Contacts of the helix formed by residues 309 - 336 (chain D) 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 309 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D SER* 4.2 9.2 + - - -
119D GLN* 2.9 33.3 + - - +
120D SER* 5.4 0.9 - - - -
121D MET 5.2 0.8 + - - -
134D ARG* 3.3 7.3 + - - -
259D TYR* 3.6 27.2 + - + +
262D MET* 3.6 22.2 - - + +
305D GLU 3.1 17.5 + - - +
306D LYS* 3.0 26.8 - - - +
308D ILE* 1.3 74.7 - - - +
310D ILE* 1.3 63.6 + - - +
311D VAL 3.2 1.1 - - - -
312D LEU* 3.1 17.7 + - + +
313D ASP* 3.9 7.8 + - - +
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D MET* 3.8 28.9 - - + -
134D ARG* 3.9 33.7 - - + +
137D LEU* 4.1 20.9 - - + -
138D ALA* 4.0 20.2 - - + +
281D ILE* 6.0 0.2 - - + -
285D LEU* 4.2 9.9 - - + -
306D LYS 3.4 20.6 - - - +
307D ILE* 3.6 18.2 - - - +
308D ILE 2.9 1.2 + - - -
309D ASN* 1.3 74.5 - - - +
311D VAL* 1.3 66.1 + - - +
312D LEU 3.0 2.8 + - - -
313D ASP* 3.0 15.8 + - - +
314D LEU* 3.2 16.7 + - + +
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Residues in contact with VAL 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D CYS* 4.5 6.8 - - + -
203D PHE* 4.7 15.6 - - + -
262D MET* 4.5 16.4 - - + -
266D VAL* 5.3 3.6 - - + -
281D ILE* 3.6 21.5 - - + -
282D THR* 3.9 23.8 - - + +
285D LEU* 3.6 22.0 - - + +
308D ILE* 3.1 20.8 + - + +
309D ASN 4.5 0.4 - - - -
310D ILE* 1.3 76.5 - - - +
312D LEU* 1.3 59.2 + - + +
313D ASP 3.4 0.2 - - - -
314D LEU* 3.9 8.4 - - - +
315D PHE* 2.9 32.4 + - - +
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Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D SER* 3.3 26.5 - - - +
255D ASN 5.6 0.7 - - - +
258D PHE* 3.7 49.0 - - + +
259D TYR* 3.8 26.7 - - + -
262D MET* 4.4 16.2 - - + -
309D ASN 3.1 14.2 + - - +
310D ILE 3.0 1.2 - - - -
311D VAL* 1.3 82.3 - - - +
313D ASP* 1.3 59.6 + - - +
315D PHE* 4.2 6.8 - - + +
316D GLY* 2.9 25.5 + - - -
602D AQ4 4.4 12.9 + - + +
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Residues in contact with ASP 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D SER* 3.8 12.8 + - - -
120D SER* 3.3 17.0 + - - -
121D MET* 3.4 22.5 + - + +
122D SER* 3.0 41.9 + - - +
309D ASN 4.2 6.4 - - - +
310D ILE* 3.0 9.4 + - - +
312D LEU* 1.3 74.4 - - - +
314D LEU* 1.3 61.4 + - - +
317D ALA* 2.9 34.0 + - - +
601D HEM 4.5 4.2 - - + +
602D AQ4 3.6 21.5 - - + -
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D MET* 4.5 1.8 - - + -
138D ALA* 3.8 35.4 - - + +
142D LEU* 4.3 19.5 - - + -
198D ILE* 3.9 3.6 - - + +
202D CYS* 4.4 8.7 - - - -
281D ILE* 3.8 37.2 - - + -
310D ILE* 3.2 19.5 + - + +
311D VAL* 4.0 6.3 - - - +
313D ASP* 1.3 76.6 - - - +
315D PHE* 1.3 58.1 + - - +
317D ALA* 5.0 0.2 - - - -
318D GLY* 2.9 27.9 + - - -
458D ILE* 4.1 3.1 - - + -
601D HEM 3.6 38.4 - - + +
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Residues in contact with PHE 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D THR* 3.6 32.5 - - + -
198D ILE* 3.9 27.1 - - + +
199D CYS* 3.9 20.6 - - + -
202D CYS* 4.3 6.5 - - - -
203D PHE* 4.0 28.3 - + + -
207D TYR* 6.5 0.4 - + - -
