Contacts of the helix formed by residues 411 - 441 (chain A) in PDB entry 1LVK
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 VAL 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A PHE* 3.3 33.5 - - + +
360A GLU* 3.3 32.5 - - - +
361A LYS* 3.9 8.7 - - + +
365A GLU 4.4 1.8 + - - -
367A ALA* 3.8 4.9 - - + +
410A ASN* 1.4 72.9 - - - +
412A GLU* 1.3 59.1 + - + +
414A SER* 3.1 3.0 + - - -
415A SER* 2.6 40.2 + - - -
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASN* 3.1 12.0 + - - +
411A VAL* 1.3 83.5 - - - +
413A LYS* 1.3 84.2 + - - +
415A SER* 3.5 6.0 + - - -
416A SER* 2.9 39.6 + - - +
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Residues in contact with LYS 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A HIS 3.8 5.3 + - - -
409A LEU* 3.3 37.2 - - + +
410A ASN* 2.6 64.7 + - - +
412A GLU* 1.3 91.6 - - - +
414A SER* 1.3 68.1 + - - +
416A SER* 3.5 5.3 + - - -
417A SER* 3.0 24.6 + - - -
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.7 24.7 - - - -
367A ALA* 3.6 1.9 - - - +
393A LEU* 4.2 10.4 - - - +
394A MET* 3.2 26.0 - - - +
409A LEU* 3.2 16.6 + - - +
410A ASN 2.7 23.8 + - - -
411A VAL 3.1 5.1 + - - -
413A LYS* 1.3 78.4 - - - +
415A SER* 1.3 63.5 + - - +
417A SER* 3.2 3.5 + - - -
418A ARG* 3.0 21.7 + - - +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.8 12.3 - - - -
411A VAL* 2.6 24.4 + - - -
412A GLU* 3.9 6.3 - - - -
413A LYS 3.1 0.2 - - - -
414A SER* 1.3 72.1 - - - +
416A SER* 1.3 59.0 + - - +
418A ARG* 2.4 35.6 + - - +
419A ASP* 2.9 31.4 + - - -
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Residues in contact with SER 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU* 2.9 26.3 + - - +
413A LYS* 3.7 7.6 - - - -
415A SER* 1.3 73.2 - - - +
417A SER* 1.3 59.5 + - - +
419A ASP* 3.1 11.1 + - - +
420A ALA* 2.8 28.4 + - - +
586A GLU* 6.0 2.5 - - - -
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Residues in contact with SER 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ALA 4.9 0.3 + - - -
393A LEU* 4.4 16.3 + - - -
409A LEU* 4.5 6.0 - - - +
413A LYS 3.0 15.9 + - - -
414A SER 3.2 4.7 + - - -
416A SER* 1.3 77.6 - - - +
418A ARG* 1.3 54.2 + - - +
420A ALA* 3.1 8.8 + - - +
421A LEU* 2.8 33.5 + - - +
592A LEU* 5.7 0.2 - - - +
593A GLN* 4.0 14.5 + - - +
596A LEU* 3.5 23.2 - - - +
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Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TYR* 3.0 25.4 - - - -
354A LEU* 2.6 50.4 + - + +
355A GLY* 3.6 9.3 + - - -
357A ILE* 2.9 36.9 + - + +
359A PHE* 3.7 19.3 - - + -
393A LEU* 4.0 17.1 - - + +
414A SER 3.0 11.5 + - - +
415A SER* 2.4 37.2 + - - +
417A SER* 1.3 74.4 - - - +
419A ASP* 1.3 76.7 + - - +
421A LEU* 3.1 5.8 + - + +
422A VAL* 2.9 23.5 + - - +
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Residues in contact with ASP 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 3.8 26.3 - - + +
306A TYR* 2.8 26.2 + - - -
