Contacts of the helix formed by residues 217 - 236 (chain B) in PDB entry 2DW1
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 ASP 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ASN* 3.0 17.9 + - - +
215B ASN* 3.1 4.4 + - + +
216B GLY* 1.3 72.3 - - - +
218B LEU* 1.3 63.2 + - - +
219B ASP* 3.2 12.0 + - - +
220B LYS* 3.1 52.3 + - + +
221B ILE* 3.4 14.0 + - - +
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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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211B VAL* 4.3 14.8 - - + -
216B GLY 3.0 21.5 + - - +
217B ASP* 1.3 68.7 + - - +
219B ASP* 1.3 68.5 + - - +
220B LYS 3.0 2.0 - - - -
221B ILE* 2.8 20.1 + - + +
222B LYS* 2.9 36.2 + - - +
250B ILE* 3.7 44.2 - - + -
252B SER* 4.6 12.1 - - - +
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ASP* 3.2 9.0 + - - +
218B LEU* 1.3 78.2 - - - +
220B LYS* 1.3 60.2 + - - +
222B LYS* 4.0 10.8 - - - +
223B THR* 3.0 45.6 + - - -
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Residues in contact with LYS 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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214B ASN* 4.5 26.4 + - - +
217B ASP* 3.1 43.8 + - + +
218B LEU 3.0 0.6 - - - -
219B ASP* 1.3 77.4 - - - +
221B ILE* 1.3 66.8 + - - +
223B THR* 4.0 5.3 - - - +
224B ARG* 3.2 21.1 + - - +
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.9 33.2 - - + -
210B MET* 3.6 23.3 - - + +
211B VAL* 4.5 5.8 - - + -
214B ASN* 2.9 40.6 - - + +
217B ASP 3.5 13.2 - - - +
218B LEU* 2.8 20.7 + - + +
220B LYS* 1.3 80.8 - - - +
222B LYS* 1.3 64.7 + - - +
224B ARG* 3.1 3.7 + - - +
225B MET* 2.9 34.1 + - + +
248B LEU* 5.8 0.2 - - + -
250B ILE* 4.5 10.5 - - + -
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Residues in contact with LYS 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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218B LEU* 2.9 38.1 + - - +
219B ASP* 4.0 8.2 - - - +
221B ILE* 1.3 78.0 - - - +
223B THR* 1.3 64.1 + - - +
225B MET* 3.1 2.7 + - - +
226B TYR* 3.0 52.3 + - + +
248B LEU* 3.8 27.4 - - + -
250B ILE* 3.8 22.7 - - + -
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Residues in contact with THR 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 ASP* 3.0 34.9 + - - -
220B LYS* 4.0 6.3 - - - +
222B LYS* 1.3 77.3 - - - +
224B ARG* 1.3 68.3 + - + +
226B TYR* 3.1 23.0 + - - +
227B GLU* 3.2 16.3 + - + +
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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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210B MET* 4.8 8.8 - - - +
220B LYS 3.2 14.8 + - - +
221B ILE* 3.1 5.8 + - - +
223B THR* 1.3 82.0 - - + +
225B MET* 1.3 67.3 + - - +
227B GLU* 3.2 8.3 + - - +
228B ILE* 2.9 33.6 + - + +
290B LEU* 5.8 0.6 - - - +
319B ASP* 2.5 31.0 + - - -
321B SER 2.7 24.9 + - - -
322B GLU* 3.3 22.8 + - - +
324B ASN* 2.7 32.2 - - - +
327B VAL* 3.2 20.4 - - - +
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Residues in contact with MET 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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204B LEU* 3.3 38.1 - - + -
206B VAL* 3.6 18.2 - - + -
210B MET* 4.8 2.7 - - - -
221B ILE* 2.9 34.5 + - + +
222B LYS* 3.1 8.5 + - - +
224B ARG* 1.3 80.1 - - - +
226B TYR* 1.3 64.6 + - + +
228B ILE* 3.2 14.0 + - - +
229B VAL* 2.9 31.1 + - - +
245B LEU* 5.2 1.3 - - + -
248B LEU* 4.6 15.7 - - + -
290B LEU* 3.3 42.0 - - + -
331B MET* 5.2 0.4 - - + -
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Residues in contact with TYR 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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222B LYS* 3.0 52.4 + - + +
223B THR* 3.1 13.7 + - - +
225B MET* 1.3 76.2 - - + +
227B GLU* 1.3 58.7 + - - +
229B VAL* 3.8 4.9 - - - +
230B ASN* 2.9 30.8 + - - +
245B LEU* 3.9 19.3 - - + -
248B LEU* 4.2 10.2 - - + +
399B ILE* 4.4 10.7 + - + +
400B SER* 3.9 20.6 - - - -
401B PRO* 3.4 43.5 - - + -
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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 THR* 3.2 12.3 + - + +
224B ARG* 3.6 10.7 - - - +
226B TYR* 1.3 81.2 - - - +
228B ILE* 1.3 59.2 + - - +
230B ASN* 3.6 7.4 + - - +
231B THR* 2.9 33.9 + - - +
324B ASN* 2.8 33.7 - - + +
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Residues in contact with ILE 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 43.5 + - + +
