Contacts of the helix formed by residues 215 - 229 (chain B) in PDB entry 1W6T
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 THR 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B PRO 4.3 0.8 + - - -
160B ILE* 3.7 21.2 - - - +
161B ALA 4.5 0.3 + - - -
162B PHE* 4.9 11.0 + - + -
165B PHE* 4.3 19.3 - - + -
214B GLY* 1.3 70.4 - - - -
216B GLU* 1.3 62.0 + - + +
218B GLY* 3.0 4.0 + - - -
219B VAL* 2.8 36.1 + - + +
241B PHE* 5.4 0.7 - - + -
262B GLU* 3.5 24.5 + - - -
277B TYR* 4.1 19.6 + - - +
281B LEU* 4.8 13.9 - - + -
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Residues in contact with GLU 216 (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 GLY 3.4 0.4 - - - -
215B THR* 1.3 81.3 - - + +
217B ASP* 1.3 53.6 + - - +
219B VAL* 4.4 2.9 - - - -
220B GLU* 2.8 49.1 + - - +
281B LEU* 5.1 6.7 - - + +
284B LYS* 3.4 26.8 + - - +
285B TYR* 3.2 27.0 + - + +
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Residues in contact with ASP 217 (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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196B ARG* 3.1 29.2 + - - -
212B PHE* 3.5 11.3 - - + -
213B GLU* 2.9 28.4 + - + +
214B GLY* 3.3 19.6 + - - +
216B GLU* 1.3 77.7 - - - +
218B GLY* 1.3 54.8 + - - +
220B GLU* 3.8 5.7 + - - +
221B THR* 2.6 41.6 + - - -
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Residues in contact with GLY 218 (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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150B ILE* 5.1 2.7 - - - -
160B ILE* 5.0 3.8 - - - -
165B PHE* 5.4 3.4 - - - -
212B PHE* 3.6 31.4 - - - -
214B GLY 3.0 8.6 + - - -
215B THR 3.0 7.3 + - - -
217B ASP* 1.3 75.5 - - - +
219B VAL* 1.3 61.1 + - - +
221B THR* 3.3 3.6 + - - -
222B ILE* 3.1 31.2 + - - +
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Residues in contact with VAL 219 (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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165B PHE* 3.8 26.4 - - + -
215B THR* 2.8 28.9 + - + +
216B GLU 3.8 3.1 - - - +
218B GLY* 1.3 70.3 - - - -
220B GLU* 1.3 58.5 + - - +
222B ILE* 3.0 12.8 + - + +
223B LEU* 2.9 28.2 + - + +
239B LEU* 3.9 19.2 - - + +
241B PHE* 4.1 14.8 - - + -
285B TYR* 3.6 46.7 - - + -
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Residues in contact with GLU 220 (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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216B GLU* 2.8 29.1 + - - +
217B ASP* 4.0 4.4 + - - +
219B VAL* 1.3 73.2 - - - +
221B THR* 1.3 57.4 + - - +
223B LEU* 3.6 11.3 - - + +
224B ALA* 2.9 29.1 + - - +
284B LYS* 3.9 12.8 + - - -
285B TYR* 2.9 36.7 + - + +
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Residues in contact with THR 221 (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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189B LEU* 3.6 22.8 - - + +
192B ILE* 4.3 10.7 - - + +
193B LEU* 4.7 2.5 - - + -
196B ARG* 2.9 30.2 + - - +
212B PHE* 3.5 22.4 - - + -
217B ASP* 2.6 27.4 + - - -
218B GLY 3.6 5.4 - - - -
219B VAL 3.2 0.2 - - - -
220B GLU* 1.3 75.1 - - - +
222B ILE* 1.3 59.5 + - - +
224B ALA* 3.4 8.1 + - - +
225B ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 222 (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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149B ILE* 4.0 15.7 - - + -
150B ILE* 3.8 22.9 - - + -
165B PHE* 3.6 33.2 - - + -
166B MET 5.3 0.7 - - - +