415A SER* 2.9 16.6 + - - +
416A SER* 3.3 14.0 - - - +
418A ARG* 1.3 90.6 + - - +
420A ALA* 1.3 57.0 + - - +
422A VAL* 3.2 3.1 + - - +
423A LYS* 2.8 39.6 + - - +
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A SER 2.8 16.4 + - - +
417A SER* 3.1 11.0 + - - +
419A ASP* 1.3 72.8 - - - +
421A LEU* 1.4 58.1 + - - +
423A LYS* 3.3 13.8 + - - +
424A ALA* 2.9 30.7 + - - +
586A GLU* 6.0 1.3 - - - +
591A PRO 3.7 23.1 - - - +
592A LEU* 3.9 9.0 - - + +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LEU* 3.3 26.9 - - + -
389A LEU* 4.2 11.2 - - + -
393A LEU* 4.6 4.9 - - + -
417A SER 2.8 13.7 + - - +
418A ARG* 3.1 9.6 + - - +
420A ALA* 1.4 73.6 - - - +
422A VAL* 1.3 64.8 + - - +
424A ALA* 3.3 1.4 + - - +
425A LEU* 2.9 38.1 + - + +
592A LEU* 3.7 20.8 - - + +
596A LEU* 4.3 15.5 - - + -
600A PHE* 3.5 42.0 - - + -
612A PHE* 4.5 8.7 - - + -
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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* 3.6 22.0 - - + -
269A VAL* 3.3 28.9 - - + -
306A TYR* 3.5 22.7 - - + +
351A ILE* 4.0 10.8 - - + +
354A LEU* 3.3 40.2 - - + -
418A ARG 2.9 10.4 + - - +
419A ASP 3.5 4.9 - - - +
421A LEU* 1.3 77.5 - - - +
423A LYS* 1.3 61.0 + - - +
425A LEU* 3.3 8.9 + - - +
426A TYR* 3.0 23.4 + - - +
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Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 3.4 50.9 - - + +
266A SER* 3.8 21.2 - - - +
268A VAL* 5.5 0.2 - - - -
269A VAL* 4.2 19.8 - - + +
419A ASP* 2.8 30.4 + - - +
420A ALA* 4.0 13.0 - - - +
422A VAL* 1.3 74.5 - - + +
424A ALA* 1.3 56.8 + - - +
426A TYR* 3.4 3.2 + - - +
427A GLY 2.9 25.1 + - - -
586A GLU* 5.7 2.4 + - - -
590A ASP* 5.7 5.4 + - - +
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 5.3 4.3 - - - +
420A ALA 2.9 17.0 + - - +
421A LEU 3.8 4.3 - - - +
423A LYS* 1.3 72.1 - - - +
425A LEU* 1.3 67.2 + - - +
427A GLY* 5.3 0.4 - - - -
428A ARG* 3.0 51.1 + - - +
592A LEU* 4.0 24.0 - - + -
612A PHE* 5.3 1.8 - - + -
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ILE* 4.8 6.4 - - + +
351A ILE* 4.2 12.3 - - + -
354A LEU* 3.6 29.2 - - + -
382A PHE* 3.8 22.2 - - + -
421A LEU* 2.9 33.2 + - + +
422A VAL* 3.3 5.8 + - - +
424A ALA* 1.3 77.3 - - - +
426A TYR* 1.3 57.8 + - - +
428A ARG* 3.8 3.5 - - - +
429A LEU* 2.9 30.7 + - - +
600A PHE* 4.1 13.5 - - + -
608A VAL* 5.0 4.0 - - + -
611A LEU* 3.8 12.3 - - + +
612A PHE* 3.4 31.2 - - + -
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Residues in contact with TYR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PHE* 2.6 38.7 + + - -
263A LEU* 4.0 17.7 - - + -
265A LYS* 5.4 2.9 - - + -
268A VAL* 3.5 26.2 - - + -
278A TYR* 3.1 36.6 - + + +
280A ILE* 3.1 11.0 - - + +
281A PHE* 3.7 20.4 - + - -
348A ILE* 3.7 17.9 - - + -
351A ILE* 3.8 21.5 - - + +
422A VAL 3.0 13.4 + - - +
423A LYS* 3.9 3.1 - - - +
425A LEU* 1.3 78.1 - - - +
427A GLY* 1.3 65.4 + - - +
429A LEU* 3.4 6.5 + - + +
430A PHE* 3.0 27.8 + + + +
