 25.6 + - - +
258D ALA* 3.9 1.3 - - - +
261D TYR* 3.5 30.5 - - + +
262D ALA* 3.5 29.8 - - + +
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Residues in contact with ARG 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLN* 3.9 11.3 + - - +
224A SER* 6.2 0.8 - - - -
227D SER* 4.5 1.0 + - - -
229D GLN* 2.8 35.3 + - - +
230D GLU* 3.4 38.7 + - - +
232D ALA* 1.3 76.3 - - - +
234D LYS* 1.3 58.0 + - + +
236D GLU* 3.4 9.2 + - - +
237D GLY* 2.8 26.7 + - - -
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Residues in contact with LYS 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLN* 3.2 42.9 + - + +
223A ILE 4.1 0.6 - - - -
224A SER* 2.7 39.3 + - - +
226A GLU* 3.1 22.8 + - - -
234A LYS* 5.4 0.9 - - - +
221D LEU* 3.8 27.8 - - + -
223D ILE* 6.1 0.4 - - + -
226D GLU* 3.9 21.9 - - + +
230D GLU* 2.9 21.5 + - - +
231D ILE* 3.5 7.4 - - + +
233D ARG* 1.3 74.8 - - + +
235D VAL* 1.3 66.0 + - - +
237D GLY* 3.1 1.4 + - - -
238D GLN* 2.9 26.9 + - + +
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Residues in contact with VAL 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 4.0 42.6 - - + -
200D VAL* 4.7 6.5 - - + -
202D THR* 4.7 1.3 - - + -
221D LEU* 3.7 16.4 - - + -
231D ILE* 2.9 31.1 + - + +
232D ALA* 3.7 7.0 - - - +
234D LYS* 1.3 74.8 - - - +
236D GLU* 1.3 63.3 + - - +
238D GLN* 3.1 12.5 + - - +
239D LEU* 3.0 40.3 + - + +
243D PRO* 4.3 10.5 - - + -
262D ALA* 4.8 1.8 - - + -
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Residues in contact with GLU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ALA 3.0 17.4 + - - +
233D ARG* 3.7 7.8 - - - +
235D VAL* 1.3 77.5 - - - +
237D GLY* 1.3 56.5 + - - +
240D GLY* 2.7 33.7 + - - -
241D CYS* 3.4 29.0 + - - +
242D LYS* 2.8 45.1 + - + +
243D PRO* 5.5 0.9 - - + +
262D ALA* 5.9 0.9 - - - +
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Residues in contact with GLY 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ALA* 3.5 37.5 - - - +
210A SER* 5.5 3.8 - - - -
222A GLN* 4.0 2.9 - - - -
233D ARG 2.8 15.6 + - - -
234D LYS 3.1 4.9 + - - -
236D GLU* 1.3 79.9 - - - +
238D GLN* 1.3 60.1 + - - +
240D GLY* 3.7 6.6 + - - -
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Residues in contact with GLN 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LYS* 5.9 0.5 + - - -
220A VAL* 5.5 10.6 + - + +
198D GLN* 5.3 1.9 + - - -
200D VAL* 3.4 18.1 - - - +
219D LEU* 3.9 34.0 - - + +
220D VAL 3.1 30.7 + - - +
221D LEU* 2.9 39.3 - - + +
234D LYS* 2.9 13.4 + - + +
235D VAL* 3.1 6.9 + - - +
237D GLY* 1.3 78.7 - - - +
239D LEU* 1.3 61.0 + - + +
240D GLY 3.7 0.2 + - - -
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D LYS* 4.1 19.5 + - + -
175D VAL 5.3 0.2 - - - +
176D LEU 5.8 0.2 - - - +
198D GLN* 4.1 33.5 + - + +
200D VAL* 3.4 35.9 - - + -
219D LEU* 3.7 11.9 - - + -
235D VAL* 3.0 16.0 + - + +
238D GLN* 1.3 77.4 - - - +
240D GLY* 1.3 59.0 + - - +
241D CYS* 3.0 29.4 + - - +
243D PRO* 3.8 40.6 - - + -
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Residues in contact with GLY 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D GLU* 2.7 17.0 + - - -
237D GLY 3.7 5.3 + - - -
238D GLN 3.4 3.2 + - - -
239D LEU* 1.3 73.9 - - - +
241D CYS* 1.3 62.9 + - - +
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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