Contacts of the helix formed by residues 229 - 240 (chain E) in PDB entry 2PGW
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 229 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254D TYR* 4.5 9.6 - - - -
257D TYR* 6.0 0.5 - - - -
223E GLN* 5.7 0.3 + - - -
225E THR* 4.7 0.3 + - - -
226E VAL* 3.5 14.5 + - - +
227E SER* 3.2 4.6 - - - +
228E TRP* 1.3 77.9 - - - +
230E ILE* 1.3 62.9 + - - +
231E PRO* 3.7 9.2 - - - +
232E ALA* 3.0 33.2 + - - +
233E MSE 3.3 17.2 + - - +
249E ALA* 5.7 0.9 - - - +
290H ALA 4.6 2.3 + - - -
291H ALA* 3.9 9.3 + - - -
292H GLY* 4.2 15.7 - - - -
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Residues in contact with ILE 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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227E SER 5.0 2.2 - - - +
228E TRP 3.9 4.5 + - - +
229E SER* 1.3 70.1 - - - +
231E PRO* 1.3 75.5 - - + +
233E MSE 3.1 9.6 + - + +
234E ALA* 3.0 20.3 + - - +
249E ALA* 4.5 20.2 - - + +
255E ASP* 4.1 10.5 - - + +
258E GLU* 3.7 27.4 - - + -
259E ILE* 3.8 24.7 - - + -
262E GLN* 3.7 21.3 - - - +
264E ALA* 3.4 24.9 - - + -
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Residues in contact with PRO 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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257D TYR* 5.3 3.1 - - + -
258D GLU* 3.5 28.3 - - - +
261D ARG* 3.7 18.2 - - - +
229E SER* 3.6 9.4 - - - +
230E ILE* 1.3 95.2 - - + +
232E ALA* 1.3 55.2 + - - +
234E ALA* 3.2 6.2 + - + +
235E HIS* 2.9 29.4 + - - +
262E GLN* 3.6 18.6 - - - +
263H ARG* 4.0 25.5 + - - +
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Residues in contact with ALA 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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203E VAL* 4.4 6.5 - - + +
225E THR* 4.1 11.0 - - - +
226E VAL* 5.4 1.6 - - + +
229E SER* 3.0 29.7 + - - +
231E PRO* 1.3 77.3 - - - +
233E MSE 1.3 61.7 + - - +
235E HIS* 3.2 3.9 - - - +
236E VAL* 3.1 27.2 + - - +
263H ARG* 3.6 22.1 - - - +
291H ALA 4.1 4.3 - - - +
292H GLY* 4.2 12.6 - - - +
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Residues in contact with MSE 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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223E GLN* 3.9 20.6 - - - +
224E PRO* 5.3 1.8 - - + -
225E THR* 3.6 17.4 + - - +
229E SER 3.3 7.8 + - - +
230E ILE* 3.1 10.4 + - + +
232E ALA* 1.3 77.3 - - - +
234E ALA* 1.3 59.9 + - - +
236E VAL* 3.2 5.3 + - - +
237E ARG* 2.9 27.2 + - - +
244E ILE* 4.2 16.9 - - + +
245E VAL 4.9 0.2 - - - +
246E ALA* 3.5 42.6 - - + -
249E ALA* 3.7 16.6 - - + -
259E ILE* 4.0 10.8 - - + -
264E ALA* 3.3 34.8 - - + +
265E ALA* 4.5 0.9 - - - -
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Residues in contact with ALA 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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230E ILE 3.0 11.1 + - - +
231E PRO* 3.6 10.5 - - + +
233E MSE 1.3 76.4 - - - +
235E HIS* 1.3 64.0 + - - +
237E ARG* 3.2 3.1 + - - +
238E GLU* 2.9 44.4 + - - +
262E GLN* 4.3 12.6 - - + +
263E ARG 4.6 1.3 - - - +
264E ALA* 3.7 28.2 + - + +