218D VAL* 5.3 10.5 - - + -
258D PHE* 4.5 21.5 - + - -
261D PHE* 6.4 2.0 - + - -
311D VAL 2.9 18.8 + - - +
312D LEU* 4.2 6.5 - - + +
314D LEU* 1.3 77.6 - - - +
316D GLY* 1.3 63.8 + - - +
318D GLY* 3.8 0.2 - - - -
319D PHE* 3.1 43.1 + + - -
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Residues in contact with GLY 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D PHE* 5.6 2.0 - - - -
312D LEU 2.9 17.9 + - - -
314D LEU 3.3 0.2 - - - -
315D PHE* 1.3 82.5 - - - +
317D ALA* 1.3 61.0 + - - +
318D GLY 3.4 0.2 + - - -
319D PHE* 3.6 20.9 - - - -
320D ASP* 3.7 12.0 - - - +
602D AQ4 3.3 32.4 + - - -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D ASP 2.9 18.1 + - - +
316D GLY* 1.3 75.4 - - - +
318D GLY* 1.3 61.9 + - - +
320D ASP* 5.3 0.4 - - - -
321D THR* 2.8 36.4 + - + +
601D HEM 3.5 34.7 - - + +
602D AQ4 3.3 33.4 + - + -
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Residues in contact with GLY 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D VAL* 4.2 1.3 - - - +
198D ILE* 4.1 12.6 - - - -
314D LEU 2.9 19.2 + - - -
315D PHE 3.8 1.1 - - - -
316D GLY 3.2 0.8 - - - -
317D ALA* 1.3 80.1 - - - +
319D PHE* 1.3 62.1 + - - +
320D ASP 3.5 0.2 + - - -
322D VAL* 3.4 27.4 + - - +
466D GLU* 5.3 0.4 - - - +
601D HEM 3.7 22.0 - - - -
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Residues in contact with PHE 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 5.9 1.6 - - - -
191D VAL* 4.5 13.9 - - + -
194D VAL* 3.9 9.0 - - - -
195D THR* 3.5 29.8 - - + +
198D ILE* 3.9 15.4 - - + +
218D VAL* 4.0 27.8 - - + -
222D ASN* 5.9 0.9 - - + -
258D PHE* 4.9 9.9 - + - -
315D PHE* 3.1 43.0 + + - -
316D GLY* 3.6 19.1 - - - -
318D GLY* 1.3 75.5 - - - +
320D ASP* 1.3 71.8 + - + +
323D THR* 2.2 36.8 + - - +
602D AQ4 3.5 28.0 - + - -
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Residues in contact with ASP 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 4.3 6.3 + - - -
225D GLY* 6.1 0.2 - - - -
316D GLY 3.7 15.8 + - - +
317D ALA* 4.7 0.9 - - - +
318D GLY 3.4 0.4 - - - -
319D PHE* 1.3 92.5 - - + +
321D THR* 1.3 63.6 + - + +
323D THR* 3.3 4.2 + - - -
324D THR* 2.8 33.1 + - - -
497D THR* 2.6 36.4 + - - +
499D LYS* 3.2 21.5 + - - -
602D AQ4 4.1 21.1 - - + +
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Residues in contact with THR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ALA* 2.8 27.3 + - + +
318D GLY 4.1 0.3 + - - -
320D ASP* 1.3 77.0 - - + +
322D VAL* 1.3 58.9 + - - +
324D THR* 3.2 4.6 + - - -
325D ALA* 2.8 29.8 + - - +
381D PHE* 3.6 11.2 - - + -
382D VAL* 4.7 2.5 - - + -
497D THR* 3.7 25.1 - - + -
601D HEM 2.9 51.2 - - + +
602D AQ4 4.9 12.6 - - + -
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Residues in contact with VAL 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D VAL* 3.9 8.7 - - + -
318D GLY 3.4 19.4 + - - +
320D ASP 3.4 0.2 - - - -
321D THR* 1.3 76.3 + - - +
323D THR* 1.3 58.3 + - - +
325D ALA* 3.2 6.5 + - - +
326D ILE* 2.9 40.6 + - + +
463D ALA* 4.2 17.0 - - + -
466D GLU* 3.6 40.2 - - + +
467D VAL* 4.1 11.0 - - + -
601D HEM 3.8 24.0 - - + -
