Contacts of the helix formed by residues 199 - 223 (chain A) in PDB entry 1N1E
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 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA* 4.0 3.4 - - - -
197A THR* 3.2 8.2 + - - +
198A THR* 1.3 76.4 + - - +
200A THR* 1.3 57.3 + - - +
201A VAL* 4.0 1.4 + - - +
202A GLY* 3.0 23.9 + - - -
203A CYS* 3.0 30.0 + - - -
250A GLY* 3.8 3.3 - - - -
251A ASP* 3.2 31.6 + - - +
252A GLY 3.2 6.4 + - - -
253A SER* 3.2 27.2 + - - +
254A ALA* 3.0 28.8 + - + +
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Residues in contact with THR 200 (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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148A LEU 5.8 1.8 - - - +
149A SER* 5.8 0.4 - - - -
150A VAL* 4.8 13.6 - - + +
171A ALA* 3.7 36.8 - - + +
172A SER* 3.7 12.6 - - - +
173A ALA* 4.0 5.0 - - + +
198A THR 2.8 18.5 + - - +
199A ASP* 1.3 69.9 - - - +
201A VAL* 1.3 73.9 + - - +
203A CYS* 3.4 2.4 + - - +
204A GLU* 3.0 32.3 + - - +
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 6.0 0.9 - - + -
199A ASP* 3.3 1.0 + - - +
200A THR* 1.3 87.2 + - - +
202A GLY* 1.3 56.9 + - - +
204A GLU* 3.2 18.2 + - - +
205A VAL* 2.9 37.1 + - + +
245A THR* 4.4 2.7 - - + +
248A LEU* 3.9 31.9 - - + +
249A GLY 5.0 1.8 - - - +
250A GLY* 3.7 31.6 - - - +
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 3.0 28.9 + - - -
201A VAL* 1.3 78.2 - - - +
203A CYS* 1.3 61.5 + - - +
205A VAL* 4.1 0.9 - - - +
206A ALA* 3.0 26.9 + - - +
241A ILE* 5.2 0.2 - - - +
245A THR* 3.8 22.0 + - - +
254A ALA* 3.8 9.4 - - - +
255A VAL* 5.3 2.3 + - - +
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Residues in contact with CYS 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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150A VAL* 4.3 11.4 - - + -
152A ALA* 4.0 15.7 - - + -
169A SER* 4.6 7.2 - - - -
171A ALA* 3.8 17.7 - - + -
197A THR* 4.2 10.8 - - - -
199A ASP 3.0 22.2 + - - +
200A THR 3.7 4.9 - - - +
201A VAL 3.3 0.2 - - - -
202A GLY* 1.3 75.0 - - - +
204A GLU* 1.3 60.4 + - - +
206A ALA* 3.7 1.4 - - - +
207A SER* 2.9 33.6 + - - -
254A ALA* 3.8 9.6 - - - +
259A ALA* 3.8 23.7 - - - +
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY 5.0 0.9 + - - +
134A PHE* 3.5 46.3 - - + +
135A PRO* 5.1 5.3 - - + +
136A ALA* 3.8 23.0 + - - +
137A GLU* 4.4 11.5 + - - +
150A VAL* 4.6 14.8 - - + +
200A THR* 3.0 18.8 + - - +
201A VAL* 3.4 28.2 + - - +
203A CYS* 1.3 74.4 - - - +
205A VAL* 1.3 67.2 + - - +
207A SER* 3.6 6.6 + - - -
208A ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 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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134A PHE* 3.7 16.4 - - + -
201A VAL* 2.9 32.4 + - + +
202A GLY 4.1 0.2 - - - +
204A GLU* 1.3 73.1 - - - +
206A ALA* 1.3 67.3 + - - +
208A ALA* 3.2 1.0 + - - -
209A VAL* 3.0 33.8 + - + +
241A ILE* 4.0 10.1 - - + +
244A LEU* 3.9 26.2 - - + -
245A THR* 3.5 25.4 - - - +
248A LEU* 3.6 28.9 - - + -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLY 3.0 19.8 + - - +
203A CYS 3.7 2.2 - - - +
205A VAL* 1.3 78.4 - - - +
207A SER* 1.3 56.9 + - - +
210A LYS* 2.9 35.9 + - - +
241A ILE* 3.9 22.7 - - + +
254A ALA 5.1 1.3 - - - +
255A VAL* 5.4 0.7 - - - -
259A ALA* 3.4 22.7 - - + +
260A GLY* 3.6 17.0 - - - -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR 5.5 0.4 - - - -
125A LYS* 3.5 37.5 - - - +
150A VAL* 5.7 0.7 - - - +
151A LEU 5.0 0.3 + - - -
152A ALA* 3.6 21.3 - - - +
203A CYS 2.9 19.3 + - - -
204A GLU* 3.9 8.2 - - - -
206A ALA* 1.3 77.7 - - - +
208A ALA* 1.3 62.0 + - - +
210A LYS* 3.4 26.8 - - - +
211A ASN* 3.7 9.2 + - - -
259A ALA 4.7 1.8 + - - -
263A ASP* 4.4 3.5 + - - -
