Contacts of the helix formed by residues 243 - 268 (chain D) in PDB entry 1D7W
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 MET 243 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 4.0 11.2 - - + -
88B GLN* 3.5 16.2 - - - +
91B GLN* 3.4 15.7 - - - +
605B HEM 1.6 75.6 - - + -
241D SER 4.2 1.8 - - - -
242D GLU* 1.3 79.1 + - - +
244D PRO* 1.4 65.0 - - + +
245D GLU* 3.2 30.3 - - - +
246D LEU* 2.9 25.7 + - + +
247D THR* 3.1 14.6 + - - -
361D LEU* 3.7 31.0 - - + -
364D VAL* 4.6 3.8 - - + -
365D PHE* 4.7 1.6 - - + -
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Residues in contact with PRO 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D SER 4.8 1.3 - - - +
243D MET* 1.4 83.1 - - + +
245D GLU* 1.3 59.7 + - - +
247D THR* 3.5 9.9 + - - +
248D SER* 2.7 36.0 + - - -
343D MET* 3.3 28.5 - - + -
364D VAL* 3.2 34.1 - - + +
367D ALA 4.2 16.6 - - - +
370D ARG* 4.7 5.2 - - + -
371D VAL* 4.2 10.8 - - + +
380D ILE* 3.7 14.2 - - + +
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Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 5.7 4.1 - - + +
87B MET* 5.1 3.5 - - + +
88B GLN* 3.1 21.0 - - - +
243D MET* 3.2 40.3 - - - +
244D PRO* 1.3 76.7 - - - +
246D LEU* 1.3 62.4 + - - +
248D SER* 3.5 4.0 + - - -
249D MET* 3.3 25.8 + - - +
342D PHE 4.5 1.4 - - - +
343D MET* 3.5 37.1 - - + +
344D PHE 5.8 0.2 - - - +
361D LEU* 3.9 3.7 - - - +
364D VAL* 4.5 0.2 - - - +
380D ILE* 3.4 22.2 - - + +
384D LEU* 3.8 25.3 - - + +
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Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN* 3.4 25.7 + - - +
91B GLN* 3.8 16.2 - - + +
92B LEU* 3.8 31.9 - - + +
95B HIS* 3.7 23.3 - - + +
239D ARG 3.2 30.7 - - - +
240D SER* 4.0 4.0 - - - +
242D GLU* 4.3 4.3 - - + -
243D MET* 2.9 11.4 + - + +
245D GLU* 1.3 72.8 - - - +
247D THR* 1.3 67.6 + - - +
248D SER 3.0 1.6 - - - -
249D MET* 2.8 15.2 + - - +
250D HIS* 3.0 33.4 + - + +
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Residues in contact with THR 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU* 6.4 0.2 - - + -
211D LEU* 3.7 13.7 - - + -
233D PHE* 3.6 34.3 - - + -
240D SER 2.5 23.4 + - - +
241D SER* 3.3 13.5 - - - -
243D MET 3.1 6.5 + - - -
244D PRO* 3.7 11.9 - - - +
246D LEU* 1.3 77.9 - - - +
248D SER* 1.3 53.3 + - - +
250D HIS* 3.2 5.5 + - - +
251D THR* 2.6 41.9 + - - +
368D SER* 5.8 1.2 - - - -
371D VAL* 4.3 15.3 - - + +
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Residues in contact with SER 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D PRO 2.7 22.0 + - - -
245D GLU 3.6 7.6 - - - -
246D LEU 3.0 0.4 - - - -
247D THR* 1.3 77.5 - - - +
249D MET* 1.3 58.5 + - - +
251D THR* 3.8 1.0 - - - -
252D LEU* 3.1 27.7 + - - +
371D VAL* 5.0 0.2 - - - +
377D ILE* 3.7 30.2 - - - +
380D ILE* 3.2 31.2 - - - +
381D LEU* 4.0 15.1 - - - +
