Contacts of the helix formed by residues 233 - 249 (chain e) in PDB entry 5JPQ
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 233 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232e LEU* 1.3 78.1 - - - +
234e ALA* 1.3 67.0 + - - +
235e SER* 3.2 6.3 - - - -
236e VAL* 3.2 8.4 + - - +
237e ALA* 3.0 20.4 + - - +
101f ASP* 4.5 22.0 + - - +
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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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91e ILE* 5.3 10.8 - - + +
95e CYS* 5.4 6.2 - - + +
206e VAL* 5.2 9.2 - - + +
207e GLY 3.5 26.5 - - - +
208e ALA* 4.3 12.6 - - + -
209e MET 4.9 6.3 + - - +
232e LEU 4.0 0.4 + - - -
233e SER* 1.3 74.6 - - - +
235e SER* 1.3 61.6 + - - +
237e ALA* 3.3 10.1 + - - +
238e CYS* 3.1 19.4 + - - +
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Residues in contact with SER 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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91e ILE 5.5 0.4 - - - -
94e GLN* 4.5 10.8 - - - -
95e CYS* 4.4 18.8 - - - +
98e THR* 4.4 20.2 - - - -
233e SER* 3.2 4.1 - - - -
234e ALA* 1.3 75.5 - - - +
236e VAL* 1.3 62.7 + - - +
238e CYS* 2.9 24.1 + - - +
239e SER* 3.0 13.5 + - - -
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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
----------------------------------------------------------
232e LEU* 4.3 6.1 - - + -
233e SER* 3.2 20.5 + - - +
235e SER* 1.3 76.0 - - - +
237e ALA* 1.3 64.5 + - - +
238e CYS 3.2 0.2 + - - -
239e SER* 3.2 9.7 + - - -
240e LYS* 3.0 22.9 + - - +
98f THR* 5.6 3.4 - - - +
101f ASP* 4.3 26.9 - - + +
102f SER* 5.3 3.4 - - - +
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Residues in contact with ALA 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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180e LEU* 5.4 12.6 - - + -
206e VAL* 5.6 7.0 - - + -
227e LEU* 5.5 8.6 - - + +
232e LEU* 4.3 12.0 - - + +
233e SER 3.0 13.3 + - - +
234e ALA* 3.4 12.1 - - - +
236e VAL* 1.3 76.2 - - - +
238e CYS* 1.3 62.4 + - - +
240e LYS* 3.4 9.0 - - - +
241e PHE* 3.2 21.1 + - - +
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Residues in contact with CYS 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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95e CYS* 5.3 9.9 - - + +
98e THR* 4.9 10.5 - - - -
99e LEU* 5.6 7.0 - - + -
234e ALA 3.1 11.3 + - - +
235e SER* 2.9 17.0 + - - +
237e ALA* 1.3 74.7 - - - +
239e SER* 1.3 64.3 + - - +
241e PHE* 3.2 5.6 + - - +
242e CYS* 2.9 25.0 + - - +
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Residues in contact with SER 239 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98e THR* 5.5 7.5 - - - -
235e SER 3.0 10.7 + - - -
236e VAL* 3.2 12.3 + - - -
238e CYS* 1.3 75.9 - - - +
240e LYS* 1.3 67.0 + - - +
242e CYS* 3.1 6.3 + - - +
243e HIS* 2.7 29.5 + - - +
239f SER* 3.7 29.2 - - - -
243f HIS* 6.4 0.9 - - - -
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Residues in contact with LYS 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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189e VAL* 4.2 5.2 - - - +
227e LEU* 4.5 19.7 - - + +
236e VAL 3.0 10.1 + - - +
237e ALA* 3.4 14.8 - - - +
239e SER* 1.3 77.9 - - - +
241e PHE* 1.3 57.8 + - - +
243e HIS* 3.9 3.0 - - - +
244e GLY* 2.9 27.7 + - - -
243f HIS* 6.1 2.9 - - - -
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Residues in contact with PHE 241 (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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189e VAL* 4.6 11.9 - - + +
204e VAL* 5.9 7.4 - - + -
237e ALA 3.2 8.4 + - - +