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Residues in contact with ALA 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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126A GLY* 3.7 24.8 - - - +
127A ILE* 3.7 32.5 - - + -
134A PHE* 3.9 4.5 - - + -
204A GLU 3.1 18.0 + - - +
205A VAL 3.2 2.7 + - - +
207A SER* 1.3 76.9 - - - +
209A VAL* 1.3 64.7 + - + +
211A ASN* 3.5 16.7 + - - +
212A VAL 3.8 2.1 + - - -
304A THR* 3.8 15.1 + - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 5.5 0.4 - - + -
205A VAL* 3.0 21.6 + - + +
208A ALA* 1.3 77.2 - - + +
210A LYS* 1.3 65.7 + - - +
212A VAL* 2.9 14.1 + - - +
213A LEU* 3.0 16.7 + - + +
240A GLU 5.0 0.2 - - - -
241A ILE* 3.5 26.2 - - + +
244A LEU* 4.0 15.7 - - + -
308A LEU* 4.0 31.2 - - + -
319A MET* 3.9 9.6 - - + -
322A CYS* 3.8 25.1 - - - -
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Residues in contact with LYS 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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125A LYS* 4.0 3.8 - - - -
206A ALA 2.9 22.7 + - - +
207A SER* 3.4 12.3 - - - +
209A VAL* 1.3 76.6 - - - +
211A ASN* 1.3 85.8 + - - +
213A LEU* 3.7 3.2 - - - +
214A ALA* 2.9 30.1 + - - +
241A ILE* 4.3 3.7 - - + +
260A GLY 5.3 0.9 - - - +
263A ASP* 3.2 27.8 + - + +
264A LEU* 3.8 35.7 - - + +
267A THR* 2.9 30.6 + - - +
268A CYS* 4.9 0.2 - - - -
400A NDE 2.7 32.5 + - - -
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Residues in contact with ASN 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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125A LYS* 4.1 12.5 + - - +
126A GLY* 5.6 0.4 - - - -
207A SER 3.7 11.7 + - - -
208A ALA* 3.5 9.4 + - - +
209A VAL 3.1 0.8 - - - -
210A LYS* 1.3 108.3 + - - +
212A VAL* 1.3 60.8 + - - +
214A ALA* 3.5 2.1 + - - -
215A ILE* 3.3 18.9 + - - +
267A THR* 4.0 0.9 - - - +
275A ASN* 3.0 37.2 + - - +
300A GLU* 3.6 22.0 - - + +
301A GLY* 3.7 14.1 - - - +
400A NDE 3.3 11.8 + - - -
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Residues in contact with VAL 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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208A ALA 4.1 2.7 - - - +
209A VAL 2.9 7.6 + - - +
211A ASN* 1.3 75.2 - - - +
213A LEU* 1.3 64.8 + - - +
215A ILE* 3.0 22.4 + - - +
216A GLY 3.3 3.8 + - - -
301A GLY* 3.7 23.1 - - - +
304A THR* 3.9 18.2 - - + -
305A ALA* 3.9 14.1 - - + -
308A LEU* 3.9 22.4 - - + -
322A CYS* 4.0 24.7 - - + +
325A ILE* 3.5 26.6 - - + +
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Residues in contact with LEU 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 VAL* 3.0 28.0 + - + +
210A LYS 3.7 1.6 - - - +
212A VAL* 1.3 75.4 - - - +
214A ALA* 1.3 56.8 + - - +
216A GLY* 3.0 4.9 + - - -
217A SER 2.9 23.0 + - - -
233A LEU* 3.7 15.0 - - + +
237A GLY* 3.5 38.6 - - - +
240A GLU* 4.3 1.3 - - - +
241A ILE* 4.2 5.8 - - + -
264A LEU* 3.7 31.2 - - + -
268A CYS* 4.1 3.4 - - - -
321A LEU* 3.8 30.3 - - + -
322A CYS* 3.9 16.8 - - - -
325A ILE* 4.0 5.3 - - + +
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Residues in contact with ALA 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 LYS 2.9 17.7 + - - +
211A ASN 3.7 6.3 - - - +
212A VAL 3.2 0.4 - - - -
213A LEU* 1.3 73.2 - - - +
215A ILE* 1.3 65.3 + - - +
217A SER* 3.3 3.5 + - - +
218A GLY 3.0 18.0 + - - -
267A THR* 3.5 40.2 - - + +
268A CYS* 3.8 11.4 - - - -
273A SER* 4.2 1.1 - - - +
275A ASN* 4.0 7.9 - - + -
276A PHE* 3.4 11.9 - - - +
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Residues in contact with ILE 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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211A ASN 3.5 9.9 - - - +
212A VAL* 3.0 10.4 + - - +
214A ALA* 1.3 77.8 - - - +
216A GLY* 1.3 55.7 + - - +
218A GLY 3.2 2.3 + - - -
219A VAL* 2.9 28.1 + - + +
275A ASN* 3.4 24.2 - - + +
