Contacts of the helix formed by residues 421 - 445 (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 PHE 421 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D ASP* 3.4 3.7 + - - +
420D ILE* 1.3 110.8 - - + +
422D LEU* 1.3 58.8 + - - +
423D PHE 3.5 1.3 - - - -
424D PRO* 3.5 21.1 - - + +
425D LYS* 3.0 35.8 + - + +
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Residues in contact with LEU 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D LEU* 4.0 37.5 - - + +
370D LEU* 4.4 8.7 - - + -
412D LEU* 3.9 29.2 - - + +
416D HIS* 3.6 42.6 - - + -
419D ASP* 3.5 33.4 + - - +
420D ILE 3.1 3.4 - - - +
421D PHE* 1.3 76.3 - - - +
423D PHE* 1.3 63.1 + - - +
425D LYS* 2.8 24.7 + - + +
426D LEU* 2.9 14.1 + - + +
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Residues in contact with PHE 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D VAL* 4.0 26.7 - - + -
408D LEU* 4.1 21.3 - - + -
409D ARG* 2.9 58.8 - - + +
412D LEU* 3.9 26.7 - - + +
413D GLN* 5.6 7.2 - - + +
420D ILE 4.7 2.1 + - - +
422D LEU* 1.3 79.5 - - - +
424D PRO* 1.3 73.5 - - + +
426D LEU* 3.1 12.8 + - + +
427D LEU* 3.2 52.8 + - + +
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Residues in contact with PRO 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D ARG* 5.6 1.6 - - - +
420D ILE 4.7 2.5 - - - +
421D PHE* 3.5 33.9 - - + +
423D PHE* 1.3 103.9 - - + +
425D LYS* 1.3 60.6 + - - +
427D LEU* 3.7 14.8 + - + +
428D GLN* 3.4 18.9 + - - +
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Residues in contact with LYS 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D LEU* 4.1 27.3 - - + +
419D ASP* 2.9 29.4 + - - +
421D PHE* 3.0 25.1 + - + +
422D LEU* 2.8 15.0 + - + +
424D PRO* 1.3 80.0 - - - +
426D LEU* 1.3 58.8 + - - +
428D GLN* 3.3 10.6 - - - +
429D LYS* 3.1 28.4 + - - +
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Residues in contact with LEU 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D PHE* 3.8 20.9 - - + -
368D LEU* 4.1 10.3 - - + -
370D LEU* 3.8 36.6 - - + -
374D ASP* 5.7 1.1 - - + +
378D PHE* 3.8 31.3 - - + -
408D LEU* 4.8 9.2 - - + -
412D LEU* 3.2 33.9 - - + -
422D LEU* 2.9 13.0 + - + +
423D PHE* 3.1 9.8 + - + +
425D LYS* 1.3 73.8 - - - +
427D LEU* 1.3 59.0 + - + +
428D GLN 3.0 1.8 - - - -
429D LYS* 2.5 25.0 + - + +
430D MET* 2.9 11.1 + - - -
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Residues in contact with LEU 427 (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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405D VAL* 5.0 5.4 - - + -
408D LEU* 5.9 1.1 - - + -
423D PHE* 3.2 54.9 + - + +
424D PRO* 4.0 13.9 - - + +
426D LEU* 1.3 77.7 - - + +
428D GLN* 1.3 63.5 + - - +
429D LYS 3.0 1.2 + - - -
430D MET* 3.2 35.3 + - + +
431D ALA* 3.3 11.6 + - - +
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Residues in contact with GLN 428 (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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424D PRO 3.4 12.2 + - - +
425D LYS* 3.3 14.1 - - - +
426D LEU 3.0 0.2 - - - -
427D LEU* 1.3 80.1 - - - +
429D LYS* 1.3 62.3 + - + +
431D ALA* 3.5 12.1 - - - +
432D ASP* 2.9 44.3 + - - +
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Residues in contact with LYS 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D PHE* 4.2 13.9 + - + -
364D LYS* 4.0 33.3 + - - +
365D PHE* 4.1 32.0 - - + +
368D LEU* 3.9 23.8 - - + -
378D PHE* 4.3 4.3 - - + -
425D LYS* 3.1 18.2 - - - +
426D LEU* 2.5 23.6 + - - +
428D GLN* 1.3 72.3 - - - +
430D MET* 1.3 53.4 + - - +
