Contacts of the helix formed by residues 417 - 445 (chain A) in PDB entry 2WW9
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 LYS 417 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ALA* 6.1 0.7 - - - -
414A ASN* 4.0 2.2 - - - +
415A VAL 3.4 0.4 - - - -
416A ALA* 1.4 74.9 - - - +
418A GLU* 1.3 95.9 + - - +
419A LEU 3.3 0.7 - - - -
420A ASN* 3.3 27.3 + - + +
421A LYS* 3.4 10.3 + - + +
31N LEU* 4.3 24.0 - - + -
35N LYS* 6.4 0.2 - - - +
37N SER* 3.3 43.5 - - - +
38N ARG 4.5 1.1 - - - +
41N LEU* 4.3 10.7 - - - +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.5 3.3 - - - +
271A PRO 5.8 0.9 - - - +
273A ARG* 5.3 4.5 - - - +
414A ASN 3.0 26.1 - - - +
415A VAL* 3.2 20.4 - - + +
417A LYS* 1.3 104.1 + - - +
419A LEU* 1.4 60.6 + - - +
421A LYS* 4.0 2.5 + - - +
422A VAL* 3.6 23.6 + - - +
79D A 4.2 3.1 - - - +
80D A 3.2 24.7 - - - +
38N ARG 4.3 1.0 - - - +
39N PRO* 4.9 0.8 - - - +
41N LEU* 3.4 26.9 - - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.7 38.4 - - + -
272A ILE* 6.5 0.9 - - + -
284A TYR* 5.9 4.0 - - + -
286A ILE* 5.1 6.5 - - + -
415A VAL* 2.9 30.2 + - + +
416A ALA* 4.0 17.5 - - + +
418A GLU* 1.4 75.8 - - - +
420A ASN* 1.4 57.6 + - - +
422A VAL 3.2 0.7 + - - -
423A ILE* 2.9 55.6 + - + +
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Residues in contact with ASN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA* 4.3 26.5 + - - +
397A ALA* 4.7 9.6 - - + +
416A ALA 3.4 14.9 + - - +
417A LYS* 3.3 26.1 + - + +
419A LEU* 1.4 77.9 - - - +
421A LYS* 1.4 56.4 + - - +
423A ILE* 5.2 1.3 - - - -
424A PRO* 3.1 28.5 - - - +
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LYS* 3.4 11.1 + - + +
418A GLU* 4.6 1.8 - - - +
419A LEU 3.3 0.8 - - - -
420A ASN* 1.4 79.8 - - - +
422A VAL* 1.4 71.5 + - + +
424A PRO* 3.6 6.2 - - - +
425A ILE* 3.3 17.8 - - + +
27B GLU* 4.8 4.9 + - - -
30B ARG* 5.3 1.0 - - - +
31B GLU* 3.2 37.1 + - - +
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 4.1 20.2 - - + -
269A GLU 5.7 0.4 - - - +
270A LEU* 3.6 27.1 - - + -
286A ILE* 6.3 0.2 - - + -
418A GLU 3.6 15.0 - - - +
419A LEU 3.2 2.4 + - - -
421A LYS* 1.4 85.0 - - + +
423A ILE* 1.4 64.6 + - - +
424A PRO 3.6 0.2 - - - -
425A ILE* 3.4 24.8 - - + +
426A ALA* 3.2 20.5 + - + +
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Residues in contact with ILE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.7 1.6 - - + -
286A ILE* 3.8 28.0 - - + -
393A ALA* 6.3 3.1 - - + -
419A LEU* 2.9 51.8 + - + +
420A ASN* 5.2 1.1 - - - -
422A VAL* 1.4 76.2 - - - +
424A PRO* 1.3 61.8 - - + +
426A ALA* 3.2 6.9 + - + +
427A ALA* 2.8 35.5 + - + +
