Contacts of the helix formed by residues 208 - 231 (chain B) in PDB entry 1YWT
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 LEU 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B THR* 3.4 41.5 - - + +
204B ASP 4.6 2.0 - - - +
205B LEU* 3.2 45.6 + - + +
206B HIS 4.6 0.2 - - - -
207B THR* 1.3 75.4 - - - +
209B SER* 1.3 79.6 + - - +
212B SER* 3.9 11.0 + - - +
213B TYR* 3.4 40.2 - - + +
216B SER* 3.5 16.4 - - - +
220B MET* 5.4 0.4 - - - -
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 3.1 9.8 - - - +
208B LEU* 1.3 103.4 + - - +
210B GLU* 1.3 67.8 + - - +
211B ASP* 2.6 33.7 + - - +
212B SER* 3.6 1.4 + - - -
213B TYR* 3.5 14.0 + - - +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 6.1 0.2 - - - -
209B SER* 1.3 79.6 + - - +
211B ASP* 1.3 63.3 + - - +
212B SER 3.7 0.2 - - - -
213B TYR* 3.9 21.7 + - + +
214B LYS 5.3 0.9 + - - -
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 2.6 21.3 + - - +
210B GLU* 1.3 81.9 - - - +
212B SER* 1.3 66.5 + - - +
213B TYR 3.8 0.2 + - - -
214B LYS* 5.4 0.7 + - - +
215B ASP* 5.4 1.0 - - - +
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR* 4.6 1.2 + - - -
166B ASN* 5.0 0.9 - - - -
167B PRO* 3.3 36.9 - - - +
208B LEU* 3.9 14.6 + - - +
209B SER* 3.6 2.1 + - - -
211B ASP* 1.3 84.8 + - - +
213B TYR* 1.3 64.9 + - - +
214B LYS* 3.5 2.7 - - - -
215B ASP* 3.3 11.1 + - - +
216B SER* 3.1 23.0 + - - -
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Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 5.3 8.3 - - + -
208B LEU* 3.4 21.1 - - + +
209B SER 3.5 16.1 + - - +
210B GLU* 3.9 19.3 - - + +
211B ASP 3.4 2.2 + - - -
212B SER* 1.3 77.3 - - - +
214B LYS* 1.3 78.9 + - + +
216B SER* 3.2 2.0 + - - -
217B THR* 3.0 52.6 + - + +
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Residues in contact with LYS 214 (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 GLU 5.3 0.8 + - - -
211B ASP 5.4 0.8 + - - +
212B SER 3.5 0.4 - - - -
213B TYR* 1.3 90.8 - - + +
215B ASP* 1.3 66.3 + - - +
217B THR* 3.6 15.2 - - - +
218B LEU* 3.2 33.0 + - - +
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Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO* 3.6 22.6 - - + +
211B ASP 5.4 0.5 - - - +
212B SER* 3.3 11.9 + - - +
213B TYR 3.2 0.8 - - - -
214B LYS* 1.3 77.2 - - - +
216B SER* 1.3 67.8 + - - +
218B LEU* 3.1 17.6 + - - +
219B ILE* 3.1 19.9 + - + +
7D TYR* 3.1 25.6 + - + +
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR 3.3 25.4 - - - -
167B PRO* 3.8 7.7 - - - +
170B LEU* 3.4 16.5 - - - +
205B LEU* 5.3 0.2 - - - +
208B LEU* 3.5 22.3 - - - +
212B SER 3.1 15.1 + - - -
213B TYR 3.2 4.7 + - - -
215B ASP* 1.3 78.6 - - - +
217B THR* 1.3 58.6 + - - +
219B ILE* 3.3 4.0 + - - +
220B MET* 2.9 37.5 + - - +
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Residues in contact with THR 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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205B LEU* 4.8 9.4 - - - +
213B TYR* 3.0 48.2 + - + +
214B LYS* 3.6 20.4 - - - +
216B SER* 1.3 78.3 + - - +
218B LEU* 1.3 64.4 + - - +
220B MET* 3.4 11.3 + - - +
221B GLN* 3.2 20.5 + - + +
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Residues in contact with LEU 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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214B LYS* 3.2 22.9 + - - +
215B ASP* 3.1 11.6 + - - +
217B THR* 1.3 78.8 - - - +
219B ILE* 1.3 61.3 + - - +
221B GLN* 3.3 10.1 + - + +
222B LEU* 3.1 45.2 + - + +
7D TYR* 4.0 25.4 - - + +
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Residues in contact with ILE 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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167B PRO* 3.2 38.1 - - + +
170B LEU* 3.5 33.9 - - + +
171B GLY* 3.9 6.5 - - - +
174B LEU* 4.1 14.6 - - + -
215B ASP 3.1 17.7 + - - +
216B SER* 3.8 5.4 - - - +
218B LEU* 1.3 73.2 - - - +
220B MET* 1.3 60.3 + - - +
222B LEU* 3.1 8.5 + - - +
223B LEU* 2.9 31.4 + - + +
7D TYR* 3.7 39.5 - - + -
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Residues in contact with MET 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR* 6.0 0.7 - - - -
170B LEU* 4.5 10.8 - - + -
198B PHE* 3.1 33.5 - - + +
201B ALA* 3.5 21.8 - - + +
202B MET* 3.4 55.0 - - + +
205B LEU* 3.9 24.2 - - + -
208B LEU* 5.4 1.1 - - - -
216B SER* 2.9 24.7 + - - +
217B THR* 3.6 8.5 - - - +
219B ILE* 1.3 78.0 - - - +
221B GLN* 1.3 62.0 + - - +
223B LEU* 3.3 13.4 + - + +
224B ARG 3.2 10.4 + - - -
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Residues in contact with GLN 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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198B PHE* 5.7 1.2 - - - -
217B THR* 3.2 14.0 + - + +