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Residues in contact with MET 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 3.7 29.8 - - + +
88B GLN* 3.9 18.8 - - + +
89B TRP* 4.1 16.6 - - + -
92B LEU* 3.9 23.3 - - + -
245D GLU 3.3 13.9 + - - +
246D LEU* 2.8 9.2 + - - +
248D SER* 1.3 78.7 - - - +
250D HIS* 1.3 57.0 - - - +
252D LEU* 3.5 9.8 + - + +
253D LEU* 3.1 35.2 + - + +
381D LEU* 3.7 25.6 - - - -
384D LEU* 4.4 1.6 - - - -
533D LEU* 4.0 28.3 - - + -
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Residues in contact with HIS 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.1 6.4 - - + +
95B HIS* 4.9 5.1 + - - +
175D MET* 3.2 49.2 + - + +
176D VAL* 5.0 6.1 - - - +
211D LEU* 3.8 19.8 - - + +
235D ALA* 3.8 9.0 - - + +
237D ASP* 4.6 6.7 - - + +
240D SER* 3.5 35.4 + - - -
246D LEU* 3.0 40.2 + - + +
247D THR 3.5 7.4 - - - +
249D MET* 1.3 74.3 - - - +
251D THR* 1.3 59.7 + - - +
253D LEU* 3.7 5.1 + - - +
254D LEU* 3.1 28.8 + - - +
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Residues in contact with THR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ALA 3.3 26.5 - - - +
210D LEU* 4.1 18.7 - - + +
211D LEU* 3.5 21.4 + - - +
247D THR* 2.6 27.1 + - - +
248D SER 3.8 4.7 - - - -
250D HIS* 1.3 73.4 - - - +
252D LEU* 1.3 61.0 + - - +
254D LEU* 3.4 4.3 + - + +
255D ARG* 3.0 51.1 + - - +
377D ILE* 4.1 11.1 - - + +
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D SER 3.1 18.8 + - - +
249D MET* 3.6 20.2 - - + +
250D HIS 3.4 0.2 - - - -
251D THR* 1.3 76.6 - - - +
253D LEU* 1.3 59.3 + - + +
255D ARG* 3.4 7.2 + - - +
256D GLU* 3.1 24.9 + - - +
377D ILE* 4.3 6.6 - - + +
381D LEU* 4.2 6.7 - - + -
533D LEU* 4.1 20.4 - - + -
536D ILE* 3.9 12.1 - - + +
537D ILE* 3.8 33.0 - - + -
540D ASN* 3.8 26.9 + - + -
541D THR* 3.8 22.0 - - + -
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 5.2 8.7 - - + -
92B LEU* 4.2 17.5 - - + -
175D MET* 3.8 21.5 - - + -
176D VAL* 3.8 32.6 - - + +
249D MET* 3.1 19.8 + - + +
250D HIS* 4.1 3.1 - - - +
252D LEU* 1.3 78.1 - - + +
254D LEU* 1.4 59.7 + - - +
256D GLU* 3.1 9.5 + - + +
257D HIS* 2.9 28.1 + - - +
284D VAL* 4.7 16.0 - - + +
287D MET* 5.7 3.8 - - + -
288D VAL* 4.2 14.4 - - + -
291D ILE* 6.3 0.7 - - + -
533D LEU* 5.7 2.2 - - + -
536D ILE* 5.0 22.7 - - + -
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Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D VAL* 4.6 5.5 - - + +
187D LEU* 5.5 0.9 - - + +
197D LEU* 3.6 42.3 - - + +
198D ALA 4.0 11.2 - - - +
199D VAL* 4.1 18.2 - - + -
209D ALA* 4.6 7.9 - - + +
210D LEU 4.1 22.7 - - - +
211D LEU* 4.0 21.3 - - + -
212D PRO* 4.8 3.1 - - + -
250D HIS 3.1 20.2 + - - +
251D THR* 3.4 6.3 + - - +
253D LEU* 1.4 74.8 - - - +
255D ARG* 1.3 62.9 + - + +
257D HIS* 3.5 4.9 - - - +
258D ASN* 3.3 22.7 + - - +
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Residues in contact with ARG 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASP* 3.0 35.4 + - - +