431D ALA 3.0 1.8 - - - -
432D ASP* 3.0 16.3 + - - +
433D LEU* 2.8 38.9 + - - +
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Residues in contact with MET 430 (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* 4.4 4.7 - - - +
378D PHE* 3.6 33.6 - - + -
381D ALA* 3.9 32.1 - - + +
382D ILE* 3.6 22.4 - - + -
385D CYS* 6.5 0.2 - - + -
401D GLN* 4.2 8.3 - - - +
405D VAL* 4.9 6.1 - - + -
408D LEU* 5.9 2.5 - - - -
426D LEU* 2.9 6.2 + - - -
427D LEU* 3.2 34.7 + - + +
429D LYS* 1.3 76.2 - - - +
431D ALA* 1.3 57.0 + - - +
433D LEU* 3.5 7.6 + - - +
434D ARG* 3.0 41.0 + - - +
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Residues in contact with ALA 431 (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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427D LEU 3.3 8.3 + - - +
428D GLN* 3.5 23.6 - - - +
430D MET* 1.3 79.2 - - - +
432D ASP* 1.3 65.2 + - - +
434D ARG* 3.3 11.4 - - - +
435D GLN* 3.2 18.5 + - - +
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Residues in contact with ASP 432 (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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361D PHE* 4.2 16.3 - - + -
428D GLN* 2.9 39.2 + - - +
429D LYS* 3.0 21.9 + - - +
431D ALA* 1.3 73.9 - - - +
433D LEU* 1.3 55.9 + - - +
435D GLN* 2.9 10.5 + - - +
436D LEU* 2.7 35.5 + - - +
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Residues in contact with LEU 433 (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* 3.6 22.9 - - + +
318D PHE* 3.8 17.5 - - + -
319D ALA* 3.6 42.2 - - + +
361D PHE* 3.4 30.5 - - + -
378D PHE* 3.9 20.4 - - + -
382D ILE* 5.7 2.2 - - + -
429D LYS 2.8 15.1 + - - +
430D MET* 3.5 8.7 - - + +
432D ASP* 1.3 77.0 - - - +
434D ARG* 1.3 64.2 + - - +
436D LEU* 2.9 20.1 + - + +
437D VAL* 3.0 18.4 + - - +
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Residues in contact with ARG 434 (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 30.5 + - - +
382D ILE* 5.0 3.0 + - - +
385D CYS* 3.3 25.3 - - - +
387D ASP* 3.2 25.5 + - - -
388D ARG* 3.6 26.6 - - - +
430D MET* 3.0 20.9 + - - +
431D ALA* 3.3 15.0 - - - +
433D LEU* 1.3 79.5 - - - +
435D GLN* 1.3 61.1 + - - +
437D VAL* 3.7 4.3 + - - +
438D THR* 3.3 23.7 + - - +
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Residues in contact with GLN 435 (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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431D ALA 3.2 12.7 + - - +
432D ASP* 2.9 17.4 + - - +
434D ARG* 1.3 74.7 - - - +
436D LEU* 1.3 64.3 + - - +
438D THR* 2.9 25.3 + - - +
439D GLU* 2.8 51.9 + - - +
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Residues in contact with LEU 436 (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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318D PHE* 4.6 15.0 - - + -
357D PRO* 3.9 35.9 - - + +
358D LYS* 4.3 24.4 + - + -
361D PHE* 3.8 37.5 - - + -
432D ASP 2.7 15.4 + - - +
433D LEU* 2.9 12.3 + - + +
435D GLN* 1.3 73.1 - - - +
437D VAL* 1.3 58.2 + - + +
439D GLU* 3.6 16.8 + - + +
440D HIS* 2.9 26.3 + - - +
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Residues in contact with VAL 437 (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 5.9 1.3 - - - +
314D TYR* 3.7 19.7 - - + -
315D GLU* 3.8 26.7 - - + +
318D PHE* 3.8 24.7 - - + -
433D LEU 3.0 14.1 + - - +
434D ARG 3.9 5.8 - - - +
436D LEU* 1.3 73.1 - - - +
438D THR* 1.3 68.4 + - - +
440D HIS* 3.0 15.7 + - + +
441D ALA* 3.0 14.0 + - - +
682H ASN* 3.4 29.3 - - + +