278A VAL* 4.6 2.9 - - + -
279A GLY* 3.2 24.5 - - - +
282A LEU* 4.1 17.0 - - + -
301A GLY* 3.7 32.8 - - - +
302A VAL* 3.7 20.2 - - + +
305A ALA* 5.8 0.2 - - + -
325A ILE* 3.9 16.2 - - + -
328A ILE* 6.2 0.2 - - + -
329A VAL* 4.2 10.1 - - + -
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Residues in contact with GLY 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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212A VAL 3.3 4.4 + - - -
213A LEU 3.0 8.9 + - - -
215A ILE* 1.3 79.6 - - - +
217A SER* 1.3 60.3 + - - +
219A VAL* 3.2 9.8 + - - +
220A ALA* 3.0 22.0 + - - +
233A LEU* 3.7 12.5 - - - +
325A ILE* 3.7 24.3 - - - +
328A ILE* 6.4 0.2 - - - -
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Residues in contact with SER 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 LEU 2.9 7.5 + - - -
214A ALA 3.7 7.6 - - - -
216A GLY* 1.3 74.0 - - - +
218A GLY* 1.3 62.4 + - - +
220A ALA* 3.2 7.4 + - - +
221A ASN* 3.1 21.7 + - - +
230A ARG* 3.6 17.1 + - - +
233A LEU* 3.8 18.0 - - - +
268A CYS* 2.5 47.9 + - - +
276A PHE* 3.7 3.8 - - - -
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Residues in contact with GLY 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 ALA 3.0 10.7 + - - -
215A ILE 3.2 2.4 + - - -
217A SER* 1.3 77.1 - - - +
219A VAL* 1.3 55.4 + - - +
221A ASN* 3.2 2.8 + - - +
222A GLY 2.9 24.6 + - - -
276A PHE* 3.3 40.0 - - - -
279A GLY 3.3 7.4 - - - -
280A LYS* 3.1 8.8 - - - -
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Residues in contact with VAL 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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215A ILE* 2.9 24.6 + - + +
216A GLY* 3.2 11.9 + - - +
218A GLY* 1.3 73.9 - - - +
220A ALA* 1.3 64.6 + - - +
222A GLY 3.2 1.4 + - - -
223A LEU* 2.9 41.9 + - + +
279A GLY* 3.3 23.1 + - - +
282A LEU* 4.2 13.5 - - + -
283A GLY* 4.0 3.7 - - - -
325A ILE* 6.1 0.2 - - + -
328A ILE* 4.3 21.8 - - + -
335A PRO* 3.9 18.2 - - + +
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Residues in contact with ALA 220 (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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216A GLY 3.0 12.4 + - - +
217A SER* 3.2 12.8 + - - +
219A VAL* 1.3 79.4 - - - +
221A ASN* 1.3 58.7 + - - +
223A LEU* 3.3 6.1 + - - +
224A GLY 3.3 0.2 + - - -
225A MET* 3.0 56.3 + - + +
226A GLY 5.9 0.9 - - - +
229A ALA* 5.2 8.3 - - + -
230A ARG* 5.5 6.5 - - + +
233A LEU* 5.1 7.4 - - + -
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Residues in contact with ASN 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 SER 3.1 8.1 + - - +
218A GLY 3.2 7.4 + - - +
220A ALA* 1.3 74.2 - - - +
222A GLY* 1.3 58.8 + - - +
224A GLY* 3.0 18.5 + - - -
225A MET 4.2 12.6 + - - +
230A ARG* 3.9 16.9 - - - +
276A PHE* 3.7 24.6 - - + -
280A LYS* 3.4 32.1 - - - +
284A LYS* 4.7 4.9 + - - -
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Residues in contact with GLY 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLY 2.9 11.1 + - - -
219A VAL 3.7 4.0 - - - -
221A ASN* 1.3 79.3 + - - +
223A LEU* 1.3 59.3 + - - +
224A GLY 3.2 1.0 + - - -
280A LYS* 3.8 24.7 - - - -
283A GLY 3.6 16.2 - - - +
284A LYS* 3.8 26.5 + - - +
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Residues in contact with LEU 223 (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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219A VAL* 2.9 37.1 + - + +
220A ALA* 3.6 6.3 - - - +
221A ASN 3.2 0.2 - - - -
222A GLY* 1.3 76.6 - - - +
224A GLY* 1.3 59.4 + - - +
225A MET* 3.7 12.3 + - + +
283A GLY 3.7 13.5 - - - +
335A PRO* 4.0 25.4 - - + +
336A ARG* 3.6 56.8 + - + +
339A LEU* 4.4 23.3 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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