Contacts of the helix formed by residues 224 - 237 (chain B) in PDB entry 4WFH
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 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASP* 5.4 3.1 + - - -
218B CYS* 4.2 2.0 - - - -
223B TRP* 1.3 76.1 - - - +
225B LYS* 1.3 68.0 + - - +
226B LEU* 3.5 8.8 + - - +
227B GLU* 2.7 41.0 + - - +
228B ALA* 2.9 21.7 + - - +
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Residues in contact with LYS 225 (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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214B THR* 5.1 2.0 - - - -
215B PHE* 6.5 0.9 - - + -
218B CYS* 3.9 19.1 - - - -
224B SER* 1.3 72.0 - - - +
226B LEU* 1.3 79.6 + - + +
228B ALA* 3.0 6.5 + - - +
229B ILE* 3.0 34.9 + - + +
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Residues in contact with LEU 226 (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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140A ASP* 3.9 50.9 - - + +
143A ARG* 3.9 20.6 - - + -
144A LEU* 4.4 26.0 - - + +
147A ILE* 5.1 3.6 - - + +
224B SER* 3.1 8.1 + - - +
225B LYS* 1.3 86.4 - - + +
227B GLU* 1.3 64.4 + - + +
229B ILE* 4.1 8.2 - - - +
230B TYR* 3.0 25.6 + - + +
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Residues in contact with GLU 227 (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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140A ASP* 5.1 4.7 - - - +
143A ARG* 4.7 13.4 + - - +
222B ASP 4.7 0.7 - - - +
223B TRP* 3.5 13.4 - - + -
224B SER* 2.7 46.6 + - - +
226B LEU* 1.3 78.4 - - + +
228B ALA* 1.3 57.4 + - - +
230B TYR* 3.3 9.9 - - - +
231B PHE* 2.8 29.9 + - - +
244B TYR* 2.5 46.9 + - + +
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Residues in contact with ALA 228 (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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214B THR* 3.4 33.2 - - - +
217B PHE* 4.3 5.8 - - + -
218B CYS* 4.2 10.3 - - - +
223B TRP* 4.1 13.4 - - + +
224B SER 2.9 12.8 + - - +
225B LYS* 3.4 10.5 - - - +
227B GLU* 1.3 74.9 - - - +
229B ILE* 1.3 60.3 + - - +
231B PHE* 3.2 3.6 + - - +
232B VAL* 2.8 32.4 + - - +
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Residues in contact with ILE 229 (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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147A ILE* 4.2 16.4 - - + -
210B VAL* 5.2 7.9 - - + -
214B THR* 3.4 29.2 - - + +
225B LYS* 3.0 28.0 + - + +
226B LEU* 4.1 5.8 - - - +
228B ALA* 1.3 71.5 - - - +
230B TYR* 1.3 67.1 + - - +
232B VAL* 3.2 0.7 + - - +
233B ILE* 2.9 39.8 + - + +
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Residues in contact with TYR 230 (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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137A LEU* 3.7 15.3 + - + +
143A ARG* 3.5 56.1 - - + -
146A CYS* 4.4 6.5 - - - -
147A ILE* 4.1 16.4 - - + +
226B LEU 3.0 19.5 + - - +
227B GLU* 3.3 7.0 - - - +
229B ILE* 1.3 76.4 - - - +
231B PHE* 1.3 59.7 + - - +
233B ILE* 3.9 0.7 - - - +
234B VAL* 2.8 57.5 + - + +
241B PHE* 3.0 20.8 - - - -
243B ASP* 2.8 38.8 + - - -
244B TYR* 3.8 18.8 - + + -
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Residues in contact with PHE 231 (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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132B TYR* 3.2 31.4 - + - -
217B PHE* 3.8 31.6 - + - -
223B TRP* 3.4 22.9 - + + -
227B GLU 2.8 14.4 + - - +