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Residues in contact with THR 438 (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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434D ARG* 3.3 13.4 + - - +
435D GLN* 2.9 22.4 + - - +
437D VAL* 1.3 82.5 - - - +
439D GLU* 1.3 70.8 + - + +
440D HIS 3.1 0.2 + - - -
441D ALA* 3.4 4.4 + - - +
442D GLN* 3.3 32.5 + - - +
682H ASN* 5.9 0.7 - - - -
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Residues in contact with GLU 439 (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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357D PRO* 5.7 1.6 - - - +
435D GLN* 2.8 47.9 + - - +
436D LEU* 4.0 20.1 - - + +
438D THR* 1.3 77.1 - - + +
440D HIS* 1.3 61.5 + - - +
442D GLN* 3.4 19.2 - - - +
443D LEU* 3.1 23.7 + - - +
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Residues in contact with HIS 440 (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* 5.4 9.9 - + - -
318D PHE* 4.0 25.5 - + + -
354D ILE* 4.3 12.2 - - + +
358D LYS* 3.1 28.9 + - - +
436D LEU 2.9 18.4 + - - +
437D VAL* 3.0 15.6 + - + +
439D GLU* 1.3 75.8 - - - +
441D ALA* 1.3 70.5 + - + +
443D LEU* 2.8 18.4 + - + +
444D VAL* 3.0 33.3 + - + +
778D 471 4.0 35.5 + - - -
682H ASN* 5.8 1.8 - - + -
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Residues in contact with ALA 441 (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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437D VAL 3.0 13.8 + - - +
438D THR* 3.9 4.3 - - - +
440D HIS* 1.3 80.2 - - - +
442D GLN* 1.3 63.6 + - - +
444D VAL* 3.0 10.5 + - - +
445D GLN* 3.0 25.3 + - - +
682H ASN* 4.0 26.7 - - + +
683H MET* 6.0 3.6 - - + -
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Residues in contact with GLN 442 (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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438D THR* 3.3 25.9 + - - +
439D GLU* 3.4 21.4 - - - +
441D ALA* 1.3 80.6 - - - +
443D LEU* 1.3 59.4 + - - +
445D GLN* 3.7 11.5 + - - +
446D ILE* 3.6 17.0 - - - +
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Residues in contact with LEU 443 (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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350D PRO* 4.0 27.4 - - + +
353D ASP* 4.0 30.3 - - + +
354D ILE* 3.9 32.5 - - + -
357D PRO* 5.6 2.2 - - + -
358D LYS* 6.2 0.4 - - - +
439D GLU 3.1 12.1 + - - +
440D HIS* 2.8 15.3 + - + +
442D GLN* 1.3 74.7 - - - +
444D VAL* 1.3 61.2 + - + +
446D ILE* 3.4 14.2 - - + +
447D ILE* 2.8 16.1 - - + +
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Residues in contact with VAL 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D PHE* 4.6 25.6 - - + -
354D ILE* 5.9 4.5 - - + -
440D HIS* 3.0 41.5 + - + +
441D ALA* 3.0 10.7 + - - +
443D LEU* 1.3 74.5 - - + +
445D GLN* 1.3 58.7 + - - +
446D ILE 2.3 20.5 + - - -
447D ILE* 2.7 24.2 + - + +
448D LYS* 3.7 9.6 + - + +
778D 471 6.5 0.2 - - - -
683H MET* 6.2 2.9 - - + -
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Residues in contact with GLN 445 (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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441D ALA 3.0 14.9 + - - +
442D GLN* 4.0 7.8 - - - +
443D LEU 3.4 0.6 - - - -
444D VAL* 1.3 75.4 - - - +
446D ILE* 1.3 69.4 + - - +
448D LYS* 4.6 21.5 - - - +
449D LYS* 4.4 17.0 + - - +
450D THR* 5.1 0.5 + - - -
683H MET* 4.3 23.5 - - - +
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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
------------------------------------------------------------
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