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Residues in contact with PRO 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLN* 5.4 11.7 - - - +
393A ALA* 5.7 6.1 - - + -
420A ASN* 3.1 33.4 - - - +
421A LYS 3.6 7.2 - - - +
423A ILE* 1.3 92.6 - - + +
425A ILE* 1.4 61.0 + - + +
427A ALA* 4.4 5.2 - - + +
428A VAL* 3.4 33.4 + - + +
28B PHE* 3.7 14.4 - - + -
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 6.3 0.2 - - + -
421A LYS* 3.3 21.3 - - + +
422A VAL* 3.4 28.9 - - + +
423A ILE 3.3 0.6 - - - -
424A PRO* 1.4 75.3 - - + +
426A ALA* 1.4 61.2 + - + +
429A THR* 3.1 31.2 + - - -
28B PHE* 4.8 7.6 - - + -
31B GLU* 3.3 61.2 - - + +
32B GLY* 4.1 1.4 - - - -
34B GLN* 4.1 15.7 - - + +
35B PHE* 4.0 16.0 - - + +
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 4.3 13.0 - - + -
286A ILE* 4.6 9.2 - - + -
288A LEU* 3.2 37.5 - - + +
422A VAL 3.2 16.7 + - - +
423A ILE* 3.2 7.7 + - - +
425A ILE* 1.4 81.2 - - + +
427A ALA* 1.4 57.3 + - - +
430A GLY* 3.1 25.0 + - - -
35B PHE* 4.3 5.8 - - - -
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Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 5.5 4.0 - - - +
291A THR* 5.2 17.8 - - + +
292A GLY* 5.8 1.0 - - - -
382A ALA* 4.7 2.5 - - - +
423A ILE* 2.8 27.2 + - + +
424A PRO* 4.3 4.9 - - + +
425A ILE 3.5 0.4 - - - -
426A ALA* 1.4 76.7 - - - +
428A VAL* 1.4 68.3 + - + +
430A GLY* 4.0 0.2 - - - -
431A ALA* 3.2 22.5 + - - +
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 3.8 28.4 - - + +
382A ALA* 4.2 20.6 - - + +
383A ASP* 5.7 3.1 - - + +
386A GLN* 4.9 15.5 - - - +
424A PRO* 3.4 20.9 + - + +
427A ALA* 1.4 78.0 - - + +
429A THR* 1.4 62.5 + - - +
431A ALA* 3.5 5.2 + - - +
432A SER* 3.3 19.8 + - - -
28B PHE* 3.8 25.4 - - + -
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Residues in contact with THR 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ILE 3.1 23.4 + - - -
428A VAL* 1.4 75.7 - - - +
430A GLY* 1.4 57.4 + - - +
431A ALA 3.3 0.2 - - - -
432A SER* 3.7 9.6 - - - -
433A VAL* 2.9 38.1 + - + +
28B PHE* 3.6 21.7 - - - -
29B VAL* 6.5 1.1 - - + -
32B GLY* 3.6 30.8 - - - +
35B PHE* 3.7 9.0 - - + -
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Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.3 16.9 - - - +
289A LEU* 5.4 3.3 - - - +
426A ALA 3.1 24.6 + - - -
427A ALA 4.0 0.4 - - - -
428A VAL 3.2 0.6 - - - -
429A THR* 1.4 77.6 - - - +
431A ALA* 1.4 59.0 + - - +
433A VAL* 4.5 0.3 - - - +
434A LEU* 3.2 27.4 + - - +
35B PHE* 3.8 17.3 - - - -
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLY* 4.6 11.8 - - - -
295A SER* 4.0 18.8 - - - +
296A VAL* 5.1 2.3 - - + +
378A GLY* 3.6 23.2 - - - +
382A ALA* 4.2 6.1 - - + -
427A ALA 3.2 13.3 + - - +
428A VAL 3.7 7.9 - - - +