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Residues in contact with GLY 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.1 11.5 - - - +
265A LYS* 3.7 24.1 - - - +
423A LYS 2.9 12.6 + - - -
424A ALA* 4.0 0.4 - - - -
426A TYR* 1.3 76.2 - - - +
428A ARG* 1.3 58.2 + - - +
430A PHE* 3.3 3.5 + - - +
431A LEU* 2.9 33.6 + - - +
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Residues in contact with ARG 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ALA* 3.0 34.0 + - - +
425A LEU* 3.9 1.6 - - - +
427A GLY* 1.3 76.0 - - - +
429A LEU* 1.3 66.8 + - - +
431A LEU* 3.2 7.6 + - + +
432A TRP* 2.9 24.1 + - - +
592A LEU* 4.0 9.9 - - - +
597A GLU* 3.0 25.8 + - - -
611A LEU* 3.1 37.8 + - + +
612A PHE* 3.2 33.5 - - - -
617A ILE* 3.7 31.2 + - + +
618A ALA* 3.5 26.3 + - - +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 3.8 26.0 - - + -
344A ILE* 4.4 17.3 - - + +
347A ILE* 4.0 25.8 - - + -
348A ILE* 4.0 16.6 - - + -
425A LEU 2.9 19.0 + - - +
426A TYR* 3.6 10.8 - - + +
427A GLY 3.4 0.2 - - - -
428A ARG* 1.3 76.6 - - - +
430A PHE* 1.3 59.3 + - - +
432A TRP* 3.2 15.8 + - + -
433A LEU* 2.7 46.7 + - + +
607A VAL* 5.1 0.9 - - + -
611A LEU* 3.7 13.2 - - + +
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Residues in contact with PHE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.9 20.2 - - + -
225A PHE* 3.8 25.6 - - + -
226A GLY* 3.7 23.3 - - - -
239A PHE* 3.8 36.3 - + + -
260A SER* 3.7 33.9 - - - -
263A LEU* 3.7 26.0 - - + -
426A TYR* 3.0 16.4 + + + +
427A GLY 3.6 4.7 - - - +
428A ARG 3.2 0.2 - - - -
429A LEU* 1.3 79.5 - - + +
431A LEU* 1.3 65.0 + - + +
433A LEU* 3.3 10.1 + - + +
434A VAL* 3.0 33.3 + - + +
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER* 4.9 11.2 - - - +
427A GLY 2.9 18.9 + - - +
428A ARG* 3.3 13.7 - - + +
430A PHE* 1.3 79.2 - - + +
432A TRP* 1.3 57.6 + - - +
434A VAL* 3.2 8.6 + - + +
435A LYS* 2.9 39.7 + - + +
616A ASN 4.9 5.2 - - - +
617A ILE* 4.1 33.2 - - + +
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Residues in contact with TRP 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PHE* 3.5 30.5 - + - -
340A GLU* 4.2 9.9 - - + -
344A ILE* 3.7 21.8 - - + -
428A ARG 2.9 16.3 + - - +
429A LEU* 3.4 12.1 - - + +
431A LEU* 1.3 73.8 - - - +
433A LEU* 1.3 77.9 + - + +
435A LYS* 3.2 3.7 + - + +
436A LYS* 2.8 62.3 + - + +
607A VAL* 3.8 31.6 - - + -
610A LYS* 4.0 26.9 - - + +
611A LEU* 3.5 19.5 - - + -
617A ILE* 3.5 26.0 - - + -
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 4.7 12.3 - - + -
222A LEU* 4.6 10.8 - - + -
225A PHE* 3.5 51.8 - - + -
331A MET* 6.0 1.3 - - - -
336A PHE* 4.2 11.0 - - + -
344A ILE* 4.1 15.9 - - + -
429A LEU* 2.7 33.3 + - + +
430A PHE* 3.4 13.2 - - + +
432A TRP* 1.3 95.8 - - + +
434A VAL* 1.3 65.4 + - - +
436A LYS* 3.2 3.2 + - - +
437A ILE* 2.9 30.0 + - - +
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 4.0 21.8 - - + -
258A ILE* 3.4 42.4 - - + +
