Contacts of the helix formed by residues 197 - 221 (chain B) in PDB entry 1XPM
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 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR 4.2 6.5 - - - +
184B ASP 2.9 13.2 + - - +
186B TRP* 4.8 2.6 - - + -
196B VAL* 1.3 74.1 - - - +
198B GLY* 1.3 63.9 + - - +
199B ALA* 3.9 5.5 + - - +
200B LEU* 2.8 53.6 + - + +
201B SER* 2.9 10.2 + - - -
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Residues in contact with GLY 198 (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 VAL* 3.4 8.7 + - - +
197B ASP* 1.3 70.6 - - - +
199B ALA* 1.3 61.9 + - - +
201B SER* 2.4 27.9 + - - -
202B LYS* 3.6 6.8 + - - +
2402B CAA 4.0 32.0 - - - +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ASP* 3.1 6.0 + - - +
198B GLY* 1.3 72.2 - - - +
200B LEU* 1.3 63.5 + - - +
202B LYS* 3.2 27.0 + - - +
203B ASP* 3.4 10.6 + - - +
2402B CAA 5.1 0.4 - - - +
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Residues in contact with LEU 200 (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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182B VAL* 3.8 27.1 - - + -
183B TYR* 4.0 15.7 - - + +
184B ASP* 4.2 3.6 - - + -
197B ASP* 2.8 42.7 + - + +
199B ALA* 1.3 75.1 - - - +
201B SER* 1.3 58.8 + - - +
203B ASP* 3.1 10.1 + - + +
204B ALA* 2.9 31.4 + - + +
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Residues in contact with SER 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 3.6 26.0 - - - +
185B PHE* 5.4 0.9 - - - -
196B VAL* 4.5 5.2 - - - -
197B ASP 2.9 9.9 + - - -
198B GLY* 2.4 23.7 + - - -
200B LEU* 1.3 78.7 - - - +
202B LYS* 1.3 55.9 + - - +
204B ALA* 4.0 1.0 - - - +
205B TYR* 3.1 28.9 + - - +
2402B CAA 3.2 45.0 + - - +
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLY 4.2 6.1 - - - +
199B ALA* 3.2 24.8 + - - +
200B LEU 3.2 1.0 - - - -
201B SER* 1.3 84.3 + - - +
203B ASP* 1.3 63.4 + - - +
205B TYR* 3.5 1.0 + - - +
206B ILE* 3.1 34.2 + - + +
236B PHE* 4.7 10.8 - - + -
239B MET* 3.7 32.3 - - + -
242B LYS* 6.2 4.0 - - + -
2402B CAA 4.5 24.0 - - + +
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA 3.4 8.2 + - - +
200B LEU* 3.1 14.9 + - + +
202B LYS* 1.3 75.2 - - - +
204B ALA* 1.3 61.1 + - - +
206B ILE* 3.5 4.6 + - - +
207B ARG* 2.9 31.8 + - - +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 4.3 13.2 - - + -
184B ASP* 4.0 18.2 - - + +
200B LEU* 2.9 24.2 + - + +
201B SER 4.0 0.4 - - - +
203B ASP* 1.3 76.2 - - - +
205B TYR* 1.3 63.1 + - - +
207B ARG* 3.9 6.4 - - - +
208B SER* 3.0 25.5 + - - -
305B TYR* 3.3 19.3 + - - +
309B SER* 5.0 2.1 + - - +
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Residues in contact with TYR 205 (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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201B SER 3.1 21.3 + - - +
202B LYS* 3.6 7.2 - - - +
204B ALA* 1.3 78.0 - - - +
206B ILE* 1.3 65.8 + - - +
208B SER* 3.4 2.9 + - - -
209B PHE* 3.1 19.5 + - + +
232B PHE* 3.7 17.4 - + - +
233B HIS* 2.8 39.9 + + - +
239B MET* 3.8 26.9 - - + -
240B GLY* 4.6 4.0 - - - -
243B ALA* 3.5 25.6 - - + -
303B PHE* 4.3 16.2 - + - -
305B TYR* 3.6 29.3 + + + -
2402B CAA 3.2 32.8 - - + -
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LYS* 3.1 20.4 + - + +
203B ASP* 4.0 4.3 - - - +