429A THR 3.3 0.2 - - - -
430A GLY* 1.4 77.1 - - - +
432A SER* 1.4 56.4 + - - +
434A LEU* 3.6 7.1 + - - +
435A SER* 3.0 30.6 + - - -
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.5 36.8 - - - +
378A GLY 5.2 0.4 - - - -
379A ILE* 3.8 19.5 - - - +
428A VAL 3.3 15.4 + - - -
429A THR* 3.7 13.9 - - - -
430A GLY 3.4 0.2 - - - -
431A ALA* 1.4 77.5 - - - +
433A VAL* 1.4 59.7 + - - +
435A SER* 3.4 8.8 + - - -
436A LEU* 3.0 21.5 + - - +
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.4 7.6 - - + -
429A THR* 2.9 30.5 + - + +
430A GLY 4.5 0.4 - - - +
432A SER* 1.4 72.5 - - - +
434A LEU* 1.4 60.3 + - - +
436A LEU* 3.3 15.1 + - + +
437A ILE* 3.1 48.5 + - + +
35B PHE* 3.8 28.3 - - + -
36B LEU* 4.1 25.6 - - + -
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 5.1 6.1 - - + -
263A LEU* 4.4 11.9 - - + -
289A LEU* 3.9 40.4 - - + +
292A GLY* 3.4 37.5 - - - +
293A CYS* 4.3 0.9 - - - +
296A VAL* 3.6 19.3 - - + -
430A GLY 3.2 20.6 + - - +
431A ALA 3.6 5.4 - - - +
433A VAL* 1.4 76.8 - - - +
435A SER* 1.4 51.7 + - - +
437A ILE* 3.4 1.8 + - - +
438A THR* 2.8 43.5 + - - +
454A VAL* 5.3 2.5 - - + +
455A VAL* 5.1 4.9 - - + -
458A ALA* 4.5 11.0 - - + -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 3.6 18.0 - - - +
299A SER* 4.5 0.9 + - - -
374A ILE* 3.2 57.6 + - - +
375A LEU* 4.2 4.5 - - - -
378A GLY* 3.9 8.8 - - - -
431A ALA 3.0 15.9 + - - -
432A SER 3.5 9.4 - - - -
433A VAL 3.3 0.4 - - - -
434A LEU* 1.4 76.0 - - - +
436A LEU* 1.4 59.2 + - - +
438A THR* 3.4 7.3 + - - -
439A VAL 3.3 8.8 + - - -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER* 4.8 8.7 - - - +
375A LEU* 3.8 29.1 - - + +
432A SER 3.0 14.9 + - - +
433A VAL* 3.6 19.3 - - + +
434A LEU 3.3 0.4 - - - -
435A SER* 1.4 76.7 - - - +
437A ILE* 1.4 60.1 + - + +
439A VAL* 3.1 28.0 - - + +
440A ILE* 3.3 25.4 + - + +
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Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 4.7 19.5 - - + +
260A VAL* 4.8 13.7 - - + +
263A LEU* 3.7 48.7 - - + -
433A VAL* 3.1 26.9 + - + +
434A LEU* 3.7 1.3 - - - +
436A LEU* 1.4 78.9 - - + +
438A THR* 1.4 59.1 + - - +
440A ILE* 3.8 19.1 - - + -
441A GLY* 3.0 21.1 + - - -
454A VAL* 5.1 4.4 - - - +
36B LEU* 5.6 3.6 - - + -
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Residues in contact with THR 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 4.0 17.6 - - + +
300A TYR* 5.5 2.7 - - + -
370A TYR* 5.2 2.5 - - - +
374A ILE* 4.9 6.7 - - + -
434A LEU* 2.8 29.2 + - - +
435A SER* 3.4 11.2 - - - +
437A ILE* 1.4 77.5 - - - +
439A VAL* 1.4 56.9 + - - +
441A GLY* 3.2 2.6 + - - -
442A GLU* 3.0 27.4 + - + +
451A ALA* 3.3 36.3 + - + +
454A VAL* 3.7 20.3 - - + +