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Residues in contact with THR 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 3.8 26.7 - - + -
190D VAL* 4.1 9.9 - - + +
191D VAL* 3.7 36.3 + - + +
194D VAL* 3.2 24.1 - - - +
319D PHE* 2.2 27.3 + - - -
320D ASP* 3.3 4.1 + - - -
322D VAL* 1.3 78.1 - - - +
324D THR* 1.3 56.9 + - - +
326D ILE* 3.3 1.9 + - - +
327D SER* 2.8 30.5 + - - -
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Residues in contact with THR 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TYR* 4.9 4.1 + - - -
320D ASP 2.8 23.7 + - - -
321D THR* 3.6 5.4 - - - -
323D THR* 1.3 73.2 - - - +
325D ALA* 1.3 57.7 + - - +
327D SER* 3.3 6.1 + - - -
328D TRP* 2.9 48.5 + - + +
381D PHE* 3.6 18.2 - - + -
497D THR* 4.2 4.6 + - - -
498D MET 3.3 26.9 - - - +
499D LYS* 3.5 30.3 + - + +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D THR 2.8 17.4 + - - +
322D VAL 3.5 5.2 - - - +
324D THR* 1.3 77.6 - - - +
326D ILE* 1.3 62.5 + - - +
328D TRP* 3.4 3.5 + - - +
329D SER* 3.0 26.9 + - - -
375D THR* 4.1 2.7 - - - +
376D PHE* 3.8 16.4 - - + -
381D PHE* 3.6 28.2 - - + -
467D VAL* 4.2 16.4 - - + -
601D HEM 4.2 2.9 - - + -
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Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D VAL* 3.7 19.5 - - + -
194D VAL* 3.9 17.7 - - + -
322D VAL* 2.9 25.7 + - + +
323D THR 3.9 2.7 - - - +
325D ALA* 1.3 72.0 - - - +
327D SER* 1.3 67.2 + - - +
329D SER* 3.2 7.8 + - - -
330D LEU* 3.0 35.8 + - + +
467D VAL* 4.3 22.4 - - + +
470D PHE* 3.7 41.3 - - + -
471D LEU* 4.6 13.2 - - + -
474D LEU* 6.5 1.1 - - + -
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Residues in contact with SER 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D PRO* 5.6 4.5 - - - +
187D TYR* 3.7 29.0 + - - +
190D VAL* 5.0 3.7 - - - +
323D THR* 2.8 19.6 + - - -
324D THR* 3.5 7.6 - - - -
326D ILE* 1.3 77.8 - - - +
328D TRP* 1.3 62.8 + - - +
330D LEU* 3.2 12.2 + - - +
331D MET* 3.1 24.1 + - - +
500D HIS* 2.5 34.0 + - - -
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Residues in contact with TRP 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D THR* 2.9 39.6 + - + +
325D ALA* 3.8 4.7 - - - +
327D SER* 1.3 76.3 - - - +
329D SER* 1.3 64.1 + - - +
331D MET* 3.1 10.8 + - + +
332D TYR* 3.0 59.7 + + + -
375D THR* 4.1 12.8 - - + -
379D SER* 4.0 12.8 - - - +
381D PHE* 3.7 13.1 - + + +
490D MET* 3.5 34.8 - - + -
492D PRO* 3.8 26.0 - - + -
498D MET* 3.0 22.3 + - + -
499D LYS* 3.5 24.2 - - - +
500D HIS* 3.8 27.3 - + + -
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Residues in contact with SER 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ALA 3.0 15.4 + - - -
326D ILE* 3.4 9.4 - - - -
328D TRP* 1.3 76.3 - - - +
330D LEU* 1.3 57.7 + - - +
332D TYR* 3.1 2.1 + - - -
333D LEU* 2.8 33.2 + - - +
371D PHE* 3.5 25.2 - - - -
372D ILE* 5.3 1.7 - - - +
375D THR* 3.5 20.2 + - - +
467D VAL* 4.8 4.2 - - - +
471D LEU* 4.0 24.1 - - - +
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Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D PRO* 3.7 28.9 - - + -
