Contacts of the helix formed by residues 197 - 221 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR 4.3 5.8 - - - +
184A ASP 2.9 13.1 + - - +
186A TRP* 5.0 2.6 - - + -
196A VAL* 1.3 73.8 - - - +
198A GLY* 1.3 65.8 + - - +
199A ALA* 3.8 6.4 + - - +
200A LEU* 3.1 39.9 + - + +
201A SER* 2.9 20.3 + - - -
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Residues in contact with GLY 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL* 3.6 7.7 + - - +
197A ASP* 1.3 70.3 + - - +
199A ALA* 1.3 61.8 + - - +
201A SER* 2.5 25.3 + - - -
202A LYS* 3.5 11.5 - - - +
1402A CAA 3.7 32.5 + - - +
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP* 3.3 6.3 + - - +
198A GLY* 1.3 72.8 - - - +
200A LEU* 1.3 62.6 + - - +
202A LYS* 3.1 21.3 + - - +
203A ASP* 3.2 18.4 - - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.0 20.6 - - + -
183A TYR* 3.7 27.1 - - + +
184A ASP* 4.0 8.3 - - - -
197A ASP* 3.0 29.9 + - + +
199A ALA* 1.3 78.1 - - - +
201A SER* 1.3 57.8 + - - +
203A ASP* 3.2 12.6 + - + +
204A ALA* 2.8 32.8 + - + +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASP* 3.6 26.6 - - - +
185A PHE* 5.4 0.2 - - - -
196A VAL* 4.6 5.4 - - - -
197A ASP 2.9 12.3 + - - -
198A GLY* 2.5 26.7 + - - -
200A LEU* 1.3 75.6 - - - +
202A LYS* 1.3 62.8 + - - +
204A ALA* 3.9 0.9 - - - +
205A TYR* 3.1 25.3 + - - +
1402A CAA 3.4 41.7 + - - +
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLY 3.5 17.0 - - - +
199A ALA* 3.1 11.6 + - - +
201A SER* 1.3 79.5 + - - +
203A ASP* 1.3 65.9 + - - +
205A TYR* 3.7 1.7 - - - +
206A ILE* 3.1 33.4 + - + +
236A PHE* 4.0 16.4 - - + -
239A MET* 3.3 32.1 - - + -
1402A CAA 4.5 12.1 - - + +
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA* 3.2 20.1 + - - +
200A LEU* 3.2 13.9 + - + +
202A LYS* 1.3 77.9 - - - +
204A ALA* 1.3 57.7 + - - +
206A ILE* 3.4 6.5 + - - +
207A ARG* 2.8 33.4 + - - +
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 4.3 18.4 - - + -
184A ASP* 4.0 15.9 - - + +
200A LEU* 2.8 20.1 + - + +
201A SER 3.9 2.9 - - - +
203A ASP* 1.3 78.0 - - - +
205A TYR* 1.3 63.3 + - - +
207A ARG* 3.9 6.1 - - - +
208A SER* 3.0 25.8 + - - -
305A TYR* 3.4 18.2 - - - +
309A SER* 5.0 2.1 + - - +
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER 3.1 18.8 + - - +
202A LYS 3.7 3.8 - - - +
204A ALA* 1.3 77.5 - - - +
206A ILE* 1.3 63.4 + - - +
208A SER* 3.4 2.9 + - - -
209A PHE* 3.1 19.6 + - + +
232A PHE* 3.6 18.4 - + - +
233A HIS* 2.9 47.6 + + - +
239A MET* 3.8 26.0 - - + -
240A GLY* 4.5 3.5 - - - -
243A ALA* 3.6 26.5 - - + -
303A PHE* 4.2 17.4 - + - -
305A TYR* 3.5 30.7 + + + -
1402A CAA 3.5 27.1 - - + -
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS* 3.1 20.4 + - + +
203A ASP* 4.0 5.8 - - - +
205A TYR* 1.3 75.7 - - - +
207A ARG* 1.3 66.8 + - - +
209A PHE* 3.2 5.3 + - + +
210A GLN* 2.9 53.4 + - - +
239A MET* 3.9 21.5 - - + -
242A LYS* 4.3 11.9 - - + +
243A ALA* 4.1 20.0 - - - +
246A SER* 3.8 14.6 - - - +
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.2 19.6 + - - -
180A GLU* 2.8 34.3 + - - +
203A ASP 2.8 22.5 + - - +
204A ALA* 3.9 5.4 - - - +
206A ILE* 1.3 74.0 - - - +
208A SER* 1.3 58.9 + - - +
210A GLN* 3.3 8.7 + - - +
211A GLN* 2.9 62.6 + - + +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A TYR* 4.3 16.7 + - - -
204A ALA 3.0 18.4 + - - -
205A TYR 3.6 1.1 - - - -
207A ARG* 1.3 76.3 - - - +
209A PHE* 1.3 61.6 + - - +
211A GLN* 3.9 0.5 - - - +
212A SER* 2.8 32.1 + - - -
303A PHE* 3.7 1.3 - - - -
305A TYR* 3.4 23.9 - - - -
309A SER* 4.8 5.0 + - - -
310A VAL 4.1 0.3 - - - -
311A GLY* 3.3 32.1 + - - -
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 3.1 13.8 + - + +
206A ILE* 3.5 9.9 - - - +
208A SER* 1.3 76.9 - - - +
210A GLN* 1.3 59.0 + - - +
212A SER* 3.8 0.7 - - - -
213A TRP* 2.9 36.7 + - + +
230A LEU* 4.4 2.9 - - + -
232A PHE* 3.3 31.4 - + - -
243A ALA* 3.7 30.1 - - + -
244A LEU* 4.9 0.2 - - - -
246A SER* 4.3 6.5 - - - -
247A ILE* 3.3 41.3 - - + -
303A PHE* 3.4 48.4 - + + -
313A PHE* 4.1 18.2 - + - -
