Contacts of the helix formed by residues 245 - 272 (chain A) in PDB entry 6DWN
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 ASN 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 4.8 8.3 - - - +
240A LEU* 3.4 23.6 + - - +
241A ARG 5.5 0.7 - - - +
243A LEU 2.8 11.2 + - - +
244A PRO* 1.3 73.7 - - - +
246A PRO* 1.3 68.4 - - - +
247A SER* 3.4 12.1 + - - -
248A LEU* 3.1 39.1 + - + +
249A ASN* 3.0 34.1 + - - +
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Residues in contact with PRO 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PRO* 3.8 7.6 - - + +
245A ASN* 1.3 87.4 - - - +
247A SER* 1.3 64.4 + - - +
249A ASN* 3.9 7.8 - - + +
250A ALA* 3.1 25.5 + - - +
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASN* 2.9 30.2 + - - +
226A GLU* 3.8 17.5 + - - +
227A VAL* 3.6 19.6 - - - +
245A ASN* 3.2 10.2 + - - -
246A PRO* 1.3 84.7 - - - +
248A LEU* 1.3 61.3 + - - +
250A ALA* 4.8 0.9 - - - -
251A PHE* 3.2 9.0 + - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 4.0 25.8 - - + -
111A THR* 4.4 18.6 - - + -
114A LEU* 4.6 6.1 - - + -
227A VAL* 4.5 12.1 - - + -
232A ASN* 5.3 0.9 - - - +
234A ALA* 4.6 11.7 - - + -
241A ARG* 3.8 31.4 - - + +
245A ASN* 3.1 29.4 + - + +
247A SER* 1.3 76.7 - - - +
249A ASN* 1.3 66.4 + - - +
251A PHE* 3.1 8.6 + - + +
252A LYS* 3.0 45.5 + - + +
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Residues in contact with ASN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU 5.5 0.4 + - - -
244A PRO* 5.4 1.4 - - - +
245A ASN* 3.0 34.2 + - - +
246A PRO* 3.9 7.1 - - + +
248A LEU* 1.3 77.8 - - - +
250A ALA* 1.3 56.7 + - - +
252A LYS* 3.2 26.6 + - - +
253A ASP* 2.9 30.0 + - - +
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ASN 5.7 3.4 - - - +
223A ASN* 4.1 15.3 - - - +
246A PRO 3.1 17.7 + - - +
247A SER* 3.8 4.5 - - - +
249A ASN* 1.3 76.5 - - - +
251A PHE* 1.3 60.7 + - - +
253A ASP* 3.8 6.8 - - - +
254A LEU* 3.1 28.1 + - - +
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Residues in contact with PHE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR* 3.6 21.3 - - - -
114A LEU* 3.9 29.2 - - + -
115A ILE* 3.9 8.7 - - + -
223A ASN* 3.9 8.7 - - - +
224A PHE* 3.6 37.2 - + - -
227A VAL* 3.9 30.3 - - + -
228A VAL* 3.8 22.7 - - + -
247A SER 3.2 13.9 + - - +
248A LEU* 3.1 14.5 + - + +
250A ALA* 1.3 77.6 - - - +
252A LYS* 1.3 61.3 + - - +
255A ASN* 3.3 44.5 + - - +
602A AQ4 4.2 6.9 - - - +
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.5 24.6 + - - +
114A LEU* 3.9 25.8 - - + -
241A ARG 4.7 6.5 + - - -
248A LEU* 3.0 32.1 + - - +
249A ASN* 3.2 23.1 + - - +
251A PHE* 1.3 77.2 - - - +
253A ASP* 1.3 64.2 + - - +
255A ASN* 3.6 4.1 + - - +
256A GLU* 3.2 34.6 + - + +
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Residues in contact with ASP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASN 2.9 16.4 + - - +
250A ALA* 3.8 8.3 - - - +
252A LYS* 1.3 77.1 - - - +
254A LEU* 1.3 62.7 + - - +
256A GLU* 3.2 19.0 + - - +
257A LYS* 3.3 33.6 + - - +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A SER 3.9 18.8 - - - +
217A LEU* 4.6 8.3 - - + +
220A LEU* 4.2 9.0 - - + +
221A ASN 4.2 7.6 - - - +
222A ASN* 2.9 39.5 - - - +
223A ASN* 5.0 0.9 - - - +
250A ALA* 3.1 14.3 + - + +
253A ASP* 1.3 78.6 - - + +