455A VAL* 5.6 0.3 - - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PRO* 6.2 0.2 - - + -
367A PHE* 3.7 24.2 - - + -
370A TYR* 3.5 31.2 - - + -
371A SER* 3.6 22.7 - - - +
374A ILE* 3.8 17.9 - - + -
435A SER 3.3 9.3 + - - +
436A LEU* 3.1 26.9 - - + +
438A THR* 1.4 75.2 - - - +
440A ILE* 1.4 60.9 + - + +
442A GLU* 3.4 8.7 + - + +
443A SER* 2.9 25.9 + - - -
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Residues in contact with ILE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 3.9 22.7 - - + -
367A PHE* 5.4 6.1 - - + -
436A LEU* 3.3 32.3 + - + +
437A ILE* 4.0 22.0 - - + +
438A THR 3.3 0.6 - - - -
439A VAL* 1.4 76.4 - - + +
441A GLY* 1.4 61.8 + - - +
443A SER* 3.0 24.0 + - - +
444A LEU* 3.3 16.5 + - + +
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Residues in contact with GLY 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 3.3 40.8 - - - +
259A ILE* 5.1 4.2 - - - +
260A VAL* 6.4 0.4 - - - -
437A ILE 3.0 15.9 + - - -
438A THR 3.2 4.7 + - - -
440A ILE* 1.4 75.8 - - - +
442A GLU* 1.4 61.1 + - - +
444A LEU* 3.9 8.6 + - - -
445A GLY 3.8 1.4 - - - +
450A ALA 4.6 4.7 - - - -
454A VAL* 4.6 10.5 - - - -
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.3 5.9 + - - -
352A PRO* 3.2 17.9 - - + +
353A PRO* 6.3 1.1 - - + -
354A THR* 2.9 33.9 + - + +
370A TYR* 2.9 25.2 + - + +
438A THR 3.0 16.6 + - - +
439A VAL* 3.6 11.7 - - + +
440A ILE 3.3 0.4 - - - -
441A GLY* 1.4 77.0 - - - +
443A SER* 1.4 60.5 + - - +
445A GLY 3.2 8.0 + - - +
447A LYS* 3.0 22.1 + - - -
450A ALA* 3.5 17.9 - - + +
451A ALA* 3.0 33.8 + - + +
----------------------------------------------------------
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PRO* 6.4 1.6 - - - -
354A THR* 4.9 3.4 - - - -
359A GLY* 3.6 21.7 - - - -
367A PHE* 3.6 29.7 - - - -
439A VAL 2.9 12.6 + - - -
440A ILE* 3.0 26.4 + - - +
442A GLU* 1.4 73.4 - - - +
444A LEU* 1.4 65.2 + - - +
445A GLY* 3.5 0.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 3.3 21.4 - - + +
255A ALA* 3.8 38.6 - - + +
256A ILE* 3.9 15.3 - - + +
259A ILE* 3.7 29.8 - - + -
357A PHE 5.1 0.5 - - - +
358A LYS* 5.2 0.9 - - - -
359A GLY 4.5 6.9 + - - -
440A ILE* 3.4 16.4 - - + +
441A GLY* 4.0 6.5 - - - +
442A GLU 3.3 0.4 - - - -
443A SER* 1.4 77.6 + - - +
445A GLY* 1.4 57.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 3.8 12.3 - - - +
256A ILE* 3.6 16.3 - - - +
354A THR* 3.5 12.3 - - - -
355A SER 4.4 0.2 - - - -
357A PHE 4.4 7.2 - - - -
359A GLY 4.9 4.0 - - - -
441A GLY 3.8 1.0 - - - +
442A GLU 3.2 6.5 + - - +
443A SER 4.2 0.9 - - - -
444A LEU* 1.4 81.1 - - - +
446A LEU* 1.4 74.4 + - - +
450A ALA* 4.1 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