Contacts of the helix formed by residues 301 - 322 (chain D) in PDB entry 1KKQ
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 301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300D LEU* 1.3 77.9 - - - +
302D LEU* 1.3 59.6 + - - +
303D ASN* 2.8 14.6 - - + +
304D ASP* 3.3 30.2 + - - +
305D GLN* 2.9 31.0 + - - +
392D LEU* 4.3 13.3 - - - +
393D ASN* 3.7 17.0 + - - +
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D LEU 3.9 0.2 + - - -
301D ASP* 1.3 74.8 + - - +
303D ASN* 1.3 63.7 + - - +
305D GLN* 3.9 20.8 - - - +
306D VAL* 2.9 30.1 + - + +
690H ARG* 4.8 13.2 - - + +
693H LEU* 4.3 20.4 - - + +
694H MET* 4.4 24.9 - - + -
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Residues in contact with ASN 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ASP* 2.8 15.4 + - + +
302D LEU* 1.3 86.1 + - - +
304D ASP* 1.3 65.2 + - - +
305D GLN 3.2 0.7 - - - -
306D VAL* 3.4 4.7 + - - +
307D THR* 2.7 29.1 + - - +
390D GLY 6.0 0.2 - - - -
392D LEU* 6.6 0.2 - - + -
690H ARG* 3.3 27.3 - - - +
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Residues in contact with ASP 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D LEU* 3.9 14.6 - - + +
301D ASP* 3.3 23.4 + - + +
303D ASN* 1.3 81.3 - - - +
305D GLN* 1.3 59.3 + - - +
307D THR* 3.2 4.1 + - - -
308D LEU* 2.9 37.2 + - - +
390D GLY 4.3 2.3 - - - +
391D LEU* 3.6 17.7 - - + -
392D LEU* 2.9 27.7 + - - +
393D ASN* 3.1 39.4 + - - +
397D ILE* 4.7 1.0 - - - +
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Residues in contact with GLN 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D LYS* 5.9 0.2 - - - +
297D PHE* 2.9 59.6 + - + +
298D ALA* 3.6 16.3 + - - +
300D LEU* 3.5 22.4 + - + -
301D ASP 2.9 22.2 + - - +
302D LEU* 3.9 22.4 - - - +
304D ASP* 1.3 78.3 - - - +
306D VAL* 1.3 56.2 + - - +
308D LEU* 4.8 0.4 - - - -
309D LEU* 3.3 29.5 + - - +
693H LEU* 4.0 22.0 - - + +
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Residues in contact with VAL 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D LEU* 2.9 37.5 - - + +
303D ASN 3.4 4.9 + - - +
304D ASP 3.2 0.6 - - - -
305D GLN* 1.3 75.4 - - - +
307D THR* 1.3 62.2 + - - +
310D LYS* 2.8 33.1 + - + +
686H GLU* 3.9 35.4 - - + +
689H ILE* 3.7 14.2 - - + +
690H ARG* 4.2 25.6 - - + +
693H LEU* 4.2 14.6 - - + -
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Residues in contact with THR 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ASN 2.7 22.2 + - - -
304D ASP* 3.2 5.3 + - - -
306D VAL* 1.3 76.4 - - - +
308D LEU* 1.3 66.3 + - - +
310D LYS* 3.2 5.9 + - - -
311D TYR* 3.1 43.9 + - + -
388D ARG* 4.2 0.7 - - + -
389D PRO 3.3 21.3 - - - +
390D GLY 3.9 9.6 + - - +
391D LEU* 3.1 31.0 - - + -
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Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D PHE* 3.9 21.8 - - + -
300D LEU* 3.6 31.0 - - + -
304D ASP 2.9 19.0 + - - +
305D GLN 4.0 4.0 - - - +
307D THR* 1.3 79.5 - - - +
309D LEU* 1.3 62.8 + - - +
311D TYR* 4.0 1.0 - - - +
312D GLY* 3.2 19.9 + - - -
383D ILE* 3.7 26.2 - - + +
384D CYS* 4.4 4.9 - - + -
385D CYS 3.7 23.6 - - - +
388D ARG* 4.2 10.7 + - + -