167B ILE* 3.6 30.7 - - + -
185B ILE* 5.5 0.2 - - + -
189B LEU* 4.9 3.8 - - + -
218B GLY 3.1 23.8 + - - +
219B VAL* 3.0 12.4 + - + +
221B THR* 1.3 73.9 - - - +
223B LEU* 1.3 59.0 + - - +
225B ALA* 3.0 8.3 + - - +
226B ILE* 2.9 29.2 + - + +
239B LEU* 3.6 20.2 - - + -
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Residues in contact with LEU 223 (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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219B VAL* 2.9 21.5 + - + +
220B GLU* 3.6 14.4 - - + +
222B ILE* 1.3 75.2 - - - +
224B ALA* 1.3 62.0 + - - +
226B ILE* 3.3 7.0 + - + +
227B GLU* 3.0 39.7 + - - +
233B PRO* 3.9 26.6 - - + +
239B LEU* 3.9 25.4 - - + -
285B TYR* 3.8 31.9 - - + -
286B PRO* 4.0 11.2 - - + -
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Residues in contact with ALA 224 (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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192B ILE* 4.0 14.6 - - + -
220B GLU 2.9 18.1 + - - +
221B THR* 3.6 9.4 - - - +
222B ILE 3.2 0.2 - - - -
223B LEU* 1.3 76.1 - - - +
225B ALA* 1.3 51.2 + - - +
227B GLU* 3.4 8.0 + - - +
228B ALA* 2.8 36.7 + - - +
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Residues in contact with ALA 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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149B ILE* 5.5 0.2 - - + -
185B ILE* 3.8 12.9 - - + +
188B ALA* 3.7 6.6 - - - +
189B LEU* 3.6 40.8 - - + +
192B ILE* 3.8 10.7 - - + +
221B THR 3.0 13.3 + - - +
222B ILE* 3.0 9.6 + - - +
224B ALA* 1.3 73.2 - - - +
226B ILE* 1.3 66.9 + - - +
228B ALA* 3.4 1.7 + - - -
229B ALA* 3.0 24.8 + - - +
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Residues in contact with ILE 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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167B ILE* 4.1 1.1 - - + -
185B ILE* 3.9 26.9 - - + -
222B ILE* 2.9 22.6 + - + +
223B LEU* 3.5 17.7 - - + +
224B ALA 3.3 0.2 - - - -
225B ALA* 1.3 76.3 - - - +
227B GLU* 1.3 60.0 + - - +
229B ALA* 3.3 10.0 + - - +
230B GLY 3.4 0.2 + - - -
231B TYR* 3.0 50.8 + - + +
233B PRO* 3.8 18.8 - - + -
237B VAL* 3.7 29.8 - - + +
239B LEU* 3.9 24.0 - - + -
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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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223B LEU* 3.0 29.4 + - - +
224B ALA* 3.8 6.7 - - - +
226B ILE* 1.3 72.5 - - - +
228B ALA* 1.3 59.5 + - - +
230B GLY* 3.0 20.6 + - - -
231B TYR 3.6 7.0 - - - +
233B PRO* 3.9 28.3 - - + +
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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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188B ALA* 4.4 10.5 - - + +
192B ILE* 4.5 9.9 - - + -
224B ALA 2.8 21.8 + - - +
225B ALA* 3.8 7.6 - - - +
227B GLU* 1.3 72.0 - - - +
229B ALA* 1.4 59.4 + - - +
230B GLY* 3.2 1.1 + - - -
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Residues in contact with ALA 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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184B GLU* 3.9 25.3 - - + +
185B ILE* 3.7 10.8 - - + -
188B ALA* 4.3 4.0 - - + +
225B ALA 3.0 16.9 + - - +
226B ILE 3.6 1.3 - - - +
227B GLU 3.2 0.6 - - - -
228B ALA* 1.4 74.1 - - - +
230B GLY* 1.3 57.7 + - - +
231B TYR* 3.2 36.7 - - + -
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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