208D ARG* 3.6 23.7 - - - +
209D ALA* 2.9 39.9 + - + +
210D LEU* 4.3 0.6 - - - +
251D THR* 3.0 28.6 + - - +
252D LEU* 3.6 5.6 - - - +
254D LEU* 1.3 75.7 - - + +
256D GLU* 1.3 60.1 + - - +
258D ASN* 3.2 7.6 + - - +
259D ARG* 2.9 25.8 + - - +
377D ILE* 3.2 28.0 - - - +
378D ASP* 4.7 1.2 + - - -
540D ASN* 2.9 46.7 + - - +
541D THR* 4.3 3.4 - - - +
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Residues in contact with GLU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D LEU 3.1 10.5 + - - +
253D LEU* 3.1 14.8 + - + +
255D ARG* 1.3 75.7 - - - +
257D HIS* 1.4 57.6 + - - +
259D ARG* 3.3 16.3 + - - +
260D LEU* 2.9 46.1 + - + +
284D VAL* 4.5 3.8 - - + -
287D MET* 3.0 44.0 - - - +
536D ILE* 4.2 14.4 - - + -
539D ASP* 4.2 6.7 - - - +
540D ASN* 3.1 25.0 + - - +
570D LEU* 5.0 0.5 - - - +
2609D ACT 4.4 4.7 - - - +
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Residues in contact with HIS 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D VAL* 5.2 0.2 - - + -
177D TYR* 2.8 37.7 + + - +
195D GLY 2.8 24.8 + - - -
196D LEU 3.9 0.6 - - - -
197D LEU* 3.4 26.7 + - + +
253D LEU 2.9 12.8 + - - +
254D LEU 3.5 9.0 - - - +
256D GLU* 1.4 77.1 - - - +
258D ASN* 1.3 82.3 + - - +
260D LEU* 3.3 3.5 + - - +
261D ALA* 3.0 25.4 + - + +
277D TYR* 3.6 21.6 - + - -
280D ALA* 3.6 25.6 - - + +
284D VAL* 4.0 10.0 - - + +
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Residues in contact with ASN 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D LEU* 3.4 26.8 - - + +
197D LEU* 2.8 45.8 + - - +
199D VAL* 3.6 19.0 - - - +
209D ALA* 5.5 1.0 - - - +
254D LEU* 3.3 11.3 + - - +
255D ARG* 3.2 9.6 + - - +
257D HIS* 1.3 85.4 - - - +
259D ARG* 1.3 63.4 + - - +
261D ALA 3.9 0.2 - - - -
262D THR* 2.9 28.6 + - - -
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Residues in contact with ARG 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ARG 2.9 16.5 + - - +
256D GLU* 3.6 14.3 + - - +
257D HIS 3.3 0.2 - - - -
258D ASN* 1.3 73.6 - - - +
260D LEU* 1.3 67.9 + - + +
262D THR* 3.2 7.2 + - - -
263D GLU* 3.1 53.4 + - + +
535D ARG* 5.0 1.6 - - - +
539D ASP* 3.1 63.8 + - - +
540D ASN* 4.0 5.4 - - - +
569D ALA* 5.0 10.5 - - - +
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Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D GLU* 2.9 40.2 + - + +
257D HIS 3.5 4.3 - - - +
259D ARG* 1.3 77.6 - - + +
261D ALA* 1.3 57.0 + - - +
263D GLU* 3.5 9.7 + - - +
264D LEU* 2.9 38.7 + - + +
280D ALA* 3.8 11.9 - - + +
283D ILE* 3.6 50.5 - - + -
284D VAL* 3.7 22.7 - - + -
287D MET* 4.4 0.4 - - + -
570D LEU* 4.1 12.8 - - + -
572D LEU* 4.1 12.3 - - + -
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 3.6 22.4 - - - +
195D GLY 4.0 11.4 - - - +
196D LEU* 3.8 15.5 - - + -
257D HIS 3.0 16.8 + - - +
258D ASN 3.9 0.2 - - - +