391D LEU* 3.8 18.6 - - + -
397D ILE* 3.7 14.8 - - + -
400D MET* 5.3 0.7 - - + -
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL* 5.9 0.4 - - + -
287D LEU* 4.1 28.0 - - + +
288D THR* 3.2 44.0 - - + +
291D ALA* 4.2 12.8 - - + -
297D PHE* 4.3 7.0 - - + -
305D GLN 3.3 13.7 + - - +
308D LEU* 1.3 80.6 - - - +
310D LYS* 1.3 57.2 + - - +
312D GLY 5.3 0.2 - - - -
313D VAL* 3.0 42.5 + - + +
383D ILE* 4.3 20.9 - - + -
689H ILE* 3.1 24.7 - - + +
693H LEU* 4.5 3.8 - - + -
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Residues in contact with LYS 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D VAL* 2.8 24.1 + - + +
307D THR* 3.2 5.4 + - - +
309D LEU* 1.3 76.8 - - - +
311D TYR* 1.3 98.9 + - + +
313D VAL* 4.6 6.2 + - - +
682H ASN 4.1 13.0 + - - -
683H MET 4.3 23.5 - - - +
684H GLY* 5.2 2.1 - - - -
685H LEU* 4.6 11.0 - - + +
686H GLU* 3.2 40.8 + - + +
689H ILE* 3.8 8.9 - - + +
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Residues in contact with TYR 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D THR* 3.1 46.7 + - + +
310D LYS* 1.3 113.8 + - + +
312D GLY* 1.3 61.5 + - - +
313D VAL 3.5 1.3 + - - -
314D TYR* 4.9 3.0 + - - +
315D GLU* 3.7 9.0 - - - +
388D ARG* 3.4 42.7 + - + +
389D PRO* 3.3 34.2 + - + +
437D VAL* 5.9 1.2 - - - +
682H ASN* 4.6 16.5 + - - +
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Residues in contact with GLY 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D LEU 3.2 14.0 + - - -
309D LEU* 4.1 1.3 - - - -
311D TYR* 1.3 76.5 - - - +
313D VAL* 1.3 63.2 + - - +
314D TYR 3.3 2.5 - - - -
315D GLU* 3.8 4.7 - - - -
316D ALA* 3.1 20.3 + - - +
382D ILE* 3.3 16.4 - - - +
383D ILE* 4.5 7.2 - - - +
388D ARG* 3.5 21.2 - - - -
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Residues in contact with VAL 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL* 4.0 29.4 - - + -
287D LEU* 3.5 29.2 - - + -
309D LEU* 3.0 28.1 + - + +
310D LYS 4.7 4.0 - - - +
311D TYR 3.5 1.2 - - - -
312D GLY* 1.3 77.7 - - - +
314D TYR* 1.3 87.8 + - + +
316D ALA* 3.4 2.3 + - - +
317D ILE* 3.0 36.9 + - + +
685H LEU* 4.2 17.7 - - + -
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Residues in contact with TYR 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D VAL* 6.4 0.9 - - + -
310D LYS 5.3 0.4 - - - -
311D TYR 4.9 1.9 + - - +
312D GLY* 4.4 0.2 - - - -
313D VAL* 1.3 95.5 - - + +
315D GLU* 1.3 62.1 + - + +
316D ALA 3.0 1.6 - - - -
317D ILE* 4.2 9.6 - - + -
318D PHE* 3.0 48.5 + + + -
437D VAL* 3.7 20.2 - - + -
440D HIS* 5.4 6.3 - + - -
778D 471 3.4 60.0 + - + +
682H ASN* 3.4 41.3 - - + +
683H MET* 4.0 13.7 - - + +
685H LEU* 4.0 19.5 - - + +
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Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D TYR 3.7 8.9 - - - +
312D GLY* 3.5 3.3 + - - +
313D VAL 3.3 0.4 - - - -
314D TYR* 1.3 77.2 - - - +
316D ALA* 1.3 58.9 + - - +
318D PHE 4.4 0.2 - - - -
319D ALA* 3.5 18.9 + - - +
382D ILE* 3.6 24.4 - - + +
388D ARG* 2.8 39.5 + - - -
430D MET* 4.4 6.8 - - - +
433D LEU* 3.6 17.8 - - + +
434D ARG* 3.5 42.0 + - - +
437D VAL* 3.8 23.7 - - + +