255A ASN* 1.3 66.0 + - - +
257A LYS* 3.2 28.6 + - + +
258A PHE* 3.0 26.4 + - + -
602A AQ4 3.6 20.4 - - - -
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Residues in contact with ASN 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU 2.9 29.2 - - - +
115A ILE* 3.6 15.2 - - - +
116A SER 5.4 4.1 + - - +
224A PHE* 4.2 3.5 - - - -
251A PHE* 3.3 34.8 + - - +
252A LYS* 4.0 4.5 - - - +
254A LEU* 1.3 75.8 - - - +
256A GLU* 1.3 61.4 + - + +
258A PHE* 3.5 4.6 + - - +
259A TYR* 3.2 22.2 + - - +
312A LEU* 5.7 0.3 - - - +
602A AQ4 2.2 53.1 + - - -
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LYS* 3.2 20.6 + - - +
253A ASP* 3.2 12.4 + - - +
254A LEU 3.2 0.8 - - - -
255A ASN* 1.3 74.4 - - + +
257A LYS* 1.3 65.8 + - + +
259A TYR* 3.3 7.4 + - - +
260A SER* 3.0 26.7 + - - +
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A SER* 4.8 12.3 + - - +
217A LEU* 4.8 9.0 - - + -
220A LEU* 5.8 3.6 - - - +
253A ASP* 3.3 31.6 + - - +
254A LEU* 3.2 29.0 + - + +
256A GLU* 1.3 74.6 - - + +
258A PHE* 1.3 53.8 + - - +
260A SER* 3.0 7.5 + - - -
261A PHE* 2.6 37.9 + - - +
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Residues in contact with PHE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.6 48.2 - - + -
222A ASN* 4.2 0.2 - - - -
254A LEU* 3.0 16.0 + - + +
255A ASN* 3.6 10.1 - - - +
256A GLU 3.3 0.2 - - - -
257A LYS* 1.3 75.4 - - - +
259A TYR* 1.3 57.7 + - - +
261A PHE* 3.1 13.1 + + - +
262A MET* 2.9 28.4 + - - +
312A LEU* 3.6 32.6 - - + +
315A PHE* 3.9 26.9 - + - -
316A GLY* 5.1 2.0 - - - -
319A PHE* 4.1 13.7 - + - -
602A AQ4 3.2 55.2 - + + -
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Residues in contact with TYR 259 (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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116A SER* 3.4 32.9 + - - -
117A ASN* 3.6 22.7 - - + +
255A ASN 3.2 13.9 + - - +
256A GLU* 3.8 7.2 - - - +
257A LYS 3.2 0.4 - - - -
258A PHE* 1.3 78.3 - - - +
260A SER* 1.3 60.2 + - - +
262A MET* 3.6 26.4 - - + +
263A GLN* 3.3 37.4 + - - +
305A GLU* 2.6 41.3 + - - +
309A ASN* 3.4 15.9 + - + +
312A LEU* 3.5 20.0 - - + -
603A CPS 3.8 14.4 - - + -
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU* 3.0 19.2 + - - +
257A LYS* 3.5 6.1 - - - -
259A TYR* 1.3 74.8 - - - +
261A PHE* 1.3 65.3 + - - +
262A MET 3.2 0.2 - - - -
263A GLN* 3.2 13.9 + - - +
264A LYS* 3.1 22.7 + - - +
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A CYS* 5.9 1.3 - - - -
203A PHE* 4.1 24.2 - + - -
207A TYR* 3.9 13.2 - + - -
213A GLU* 3.2 45.8 - - + -
217A LEU* 4.5 24.0 - - + -
257A LYS 2.6 17.7 + - - +
258A PHE* 3.3 16.4 - + - +
260A SER* 1.3 72.3 - - - +
262A MET* 1.3 66.1 + - - +
264A LYS* 3.3 11.6 + - + +
265A MET* 3.0 61.8 + - + +
312A LEU* 5.9 3.8 - - + -
315A PHE* 5.4 8.5 - + - -
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Residues in contact with MET 262 (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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203A PHE* 6.2 4.0 - - + -
258A PHE 2.9 12.4 + - - +
259A TYR* 3.6 51.4 - - + +
260A SER 3.2 0.2 - - - -
261A PHE* 1.3 79.5 - - - +
263A GLN* 1.3 56.0 + - + +
265A MET* 2.8 7.3 + - - +
266A VAL* 2.6 52.2 + - + +
305A GLU* 5.7 0.4 - - + -
308A ILE* 4.3 10.8 - - + +