225B MET* 3.2 16.8 + - - +
227B GLU* 1.3 74.8 - - - +
229B VAL* 1.3 62.3 + - - +
231B THR* 3.1 8.3 + - - -
232B VAL* 2.9 26.2 + - - +
290B LEU* 5.5 0.7 - - + -
324B ASN* 4.2 23.1 - - + +
327B VAL* 3.5 28.7 - - + -
328B ALA* 4.0 20.6 - - - +
331B MET* 3.5 29.2 - - + -
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Residues in contact with VAL 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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202B LEU* 4.3 13.7 - - + -
204B LEU* 3.7 25.8 - - + -
225B MET 2.9 21.0 + - - +
226B TYR* 3.8 4.5 - - - +
228B ILE* 1.3 72.5 - - - +
230B ASN* 1.3 68.5 + - - +
232B VAL* 2.9 9.7 + - - +
233B ASN* 2.8 20.6 + - - +
243B VAL* 4.3 23.6 - - + +
244B ALA* 5.0 0.2 - - - -
245B LEU* 4.2 34.5 - - + +
331B MET* 4.4 4.9 - - + -
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Residues in contact with ASN 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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226B TYR 2.9 18.9 + - - +
227B GLU* 3.7 8.2 - - - +
229B VAL* 1.3 77.1 - - - +
231B THR* 1.3 60.6 + - - +
233B ASN* 2.8 26.7 + - - +
234B GLU* 2.9 37.8 + - - +
403B VAL* 4.6 17.3 - - + +
406B ASN* 3.9 28.3 - - - +
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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
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227B GLU* 2.9 19.2 + - - +
228B ILE* 3.4 9.6 - - - -
230B ASN* 1.3 83.7 + - - +
232B VAL* 1.3 62.8 + - - +
234B GLU* 3.2 15.8 + - + +
235B ILE* 3.0 39.5 + - + +
324B ASN* 5.8 3.4 - - - +
325B LEU* 4.3 15.7 - - + -
328B ALA* 3.7 22.4 - - + -
367B THR* 5.2 2.7 - - + -
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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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228B ILE 2.9 18.7 + - - +
229B VAL* 2.9 9.8 + - - +
231B THR* 1.3 75.4 - - - +
233B ASN* 1.3 63.7 + - - +
235B ILE* 3.1 11.9 + - - +
236B TYR* 3.0 37.6 + - + -
243B VAL* 3.7 28.0 - - + -
328B ALA* 3.9 24.0 - - - +
331B MET* 3.7 27.1 - - + -
332B ALA* 4.4 4.0 - - + +
335B MET* 4.4 8.5 - - - -
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Residues in contact with ASN 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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229B VAL 2.8 9.2 + - - +
230B ASN* 3.1 15.3 - - - +
232B VAL* 1.3 76.9 - - - +
234B GLU* 1.3 62.6 - - - +
236B TYR* 3.3 10.4 + - - +
237B ARG* 3.4 11.4 + - - +
241B ILE 4.5 0.9 - - - +
242B HIS* 3.3 20.4 - - - +
243B VAL* 2.6 54.1 + - - +
406B ASN* 3.1 33.1 + - - +
408B LEU* 4.2 10.0 - - + +
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Residues in contact with GLU 234 (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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230B ASN* 2.9 39.8 + - - +
231B THR* 3.6 17.5 + - + +
233B ASN* 1.3 79.7 - - + +
235B ILE* 1.3 62.6 + - + +
237B ARG* 3.2 24.6 - - - +
238B TYR 4.8 0.2 + - - -
406B ASN* 6.3 2.0 - - + -
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Residues in contact with ILE 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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231B THR* 3.0 33.5 + - + +
232B VAL* 3.1 11.4 + - - +
234B GLU* 1.3 79.1 - - + +
236B TYR* 1.3 56.2 + - + +
237B ARG 3.2 3.4 + - - -
238B TYR* 4.3 8.3 + - - +
239B MET* 4.4 1.9 - - - +
325B LEU* 4.8 2.7 - - + -
328B ALA* 4.5 14.1 - - + -
329B VAL* 4.9 3.1 - - + +
332B ALA* 4.3 12.8 - - + -
356B ILE* 3.3 31.4 - - + -
367B THR* 3.5 43.9 - - + +
369B PHE* 3.6 22.1 - - + -
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Residues in contact with TYR 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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232B VAL* 3.0 34.1 + - + +
233B ASN 3.3 3.1 + - - +
235B ILE* 1.3 75.8 - - - +
237B ARG* 1.3 62.3 + - - +
238B TYR 3.6 0.4 - - - -
239B MET* 3.3 31.7 + - + +
241B ILE* 2.7 54.3 + - + +
243B VAL* 3.9 14.1 - - + -
332B ALA* 2.8 31.0 + - + -
335B MET* 3.4 10.1 - - + -
336B GLY* 2.8 36.1 + - - -
339B LEU* 3.3 23.6 - - + -
369B PHE* 3.6 20.3 - + - -
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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
------------------------------------------------------------
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