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D LEU* 3.7 29.4 - - + -
312D GLY 3.1 15.6 + - - +
313D VAL 3.7 4.3 - - - +
314D TYR 3.0 0.2 - - - -
315D GLU* 1.3 79.0 - - - +
317D ILE* 1.3 66.5 + - - +
318D PHE 3.3 0.2 - - - -
319D ALA* 3.3 4.6 + - - +
320D MET* 3.0 31.2 + - + +
379D VAL* 4.1 15.7 - - + -
382D ILE* 4.1 9.9 - - + -
383D ILE* 4.8 2.0 - - + -
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D SER* 5.1 2.2 - - - -
283D THR* 3.4 33.7 - - + +
284D VAL* 5.0 5.8 - - + -
287D LEU* 3.8 15.9 - - + -
313D VAL* 3.0 28.3 + - + +
314D TYR* 3.2 16.5 + - + +
316D ALA* 1.3 77.2 - - - +
318D PHE* 1.3 69.9 + - + +
320D MET* 3.7 9.1 + - + +
321D LEU* 2.8 33.1 + - + +
778D 471 4.2 33.0 - - + -
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Residues in contact with PHE 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D TYR* 3.0 37.6 + + + +
317D ILE* 1.3 79.8 - - + +
319D ALA* 1.3 69.6 + - - +
321D LEU* 3.3 23.0 + - + +
322D SER* 3.5 9.5 + - - -
358D LYS* 3.9 38.4 - - + -
361D PHE* 4.3 4.7 - - + -
433D LEU* 3.8 16.2 - - + -
436D LEU* 4.6 15.0 - - + -
437D VAL* 3.8 27.8 - - + -
440D HIS* 4.0 31.9 - + + -
778D 471 4.3 22.9 - + + -
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D GLU 3.5 20.2 + - - +
316D ALA* 3.3 6.6 + - - +
318D PHE* 1.3 80.7 - - - +
320D MET* 1.3 62.5 + - - +
322D SER* 3.2 18.5 + - - -
323D SER* 4.4 1.4 + - - -
361D PHE* 4.4 6.1 - - - -
365D PHE* 3.8 12.4 - - + -
375D ILE* 5.7 1.9 - - + +
378D PHE* 3.9 21.5 - - + -
379D VAL* 4.6 5.8 - - + -
382D ILE* 6.2 0.2 - - + -
433D LEU* 3.6 21.6 - - + +
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Residues in contact with MET 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TYR* 4.2 17.0 - - + +
218D PHE* 3.6 43.3 - - + -
220D MET 6.0 0.9 - - - +
283D THR* 6.2 4.7 - - + -
286D GLU* 5.9 0.2 - - - +
287D LEU* 4.5 11.9 - - + -
316D ALA 3.0 19.2 + - - +
317D ILE* 4.2 7.6 - - + +
319D ALA* 1.3 78.3 - - - +
321D LEU* 1.3 64.6 + - - +
323D SER* 2.9 30.3 + - - +
324D VAL* 4.2 2.8 + - - +
375D ILE* 4.2 12.1 - - + -
379D VAL* 3.4 28.3 - - + -
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ILE* 2.8 23.3 + - + +
318D PHE* 3.4 30.1 - - + +
319D ALA 3.2 0.4 - - - -
320D MET* 1.3 77.4 - - - +
322D SER* 1.3 61.4 + - - +
323D SER 3.1 0.5 + - - -
324D VAL* 3.3 23.8 - - + +
325D MET* 3.3 30.6 - - + +
330D MET* 3.5 25.4 - - + -
355D MET* 4.5 5.8 - - + -
358D LYS* 4.0 15.3 - - + -
778D 471 4.0 21.1 - - + +
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Residues in contact with SER 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ARG* 4.0 0.2 + - - -
318D PHE 3.5 7.3 + - - -
319D ALA 3.2 15.0 + - - -
320D MET 3.0 1.6 + - - -
321D LEU* 1.3 76.8 - - - +
323D SER* 1.3 61.9 + - - +
325D MET* 3.3 15.5 + - - +
361D PHE* 3.7 7.3 - - - -
362D ALA* 3.6 30.1 - - - +
365D PHE* 3.6 23.7 - - - -
366D ASN* 3.3 27.5 + - - +
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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
------------------------------------------------------------
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