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Residues in contact with HIS 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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203E VAL* 3.7 16.7 - - + +
207E ILE* 4.9 0.4 - - + -
231E PRO 2.9 14.6 + - - +
232E ALA* 3.2 13.7 - - - +
234E ALA* 1.3 78.1 - - - +
236E VAL* 1.3 64.0 + - - +
238E GLU* 3.6 6.6 + - - +
239E LYS* 3.5 18.1 + - + +
237H ARG* 3.2 32.6 + - - +
263H ARG* 3.0 42.1 + - + +
265H ALA 3.4 25.8 - - - -
266H ASP* 2.8 23.6 + - - -
293H LEU* 4.5 0.9 - - + -
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Residues in contact with VAL 236 (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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203E VAL* 4.0 25.6 - - + +
206E ALA* 3.9 19.5 - - + +
207E ILE* 4.5 4.7 - - + -
210E CYS* 5.2 0.4 - - - -
224E PRO* 4.4 14.6 - - + -
225E THR* 3.5 24.9 - - + -
232E ALA 3.1 14.6 + - - +
233E MSE 3.7 5.8 - - - +
235E HIS* 1.3 76.6 - - - +
237E ARG* 1.3 66.6 + - - +
239E LYS* 3.0 15.5 + - - +
240E VAL* 3.0 33.1 + - + +
244E ILE* 4.8 2.5 - - + -
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Residues in contact with ARG 237 (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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235A HIS* 3.2 33.9 + - - +
238A GLU* 5.7 3.0 + - - -
239A LYS* 2.8 46.6 + - - +
233E MSE 2.9 16.3 + - - +
234E ALA 3.6 3.1 + - - +
236E VAL* 1.3 78.5 - - - +
238E GLU* 1.3 82.7 + - - +
239E LYS 3.1 0.7 + - - -
240E VAL* 3.5 6.1 - - - +
242E ILE 5.3 1.0 - - - +
244E ILE* 3.9 21.7 - - + +
263E ARG* 2.7 36.2 + - - +
264E ALA 3.8 4.3 - - - +
265E ALA* 3.8 22.4 - - - +
266E ASP* 3.6 30.1 + - - +
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Residues in contact with GLU 238 (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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238A GLU* 6.0 2.7 - - - +
239A LYS* 3.0 16.9 + - - +
234E ALA* 2.9 34.1 + - - +
235E HIS* 4.0 6.7 - - - +
237E ARG* 1.3 98.3 + - - +
239E LYS* 1.3 62.7 + - + +
262E GLN 4.9 4.0 - - - +
263E ARG* 6.1 0.2 - - - +
237H ARG* 6.0 0.8 + - - +
238H GLU* 4.6 11.3 - - - +
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Residues in contact with LYS 239 (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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239A LYS* 3.9 1.3 + - - -
207E ILE* 4.1 31.7 - - + +
235E HIS 3.5 11.0 + - - +
236E VAL 3.0 8.5 + - - +
238E GLU* 1.3 85.4 - - + +
240E VAL* 1.3 62.4 - - - +
241E GLY 4.1 0.3 + - - -
237H ARG* 2.9 47.5 + - - +
238H GLU* 3.1 25.1 + - + +
239H LYS 4.0 1.6 + - - -
240H VAL 2.6 31.1 + - - +
241H GLY* 4.9 4.5 - - - -
242H ILE 6.4 0.4 - - - -
266H ASP* 6.1 0.2 - - - -
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Residues in contact with VAL 240 (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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239A LYS* 2.8 28.4 + - - -
207E ILE* 3.7 28.5 - - + +
210E CYS* 3.5 33.4 - - + -
236E VAL* 3.0 21.5 + - + +
237E ARG 3.5 2.8 - - - +
239E LYS* 1.3 79.5 - - - +
241E GLY* 1.3 61.2 + - - +
242E ILE 3.5 19.9 + - - +
244E ILE* 3.9 22.9 - - + -
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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