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 2.9 33.6 + - + +
207A ARG* 3.8 8.2 - - - +
209A PHE* 1.3 77.0 - - + +
211A GLN* 1.3 65.4 + - - +
213A TRP* 3.9 4.2 - - - +
214A ASN* 2.9 44.2 + - - +
246A SER* 3.3 42.0 + - - +
247A ILE* 4.3 12.3 - - + +
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Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.7 44.2 + - + +
207A ARG* 2.9 53.1 + - + +
210A GLN* 1.3 84.3 + - - +
212A SER* 1.3 62.6 + - - +
214A ASN* 3.6 13.2 + - - +
215A GLU* 3.2 23.9 + - - +
101B PHE* 4.1 10.6 - - + -
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Residues in contact with SER 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A VAL* 3.6 12.7 - - - +
177A ALA 5.8 0.4 - - - -
178A TYR* 3.5 22.3 + - - +
208A SER 2.8 21.7 + - - -
209A PHE 3.8 2.9 - - - -
211A GLN* 1.3 74.3 - - - +
213A TRP* 1.3 66.3 + - - +
215A GLU* 3.4 3.0 + - - -
216A TYR* 3.0 24.1 + - - +
303A PHE* 3.8 11.6 - - - -
311A GLY 3.7 14.6 + - - -
313A PHE* 4.2 19.7 - - - -
101B PHE* 5.4 0.4 - - - -
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Residues in contact with TRP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 2.9 26.6 + - + +
210A GLN* 3.9 2.7 - - - +
212A SER* 1.3 76.8 - - - +
214A ASN* 1.3 72.0 + - - +
216A TYR* 3.1 17.9 + + - +
217A ALA* 2.8 42.8 + - + +
222A LYS 4.6 0.7 - - - -
223A SER* 3.7 28.0 - - - -
224A LEU* 3.5 41.5 - - + +
227A PHE* 3.5 24.9 - + - -
247A ILE* 4.2 26.6 - - + +
313A PHE* 3.5 36.0 - + + +
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Residues in contact with ASN 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN* 2.9 32.6 + - - +
211A GLN* 3.9 15.7 + - - +
213A TRP* 1.3 92.1 + - - +
215A GLU* 1.3 61.0 + - - +
217A ALA* 3.5 5.7 + - - +
218A LYS* 3.1 23.4 + - - +
247A ILE* 5.9 0.7 - - - +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A VAL* 3.8 7.9 - - + -
211A GLN 3.2 8.3 + - - +
212A SER 4.0 2.9 - - - +
214A ASN* 1.3 75.6 - - - +
216A TYR* 1.3 61.8 + - - +
218A LYS* 3.3 24.4 + - - +
219A ARG* 2.8 73.4 + - - +
101B PHE* 3.5 52.4 - - + -
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Residues in contact with TYR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASP* 2.7 59.8 + - + -
176A VAL* 3.6 12.0 - - + +
212A SER 3.0 18.0 + - - +
213A TRP* 3.4 20.6 - + - +
215A GLU* 1.3 77.0 - - - +
217A ALA* 1.3 65.4 + - - +
219A ARG* 3.3 3.5 + - - +
220A GLN* 2.9 33.7 + - + +
222A LYS* 3.5 27.6 - - + +
227A PHE* 3.6 24.2 - + - -
313A PHE* 3.5 29.8 - + + -
314A TYR* 4.2 3.4 - - - -
315A SER* 3.5 11.8 + - - -
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TRP* 2.8 37.8 + - + +
214A ASN* 3.7 7.2 - - - +
216A TYR* 1.3 79.7 - - - +
218A LYS* 1.3 58.0 + - - +
221A GLY* 2.8 27.9 + - - -
222A LYS 3.2 28.8 + - - +
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ASN 3.1 16.4 + - - +
215A GLU* 3.6 26.4 + - - +
216A TYR 3.2 0.2 - - - -
217A ALA* 1.3 80.1 - - - +
219A ARG* 1.3 63.0 + - + +
221A GLY* 3.6 7.0 + - - -
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Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 4.8 4.0 + - - -
176A VAL* 3.5 28.7 - - - +
215A GLU* 2.8 48.2 + - - +
216A TYR* 3.9 2.7 - - - +
218A LYS* 1.3 77.1 - - + +
220A GLN* 1.3 77.0 + - - +
221A GLY 3.8 0.2 + - - -
99B GLN* 5.1 1.4 + - - -
101B PHE* 3.7 31.9 + - - +
131B GLU* 5.8 1.8 + - - -
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Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU 4.7 3.5 + - - +
174A ASP* 3.5 31.8 + - + +
216A TYR* 2.9 42.9 + - + +
219A ARG* 1.3 94.5 + - - +
221A GLY* 1.3 64.6 + - - +
222A LYS* 3.6 29.4 - - + +
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Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA 2.8 11.2 + - - -
218A LYS 3.6 5.0 + - - -
219A ARG 3.5 2.8 - - - -
220A GLN* 1.3 80.2 - - - +
222A LYS* 1.3 59.9 + - - +
226A ASP* 4.7 1.2 - - - +
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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