228B ALA 3.4 7.2 - - - +
229B ILE 3.2 0.2 - - - -
230B TYR* 1.3 79.2 - - - +
232B VAL* 1.3 64.4 + - - +
233B ILE 3.2 0.2 + - - -
234B VAL* 3.7 5.0 - - + +
235B THR* 2.5 37.5 + - - -
244B TYR* 3.2 38.1 - - + -
245B VAL* 3.8 6.5 - - - -
246B ALA* 3.6 27.4 - - + -
261B VAL* 5.6 1.3 - - + -
264B TRP* 4.3 10.5 - + - -
265B ILE* 6.1 0.7 - - + -
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Residues in contact with VAL 232 (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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210B VAL* 4.3 22.7 - - + -
213B PRO* 4.0 13.5 - - + -
214B THR* 3.5 20.9 - - + +
217B PHE* 4.2 8.5 - - + -
228B ALA 2.8 19.9 + - - +
229B ILE* 3.5 8.1 - - - +
231B PHE* 1.3 76.6 - - - +
233B ILE* 1.3 69.2 + - + +
235B THR* 3.1 3.5 + - - -
236B LEU* 2.9 45.9 + - + +
264B TRP* 4.0 22.7 - - + -
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Residues in contact with ILE 233 (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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147A ILE* 3.6 44.4 - - + +
150A ALA* 5.6 2.7 - - + -
151A LEU* 4.4 20.0 - - + -
210B VAL* 5.2 8.7 - - + -
229B ILE* 2.9 32.5 + - + +
230B TYR 4.1 1.3 - - - +
232B VAL* 1.3 79.3 - - + +
234B VAL* 1.3 58.6 + - + +
235B THR 2.9 5.4 + - - -
236B LEU* 4.3 3.1 - - - +
237B THR* 2.5 50.2 + - + +
272B PHE* 5.1 12.3 - - + -
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A CYS* 5.3 3.8 - - - -
147A ILE* 6.0 1.1 - - + -
132B TYR* 5.4 2.9 - - + -
230B TYR* 2.8 62.7 + - + +
231B PHE* 3.7 6.5 - - + +
233B ILE* 1.3 75.0 - - + +
235B THR* 1.3 58.7 + - - +
237B THR* 3.1 14.3 + - - -
239B VAL* 3.1 10.4 + - + -
240B GLY* 3.0 20.1 + - - +
241B PHE* 3.5 46.4 - - + +
242B GLY 5.2 0.7 - - - +
243B ASP* 5.2 2.0 - - - +
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Residues in contact with THR 235 (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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130B ILE* 3.8 24.4 - - + +
132B TYR* 2.7 36.6 + - + +
231B PHE* 2.5 30.2 + - - -
232B VAL* 3.2 10.5 - - - -
233B ILE 2.9 0.4 - - - -
234B VAL* 1.3 78.4 - - - +
236B LEU* 1.3 63.0 + - + +
237B THR 3.2 0.2 - - - -
238B THR* 2.8 21.8 + - - +
240B GLY 5.0 0.9 - - - +
264B TRP* 4.3 13.5 - - + -
265B ILE* 4.3 14.8 - - + -
269B LEU* 4.4 1.0 - - - +
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Residues in contact with LEU 236 (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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209B PHE* 3.8 26.0 - - + +
210B VAL* 4.7 2.9 - - + -
232B VAL* 2.9 26.3 + - + +
233B ILE* 3.2 2.4 + - - +
235B THR* 1.3 81.2 - - + +
237B THR* 1.3 59.0 + - - +
238B THR* 3.1 2.4 + - - +
264B TRP* 3.9 23.1 - - + -
265B ILE* 4.5 9.0 - - + +
268B GLY* 4.1 31.0 - - - +
269B LEU* 3.4 24.3 - - + +
272B PHE* 3.8 48.1 - - + +
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Residues in contact with THR 237 (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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129A THR* 3.8 13.9 - - - +
150A ALA* 4.9 4.7 - - + +
151A LEU* 4.8 7.4 - - + -
154A ILE* 3.8 20.4 - - + +
233B ILE* 2.5 38.7 + - + +
234B VAL* 3.1 12.6 + - - -
236B LEU* 1.3 75.5 - - - +
238B THR* 1.3 74.5 + - - +
239B VAL* 3.2 19.5 + - + +
272B PHE* 4.3 19.3 - - + -
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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