205B TYR* 1.3 75.4 - - - +
207B ARG* 1.3 59.9 + - - +
209B PHE* 3.2 5.5 + - + +
210B GLN* 2.9 45.2 + - - +
239B MET* 3.9 21.5 - - + -
242B LYS* 4.2 23.3 - - + +
243B ALA* 4.1 9.6 - - + +
246B SER* 3.7 28.3 - - - +
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Residues in contact with ARG 207 (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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178B TYR* 3.2 20.3 + - + -
180B GLU* 2.7 33.7 + - - +
203B ASP 2.9 20.0 + - - +
204B ALA* 3.9 6.1 - - - +
206B ILE* 1.3 76.0 - - - +
208B SER* 1.3 57.9 + - - +
210B GLN* 3.2 9.6 + - - +
211B GLN* 2.8 63.4 + - + +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 4.2 18.2 + - - -
204B ALA 3.0 19.2 + - - -
205B TYR 3.6 0.7 - - - -
207B ARG* 1.3 75.9 - - - +
209B PHE* 1.3 56.4 + - - +
211B GLN* 4.0 0.7 - - - +
212B SER* 2.8 37.4 + - - -
303B PHE* 3.6 1.5 - - - -
305B TYR* 3.5 22.6 - - - -
309B SER* 4.8 5.3 + - - -
310B VAL 4.0 0.2 - - - -
311B GLY* 3.2 33.1 + - - -
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Residues in contact with PHE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 3.1 11.3 + - + +
206B ILE* 3.5 9.9 - - - +
208B SER* 1.3 81.0 - - - +
210B GLN* 1.3 58.8 + - - +
212B SER* 3.8 0.5 - - - -
213B TRP* 2.9 36.3 + - + +
230B LEU* 4.3 2.9 - - + -
232B PHE* 3.3 32.3 - + - -
243B ALA* 3.7 28.0 - - + -
246B SER* 4.3 6.3 - - - -
247B ILE* 3.3 42.0 - - + -
303B PHE* 3.4 49.3 - + + -
313B PHE* 4.2 17.3 - + - -
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Residues in contact with GLN 210 (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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206B ILE* 2.9 32.9 + - + +
207B ARG* 3.2 8.1 + - - +
209B PHE* 1.3 79.3 - - + +
211B GLN* 1.3 65.8 + - - +
213B TRP* 3.9 3.8 - - - +
214B ASN* 2.9 44.4 + - - +
246B SER* 3.5 39.3 + - - +
247B ILE* 4.1 15.9 - - + +
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Residues in contact with GLN 211 (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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101A PHE* 4.0 11.1 - - + -
178B TYR* 3.6 44.1 + - + +
207B ARG* 2.8 53.7 + - + +
210B GLN* 1.3 81.6 + - - +
212B SER* 1.3 61.2 + - - +
214B ASN* 3.9 15.5 + - - +
215B GLU* 3.2 23.9 + - - +
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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
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101A PHE* 5.3 0.9 - - - -
176B VAL* 3.6 12.3 - - - +
177B ALA 5.7 0.2 - - - -
178B TYR* 3.4 22.7 - - - +
208B SER 2.8 22.2 + - - -
209B PHE 3.8 2.5 - - - -
211B GLN* 1.3 76.9 - - - +
213B TRP* 1.3 65.0 + - - +
215B GLU* 3.5 2.4 + - - +
216B TYR* 3.0 23.2 + - - +
303B PHE* 3.7 12.1 - - - -
311B GLY 3.7 15.2 + - - -
313B PHE* 4.2 18.6 - - - -
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Residues in contact with TRP 213 (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* 2.9 25.5 + - + +
210B GLN* 3.9 2.5 - - - +
212B SER* 1.3 75.3 - - - +
214B ASN* 1.3 74.3 + - - +
216B TYR* 3.1 20.7 + + - +
217B ALA* 2.8 46.6 + - + +
222B LYS 4.4 0.7 - - - -
223B SER* 3.6 26.2 - - - -
224B LEU* 3.5 41.8 - - + +
227B PHE* 3.5 24.5 - + - -
247B ILE* 4.3 24.4 - - + +
313B PHE* 3.5 33.3 - + + +