260D LEU* 1.3 77.5 - - - +
262D THR* 1.4 56.0 - - - +
264D LEU* 4.4 4.5 - - - -
265D LYS* 3.0 27.5 + - - +
276D LEU* 3.6 12.6 - - + +
280D ALA* 4.0 12.1 - - + +
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Residues in contact with THR 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 6.0 1.6 - - - +
196D LEU* 4.5 7.5 - - - +
258D ASN 2.9 17.8 + - - -
259D ARG* 3.4 11.4 - - - -
260D LEU 3.2 0.2 - - - -
261D ALA* 1.4 73.3 - - - +
263D GLU* 1.3 70.2 + - + +
265D LYS* 3.0 18.4 + - - +
266D SER* 3.1 20.0 + - - +
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Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D ARG* 3.1 56.6 + - - +
260D LEU* 3.9 8.1 - - - +
262D THR* 1.3 83.4 - - + +
264D LEU* 1.3 57.9 + - - +
266D SER* 3.2 8.3 + - - -
267D LEU* 2.9 38.5 + - + +
570D LEU 5.6 1.4 - - - +
572D LEU* 3.5 27.1 - - + +
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D LEU 2.9 29.6 + - - +
261D ALA* 3.8 0.4 - - - +
263D GLU* 1.3 76.3 - - - +
265D LYS* 1.3 57.2 + - - +
267D LEU* 3.6 5.2 - - + +
268D ASN* 2.8 35.6 + - - +
271D TRP* 3.9 12.8 - - + -
276D LEU* 3.7 19.2 - - + +
279D GLU* 3.9 16.8 - - + -
280D ALA* 3.9 26.7 - - + +
283D ILE* 4.1 10.1 - - + -
572D LEU* 4.0 18.6 - - + -
575D TRP* 3.9 33.4 - - + -
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Residues in contact with LYS 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D GLN* 4.9 8.5 + - - +
194D LEU* 3.9 28.4 - - + +
261D ALA 3.0 15.7 + - - +
262D THR* 3.0 15.0 + - - +
264D LEU* 1.3 78.1 - - - +
266D SER* 1.4 59.2 + - - +
268D ASN 4.5 1.3 - - - -
269D PRO* 3.4 46.6 + - + +
271D TRP 4.4 6.7 + - - +
276D LEU* 3.5 24.4 - - + +
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Residues in contact with SER 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D THR* 3.1 17.5 + - - +
263D GLU* 3.2 10.3 + - - -
265D LYS* 1.4 77.1 - - - +
267D LEU* 1.3 65.6 + - - +
269D PRO* 4.1 10.4 - - - +
576D ARG* 3.6 8.0 + - - -
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Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D GLU* 2.9 27.3 + - + +
264D LEU* 3.6 10.5 - - + +
265D LYS 3.3 0.2 - - - -
266D SER* 1.3 82.5 - - - +
268D ASN* 1.3 74.3 + - - +
269D PRO* 3.7 4.0 - - - +
572D LEU* 4.1 29.4 - - + +
573D ALA* 4.6 6.5 - - - -
575D TRP 5.3 0.4 - - - +
576D ARG* 2.5 75.1 + - + +
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Residues in contact with ASN 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D LEU* 2.8 11.4 + - - +
265D LYS* 3.6 6.7 - - - +
267D LEU* 1.3 88.1 - - - +
269D PRO* 1.3 66.7 - - - +
270D ARG* 3.3 3.4 - - + -
271D TRP* 3.0 66.0 + - + +
575D TRP 2.8 26.0 + - - -
576D ARG* 3.4 2.6 - - - +
577D GLU* 2.6 32.9 + - + +
578D ALA 3.9 1.0 + - - -
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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