190D VAL* 4.1 18.4 - - + -
326D ILE* 3.0 25.4 + - + +
327D SER* 3.2 9.2 + - - +
329D SER* 1.3 74.4 - - - +
331D MET* 1.3 62.7 + - - +
333D LEU* 3.2 18.7 + - + +
334D VAL* 3.0 26.2 + - - +
471D LEU* 4.6 11.0 - - + -
474D LEU* 5.7 4.3 - - + -
475D LEU* 5.8 0.2 - - + -
480D PHE* 4.0 36.5 - - + +
506D PHE* 3.7 18.3 - - + -
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Residues in contact with MET 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D PRO* 6.0 0.4 - - + -
327D SER 3.1 15.5 + - - +
328D TRP* 3.1 11.6 + - + +
330D LEU* 1.3 76.0 - - - +
332D TYR* 1.3 56.7 + - - +
334D VAL* 3.2 8.2 - - - +
335D MET* 3.0 31.9 + - - +
488D VAL* 3.6 28.3 - - + -
489D ASP 4.1 11.7 - - - +
490D MET* 3.7 22.9 - - + -
500D HIS* 3.4 46.7 - - + +
501D ALA 4.2 5.6 - - - +
503D CYS* 4.5 3.8 - - + -
506D PHE* 3.7 26.2 - - + -
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Residues in contact with TYR 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D TRP* 3.0 55.5 + + + -
329D SER 3.6 5.2 - - - +
331D MET* 1.3 74.2 - - - +
333D LEU* 1.3 61.4 + - - +
336D ASN* 2.9 42.5 + - - +
339D VAL* 4.6 0.5 - - - +
371D PHE* 4.1 4.7 - - + -
375D THR* 3.9 13.7 - - + -
378D HIS* 3.3 39.1 + + + -
379D SER* 3.4 29.1 + - - -
427D PHE* 3.4 43.1 - + + -
490D MET* 3.7 19.7 - - + -
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Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D SER 2.8 25.1 + - - +
330D LEU* 3.2 24.9 + - + +
332D TYR* 1.3 73.0 - - - +
334D VAL* 1.3 60.2 + - - +
336D ASN 3.1 22.9 - - - +
337D PRO 3.5 0.5 - - - -
339D VAL* 4.3 1.8 - - + -
340D GLN* 3.3 40.9 + - + +
343D ILE* 3.9 19.5 - - + -
371D PHE* 3.4 30.1 - - + -
471D LEU* 4.5 6.1 - - + -
475D LEU* 4.0 28.7 - - + -
480D PHE* 5.1 4.5 - - + -
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Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D LEU 3.0 13.2 + - - +
331D MET* 3.2 15.7 - - - +
333D LEU* 1.3 77.0 - - - +
335D MET* 1.3 76.9 + - + +
336D ASN 3.4 0.7 + - - -
337D PRO* 3.5 16.2 - - - +
340D GLN* 4.6 5.6 - - - +
480D PHE* 5.0 2.7 - - + +
481D SER* 3.2 16.8 - - - +
482D VAL* 3.1 49.2 - - + +
488D VAL* 5.5 1.1 - - + -
506D PHE* 3.9 22.7 - - + -
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Residues in contact with MET 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D MET 3.0 20.9 + - - +
334D VAL* 1.3 81.9 - - + +
336D ASN* 1.3 72.3 + - - +
337D PRO* 3.5 6.6 - - - +
482D VAL* 3.9 21.5 - - + -
486D VAL* 5.5 1.1 - - + +
488D VAL* 3.2 44.0 - - + +
490D MET* 3.8 28.3 - - + -
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Residues in contact with ASN 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D TYR* 2.9 32.9 + - - +
333D LEU 3.1 9.8 - - - +
335D MET* 1.3 90.3 + - - +
337D PRO* 1.3 66.7 - - - +
338D ARG* 3.0 9.0 + - + +
339D VAL* 3.1 34.8 + - + +
340D GLN 3.4 1.4 + - - -
427D PHE* 3.9 30.7 - - + +
490D MET* 5.5 0.4 - - - +
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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).
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