238e CYS* 3.2 8.7 + - - +
240e LYS* 1.3 77.4 - - - +
242e CYS* 1.3 69.4 + - - +
243e HIS 3.1 0.3 + - - -
244e GLY* 3.7 0.3 - - - -
245e ALA* 2.9 26.8 + - - +
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Residues in contact with CYS 242 (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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98e THR 5.7 1.8 - - - +
99e LEU* 6.3 1.3 - - - -
102e SER* 4.4 22.4 - - - -
104e ILE* 5.0 10.2 - - + +
238e CYS 2.9 13.2 + - - +
239e SER* 3.4 11.0 - - - +
241e PHE* 1.3 76.3 - - - +
243e HIS* 1.3 53.0 + - + +
245e ALA* 3.2 5.0 + - - +
246e GLU* 2.7 37.6 + - - +
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Residues in contact with HIS 243 (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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239e SER* 2.7 22.4 + - - +
240e LYS* 4.1 2.2 - - - +
242e CYS* 1.3 73.3 - - + +
244e GLY* 1.3 64.0 + - - +
246e GLU* 3.1 8.6 + - - +
247e ASP* 2.9 24.2 + - - +
239f SER* 6.0 1.1 - - - -
240f LYS* 5.4 6.7 - - - -
243f HIS* 4.2 25.1 - - + -
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Residues in contact with GLY 244 (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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189e VAL* 3.9 16.2 - - - -
190e GLN* 3.7 16.4 - - - -
240e LYS 2.9 17.6 + - - -
241e PHE 3.7 0.7 - - - -
243e HIS* 1.3 75.2 - - - +
245e ALA* 1.3 56.2 + - - +
247e ASP* 3.3 7.7 - - - +
248e ALA* 2.9 25.8 + - - +
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Residues in contact with ALA 245 (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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41e MET* 5.5 11.7 - - + -
104e ILE* 6.1 2.2 - - + -
189e VAL* 4.9 1.0 - - + +
193e ILE* 4.8 11.0 - - + -
241e PHE 2.9 18.2 + - - +
242e CYS* 3.7 3.4 - - - +
244e GLY* 1.3 74.1 - - - +
246e GLU* 1.3 61.2 + - - +
248e ALA* 3.6 8.4 - - - +
249e TRP* 2.8 32.9 + - - +
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Residues in contact with GLU 246 (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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103e PRO* 5.2 9.4 - - + -
104e ILE* 5.1 12.2 - - + +
242e CYS 2.7 20.9 + - - +
243e HIS* 3.4 9.9 - - - +
245e ALA* 1.3 72.2 - - - +
247e ASP* 1.3 56.5 + - - +
249e TRP* 3.1 2.6 + - - -
250e ASN 2.9 10.2 + - - -
251e ILE* 2.9 53.3 + - + +
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Residues in contact with ASP 247 (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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190e GLN* 4.8 8.7 - - + -
243e HIS 2.9 11.9 + - - +
244e GLY* 3.3 13.0 - - - +
246e GLU* 1.3 76.0 - - - +
248e ALA* 1.3 63.3 + - - +
249e TRP 3.2 0.5 + - - -
250e ASN* 3.3 11.1 + - - -
251e ILE 4.1 3.5 + - - +
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Residues in contact with ALA 248 (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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190e GLN* 4.0 14.5 - - - +
193e ILE* 3.6 32.3 - - + -
194e GLU* 4.8 5.6 - - + +
244e GLY 2.9 16.4 + - - +
245e ALA 3.3 5.8 + - - +
247e ASP* 1.3 76.7 - - - +
249e TRP* 1.3 59.3 + - + +
250e ASN* 3.3 1.8 + - - +
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Residues in contact with TRP 249 (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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109e LYS* 6.5 1.1 - - + -
245e ALA 2.8 18.0 + - - +
246e GLU* 4.1 2.9 - - - +
248e ALA* 1.3 76.7 - - + +
250e ASN* 1.3 72.0 + - - +
251e ILE* 3.3 6.8 + - + +
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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