309A ASN* 3.6 32.3 - - + +
311A VAL* 4.8 9.2 - - + -
312A LEU* 4.5 17.5 - - + -
603A CPS 3.9 17.5 - - + -
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Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A TYR* 3.3 21.4 + - - +
260A SER* 3.2 14.0 + - - +
262A MET* 1.3 76.4 - - + +
264A LYS* 1.3 64.5 + - - +
266A VAL* 4.0 6.0 - - - +
267A LYS* 2.8 52.4 + - - +
603A CPS 3.6 55.8 - - + +
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 4.4 13.8 - - - +
213A GLU* 2.9 34.9 + - - +
260A SER 3.1 12.3 + - - +
261A PHE* 3.4 15.9 - - + +
263A GLN* 1.3 76.6 - - - +
265A MET* 1.3 58.3 + - - +
267A LYS* 3.7 6.6 - - - +
268A GLU* 3.0 59.6 + - + +
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Residues in contact with MET 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A CYS* 5.1 1.3 - - - -
203A PHE* 3.4 49.8 - - + -
205A ARG* 2.8 44.0 - - - +
207A TYR* 4.0 2.7 - - + +
261A PHE* 3.0 50.6 + - + +
262A MET* 2.8 15.0 + - + +
264A LYS* 1.3 74.5 - - - +
266A VAL* 1.3 61.1 + - + +
268A GLU* 3.3 8.3 + - - +
269A HIS* 2.8 41.4 + - + +
282A THR* 5.3 2.0 - - + +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A MET* 2.6 37.1 + - + +
263A GLN* 4.0 5.4 - - - +
265A MET* 1.3 72.6 - - + +
267A LYS* 1.3 57.1 + - - +
269A HIS* 3.3 6.1 + - - +
270A TYR* 2.9 27.6 + - - +
282A THR* 4.5 12.1 - - + -
286A ILE* 4.2 13.1 - - + +
308A ILE* 3.4 33.7 - - + -
311A VAL* 5.5 2.7 - - + -
603A CPS 3.8 37.2 - - + -
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLN* 2.8 45.5 + - - +
264A LYS* 3.7 6.1 - - - +
266A VAL* 1.3 74.5 - - - +
268A GLU* 1.3 65.8 + - + +
270A TYR* 3.2 6.4 + - - +
271A LYS* 3.1 24.4 + - - +
603A CPS 3.8 30.7 - - + -
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 3.2 29.0 + - - -
264A LYS* 3.0 46.8 + - + +
265A MET* 3.7 8.2 - - - +
267A LYS* 1.3 76.2 - - + +
269A HIS* 1.3 63.1 + - + +
271A LYS* 3.8 5.2 + - - +
272A THR* 3.2 31.1 + - - +
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 3.1 25.1 + - + -
205A ARG* 5.4 3.8 - - - -
265A MET* 2.8 38.9 + - + +
266A VAL 3.7 4.0 - - - +
267A LYS 3.1 0.4 - - - -
268A GLU* 1.3 81.4 - - + +
270A TYR* 1.3 60.1 + - - +
271A LYS 3.1 1.6 - - - -
272A THR* 3.2 1.1 + - - -
273A PHE* 2.8 33.7 + - - +
279A ARG* 3.4 17.0 + - - +
280A ASP* 2.9 25.3 + - - -
282A THR* 3.5 20.1 - - + -
283A ASP* 3.1 26.0 - - - +
286A ILE* 3.9 11.4 - - + -
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A VAL 2.9 16.9 + - - +
267A LYS* 3.2 5.8 + - - +
269A HIS* 1.3 75.8 - - - +
271A LYS* 1.3 66.2 + - - +
272A THR 3.5 0.2 + - - -
273A PHE* 3.5 16.4 + - + +
286A ILE* 4.1 20.8 - - + +
290A GLN* 4.9 15.5 - - + -
603A CPS 3.7 50.2 + - + -
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS 3.1 16.3 + - - +
268A GLU* 4.0 7.6 - - - +
270A TYR* 1.3 83.6 - - - +
272A THR* 1.3 64.3 + - + +
273A PHE 3.6 2.9 + - - +
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU 3.2 18.1 + - - +
269A HIS 3.2 1.0 + - - -
271A LYS* 1.3 87.1 - - + +
273A PHE* 1.3 64.6 + - - +
274A GLU* 3.3 6.1 + - - +
279A ARG* 2.7 41.2 + - - -
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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
------------------------------------------------------------
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