260A SER* 4.2 14.6 - - - +
430A PHE* 3.0 33.7 + - + +
431A LEU* 3.6 9.4 - - + +
432A TRP 3.2 0.2 - - - -
433A LEU* 1.3 76.6 - - - +
435A LYS* 1.3 57.9 + - + +
437A ILE* 3.2 9.0 + - - +
438A ASN* 2.8 31.9 + - - +
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Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 2.9 25.9 + - + +
432A TRP* 3.8 5.4 - - + +
434A VAL* 1.3 77.4 - - + +
436A LYS* 1.3 65.4 + - + +
438A ASN* 3.1 11.2 + - - +
439A ASN* 2.9 38.2 + - - +
614A ASP* 3.7 15.6 + - - -
616A ASN* 3.6 33.4 - - + +
617A ILE* 4.4 19.3 - - + -
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Residues in contact with LYS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLY 5.0 4.8 + - - -
336A PHE* 3.4 33.0 - - + -
340A GLU* 3.4 27.1 + - - -
432A TRP* 2.8 64.4 + - + +
435A LYS* 1.3 80.5 - - + +
437A ILE* 1.3 63.7 + - - +
439A ASN* 3.2 27.0 - - - +
440A VAL* 3.3 16.3 + - - +
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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
----------------------------------------------------------
218A ALA* 3.8 33.0 - - + -
221A ILE* 4.2 15.7 - - + -
222A LEU* 4.0 30.7 - - + -
258A ILE* 4.2 11.2 - - + -
334A VAL* 4.3 16.2 - - + -
336A PHE* 4.2 17.7 - - + -
433A LEU 2.9 20.7 + - - +
434A VAL* 3.5 4.9 - - - +
436A LYS* 1.3 75.2 - - - +
438A ASN* 1.3 68.4 + - - +
440A VAL* 3.1 2.9 + - - +
441A LEU* 2.9 35.7 + - + +
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Residues in contact with ASN 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA 4.3 0.2 - - - +
257A SER* 3.4 15.0 + - - -
258A ILE* 2.8 51.4 + - - +
434A VAL* 2.8 28.9 + - - +
435A LYS* 3.1 10.9 + - - +
437A ILE* 1.3 76.3 - - - +
439A ASN* 1.3 59.5 + - - +
441A LEU* 4.3 2.7 - - - +
442A CYS* 2.5 43.6 + - + +
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Residues in contact with ASN 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LYS* 2.9 27.2 + - - +
436A LYS* 3.2 25.2 + - + +
438A ASN* 1.3 78.7 - - - +
440A VAL* 1.3 67.1 + - + +
442A CYS 4.1 7.8 - - - +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 5.0 3.8 - - - +
214A GLN* 3.4 34.5 - - - +
334A VAL* 3.8 27.6 - - + +
335A GLY* 5.6 3.1 - - - +
436A LYS* 3.5 16.8 - - - +
437A ILE 3.1 7.1 + - - +
439A ASN* 1.3 83.7 - - + +
441A LEU* 1.3 68.3 + - + +
442A CYS 4.5 1.4 - - - +
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.9 17.9 - - + +
214A GLN* 3.5 33.4 - - + +
215A ILE* 3.6 28.3 - - + +
218A ALA* 4.3 8.3 - - + -
254A SER 4.5 1.0 - - - +
255A GLY* 3.2 10.9 - - - -
256A ALA* 3.0 40.6 + - + +
258A ILE* 5.1 7.2 - - + -
334A VAL* 5.4 2.0 - - + -
437A ILE* 2.9 39.1 + - + +
438A ASN* 4.7 0.9 - - - +
440A VAL* 1.3 82.8 - - + +
442A CYS* 1.3 65.8 + - - +
443A SER* 3.5 0.3 + - - -
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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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