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Residues in contact with ASN 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 GLN* 2.9 35.7 + - - +
211B GLN* 3.9 17.7 + - - +
212B SER 3.4 0.2 - - - -
213B TRP* 1.3 89.3 + - - +
215B GLU* 1.3 61.4 + - - +
217B ALA* 3.4 5.0 + - - +
218B LYS* 3.0 24.1 + - - +
247B ILE* 6.0 0.3 - - - +
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Residues in contact with GLU 215 (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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101A PHE* 3.4 51.2 - - + -
176B VAL* 3.7 11.0 - - + -
211B GLN 3.2 7.4 + - - +
212B SER 4.0 3.6 - - - +
214B ASN* 1.3 75.6 - - - +
216B TYR* 1.3 61.3 + - - +
218B LYS* 3.3 24.3 + - - +
219B ARG* 2.8 73.4 + - - +
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Residues in contact with TYR 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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174B ASP* 2.7 59.5 + - + -
176B VAL* 3.5 12.7 - - + +
212B SER 3.0 18.1 + - - +
213B TRP* 3.1 19.3 + + - +
215B GLU* 1.3 77.2 - - - +
217B ALA* 1.3 66.9 + - - +
219B ARG* 3.3 4.3 + - - -
220B GLN* 2.9 33.3 + - + +
222B LYS* 3.5 32.1 - - + +
227B PHE* 3.6 21.5 - + - -
313B PHE* 3.6 29.4 - + + -
314B TYR* 4.3 3.6 - - - -
315B SER* 3.5 10.5 - - - -
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Residues in contact with ALA 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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213B TRP* 2.8 40.0 + - + +
214B ASN* 3.8 6.3 - - - +
216B TYR* 1.3 79.9 - - - +
218B LYS* 1.3 53.8 + - - +
221B GLY* 2.7 34.5 + - - -
222B LYS 3.2 24.2 + - - +
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Residues in contact with LYS 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 ASN 3.0 18.6 + - - +
215B GLU* 3.5 25.1 + - - +
216B TYR 3.2 0.2 - - - -
217B ALA* 1.3 78.9 - - - +
219B ARG* 1.3 63.6 + - + +
221B GLY* 3.6 6.6 + - - -
221C GLY 5.8 0.2 - - - +
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Residues in contact with ARG 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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99A GLN* 5.1 2.0 + - - -
101A PHE* 3.7 31.1 + - - +
131A GLU* 5.6 4.0 + - - -
175B ALA 4.8 5.1 + - - -
176B VAL* 3.7 27.5 - - - +
215B GLU* 2.8 47.6 + - - +
216B TYR* 3.9 3.6 - - - +
218B LYS* 1.3 78.1 - - + +
220B GLN* 1.3 77.5 + - - +
220C GLN 5.4 1.0 - - - +
221C GLY 5.2 4.3 - - - +
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLU 4.7 3.7 + - - +
174B ASP* 3.6 30.4 + - + +
216B TYR* 2.9 42.4 + - + +
219B ARG* 1.3 91.8 + - + +
221B GLY* 1.3 63.0 + - - +
222B LYS* 3.3 28.3 + - + +
219C ARG 5.4 1.0 - - - +
220C GLN* 3.8 17.7 - - - +
221C GLY* 5.5 0.7 - - - -
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Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ALA 2.7 16.6 + - - -
218B LYS 3.6 5.4 + - - -
219B ARG 3.5 2.2 - - - -
220B GLN* 1.3 75.8 - - - +
222B LYS* 1.3 59.6 + - - +
226B ASP* 4.8 0.3 - - - +
219C ARG 5.3 4.3 - - - +
221C GLY* 4.9 16.3 + - - -
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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
------------------------------------------------------------
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