218B LEU* 3.6 14.8 - - + +
219B ILE 3.2 0.2 - - - -
220B MET* 1.3 74.9 - - - +
222B LEU* 1.3 67.2 + - + +
224B ARG* 3.1 25.1 + - - +
225B ASP* 2.9 49.2 + - - +
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Residues in contact with LEU 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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174B LEU* 3.6 31.2 - - + -
218B LEU* 3.1 32.9 + - + +
219B ILE* 3.1 9.3 + - - +
221B GLN* 1.3 76.5 - - + +
223B LEU* 1.3 63.3 + - - +
225B ASP* 3.3 12.4 + - - +
226B ASN* 3.1 28.1 + - - -
5D HIS* 4.0 25.0 - - + +
6D SEP 4.0 9.2 - - - +
7D TYR* 3.8 26.7 - - + -
9D ALA* 5.7 6.7 - - + -
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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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170B LEU* 4.3 12.1 - - + +
173B ALA 4.9 0.9 - - - -
174B LEU* 3.7 37.9 - - + +
177B SER* 4.7 0.7 - - - +
194B ALA* 4.1 32.3 - - + +
197B THR* 3.9 25.8 - - + -
198B PHE* 4.1 19.1 - - + -
219B ILE* 2.9 21.9 + - + +
220B MET* 3.4 17.5 - - + +
221B GLN 3.2 0.2 - - - -
222B LEU* 1.3 77.2 - - - +
224B ARG* 1.3 57.3 + - - +
226B ASN* 3.3 5.7 + - - +
227B LEU* 2.9 33.1 + - - +
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Residues in contact with ARG 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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195B LYS* 6.1 1.2 - - - +
198B PHE* 3.1 45.5 - - + -
220B MET 3.2 7.2 + - - +
221B GLN* 3.1 28.4 + - - +
223B LEU* 1.3 76.8 - - - +
225B ASP* 1.3 67.4 + - - +
227B LEU* 3.0 18.5 + - + +
228B THR* 2.9 34.3 + - - +
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Residues in contact with ASP 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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221B GLN* 2.9 46.2 + - - +
222B LEU* 3.3 12.4 + - - +
224B ARG* 1.3 76.7 - - - +
226B ASN* 1.3 58.2 + - - +
228B THR* 3.3 6.9 + - - -
229B LEU* 2.9 29.5 + - - +
5D HIS* 3.5 31.6 + - + +
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Residues in contact with ASN 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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174B LEU* 3.2 24.2 - - - +
178B VAL* 4.2 5.5 - - - +
194B ALA* 5.6 0.2 - - + -
222B LEU 3.1 12.3 + - - -
223B LEU* 3.5 7.6 - - + +
225B ASP* 1.3 73.0 - - - +
227B LEU* 1.3 60.6 + - - +
229B LEU* 3.2 4.9 + - - +
230B TRP* 2.7 58.8 + - + -
4D SER* 3.0 15.1 - - - -
5D HIS* 2.7 52.2 + - - -
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Residues in contact with LEU 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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191B ILE* 3.6 41.7 - - + +
194B ALA* 4.1 14.6 - - + +
195B LYS* 4.0 30.7 - - + +
198B PHE* 4.7 4.5 - - + -
223B LEU 2.9 19.8 + - - +
224B ARG* 3.4 30.1 - - + +
226B ASN* 1.3 74.5 - - - +
228B THR* 1.3 62.6 + - - +
230B TRP* 3.9 5.7 - - - +
231B THR* 3.1 31.9 + - - +
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Residues in contact with THR 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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224B ARG* 2.9 21.0 + - - +
225B ASP* 3.5 10.7 - - - -
227B LEU* 1.3 77.8 - - - +
229B LEU* 1.3 64.6 + - - +
231B THR* 3.3 21.4 + - - +
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Residues in contact with LEU 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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181B TYR* 4.9 1.8 + - + -
225B ASP 2.9 16.1 + - - +
226B ASN* 3.7 4.9 - - - +
228B THR* 1.3 78.6 - - - +
230B TRP* 1.3 68.4 + - + +
231B THR 3.5 2.8 + - - -
1D MET* 4.7 9.8 - - - +
2D ALA* 3.9 30.7 - - + +
3D ARG 3.9 10.5 - - - +
4D SER* 3.9 34.5 - - - +
5D HIS* 5.4 5.8 - - - +
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Residues in contact with TRP 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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177B SER* 3.5 33.4 - - - -
178B VAL* 4.0 4.7 - - - -
181B TYR* 3.4 67.0 + + + -
190B ALA* 3.6 26.5 - - + -
191B ILE* 3.9 36.7 - - + +
194B ALA* 3.8 12.3 - - + -
226B ASN* 2.7 48.1 + - + +
227B LEU* 3.9 5.6 - - - +
229B LEU* 1.3 83.4 - - + +
231B THR* 1.3 58.9 + - - +
4D SER* 3.4 29.2 - - - -
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Residues in contact with THR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ILE* 4.2 18.5 - - - +
227B LEU* 3.1 19.1 + - - +
228B THR* 3.3 14.4 + - - +
229B LEU 4.5 2.9 - - - -
230B TRP* 1.3 81.6 - - - +
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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
------------------------------------------------------------
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