Contacts of the helix formed by residues 236 - 248 (chain E) in PDB entry 4O9U
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 ARG 236 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232E GLU 5.2 11.7 + - - +
233E GLU* 5.4 7.6 + - - -
234E GLU 3.0 3.1 - - - +
235E LYS* 1.3 77.4 - - - +
237E ILE* 1.3 76.0 + - + +
238E GLN 3.3 1.3 - - - -
239E HIS* 3.1 8.0 + - + +
240E GLU* 2.5 75.6 + - + +
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Residues in contact with ILE 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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216E LEU* 5.2 0.3 - - - +
217E PRO* 4.2 30.7 - - + +
218E ILE* 4.8 15.5 - - + -
233E GLU* 3.9 25.4 - - - +
234E GLU* 3.4 7.0 + - + +
236E ARG* 1.3 95.1 - - + +
238E GLN* 1.3 64.1 + - - +
239E HIS 3.1 1.3 - - - -
240E GLU* 4.1 7.9 - - + +
241E ALA* 3.1 29.9 + - + +
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Residues in contact with GLN 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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196E TYR* 4.7 8.1 + - - +
198E VAL* 5.3 1.8 - - - +
216E LEU* 3.1 34.8 - - + +
218E ILE* 3.0 41.5 + - + +
220E ALA* 3.8 21.0 - - - +
230E LEU* 3.6 24.2 - - + +
234E GLU 3.1 21.0 + - - +
235E LYS* 4.0 10.3 - - + +
237E ILE* 1.3 76.2 - - - +
239E HIS* 1.3 50.6 + - - +
242E LEU* 2.5 42.1 + - + +
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Residues in contact with HIS 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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235E LYS 3.2 15.3 + - - +
236E ARG* 3.1 13.6 + - + +
238E GLN* 1.3 79.9 - - - +
240E GLU* 1.3 54.4 + - + +
242E LEU* 4.4 2.0 - - - +
243E ARG* 2.7 44.4 + - - +
268E THR* 2.9 39.7 + - + +
270E ASP* 2.7 29.7 + - - -
271E MET* 3.1 27.6 - - + +
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Residues in contact with GLU 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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236E ARG* 2.5 55.4 + - + +
237E ILE* 4.2 8.1 - - + +
239E HIS* 1.3 70.3 - - + +
241E ALA* 1.3 59.9 + - - +
242E LEU 3.1 1.1 - - - -
243E ARG* 3.0 33.0 + - - +
244E ASP* 2.9 35.9 + - - +
274E ARG* 5.9 0.6 + - - +
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Residues in contact with ALA 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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216E LEU* 4.0 9.9 - - + -
217E PRO* 3.9 27.8 - - + -
237E ILE* 3.1 16.9 + - + +
240E GLU* 1.3 78.5 - - - +
242E LEU* 1.3 56.2 + - - +
243E ARG 3.2 0.2 - - - -
244E ASP* 3.9 6.7 - - - +
245E HIS* 3.1 41.6 + - + +
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Residues in contact with LEU 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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171E MET* 5.6 2.7 - - + -
173E MET* 4.4 12.1 - - + -
196E TYR* 3.7 54.5 - - + +
214E ILE* 5.5 1.8 - - + -
216E LEU* 4.0 9.1 - - + +
238E GLN* 2.5 35.6 + - + +
239E HIS* 3.3 6.7 - - - +
240E GLU 3.1 0.4 - - - -
241E ALA* 1.3 78.6 - - - +
243E ARG* 1.3 56.1 + - - +
245E HIS* 4.4 2.7 - - + -
246E VAL* 2.9 34.3 - - + +
266E LEU* 4.5 13.9 - - + +
271E MET* 3.6 22.8 - - + +
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Residues in contact with ARG 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 HIS* 2.7 25.3 + - - +
240E GLU* 3.0 33.2 + - - +
242E LEU* 1.3 76.7 - - - +
244E ASP* 1.3 59.8 + - - +
246E VAL* 4.1 3.1 - - - +
247E ALA* 3.2 24.6 + - - +
270E ASP* 2.6 59.4 + - - +
271E MET* 3.7 24.3 - - + +
274E ARG* 3.1 40.9 - - + +
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Residues in contact with ASP 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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240E GLU* 2.9 18.2 + - - +
241E ALA* 3.7 7.7 + - - +
243E ARG* 1.3 78.2 - - - +
245E HIS* 1.3 64.7 + - + +
247E ALA* 3.4 16.7 + - - +
248E GLY 3.8 3.6 + - - -
274E ARG* 4.0 18.1 + - - -
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Residues in contact with HIS 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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171E MET* 3.8 14.1 - - + -
194E PHE* 5.7 4.0 - + - -
214E ILE* 4.5 24.3 - - + +
215E GLU 5.6 3.8 + - - -
216E LEU* 4.5 12.5 - - + -
217E PRO* 6.4 0.2 - - + -
241E ALA* 3.1 32.1 + - + +
242E LEU* 4.9 4.0 - - + +
244E ASP* 1.3 76.9 - - + +
246E VAL* 1.3 63.3 + - - +
247E ALA 3.5 0.3 + - - -
248E GLY* 3.7 5.2 + - - -
249E MET* 3.3 29.1 - - - +
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Residues in contact with VAL 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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171E MET* 3.6 23.6 - - + -
173E MET* 3.6 16.8 - - + -
242E LEU* 2.9 28.8 + - + +
243E ARG* 4.2 3.8 - - - +
244E ASP 3.4 0.4 - - - -
245E HIS* 1.3 74.8 - - + +
247E ALA* 1.3 65.0 + - - +
249E MET* 3.2 22.9 + - - +
252E LEU* 3.8 11.4 - - + -
267E LEU* 3.6 25.8 - - + -
271E MET* 4.8 6.1 - - + +
275E LEU* 3.4 24.6 - - + +
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Residues in contact with ALA 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E ARG 3.2 17.2 + - - +
244E ASP* 3.4 15.0 - - - +
245E HIS 3.3 0.2 - - - -
246E VAL* 1.3 76.6 - - - +
248E GLY* 1.3 57.1 + - - +
249E MET 3.3 5.4 + - - +
271E MET 5.8 0.4 - - - -
274E ARG* 3.6 40.4 - - - +
275E LEU* 4.6 2.3 - - - -
276E LYS* 3.7 26.5 + - - +
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Residues in contact with GLY 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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169E LYS* 4.2 15.1 - - - +
244E ASP 3.8 4.4 + - - -
245E HIS 3.7 5.4 + - - -
246E VAL 3.3 0.4 - - - -
247E ALA* 1.3 76.5 - - - +
249E MET* 1.3 74.0 + - - +
276E LYS* 4.8 9.2 - - - -
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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