Contacts of the helix formed by residues 438 - 461 (chain A) in PDB entry 6UZA
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 GLY 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A TRP 5.4 0.2 - - - -
393A GLU* 3.8 13.9 - - - -
394A ASN* 4.9 4.5 - - - -
395A LEU* 6.3 1.6 - - - -
434A LYS 4.2 2.6 + - - -
435A ILE 3.2 13.6 + - - -
437A ARG* 1.3 82.2 - - - +
439A PRO* 1.3 75.9 - - - +
440A PHE 3.4 2.5 - - - -
441A MET* 3.8 2.8 + - - -
442A LYS* 3.2 22.7 + - - +
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Residues in contact with PRO 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ARG* 4.6 6.1 - - - +
390A ILE 3.4 26.7 - - - +
391A TRP* 3.6 33.8 - - + +
393A GLU* 3.8 12.3 - - + +
437A ARG 4.4 1.6 - - - +
438A GLY* 1.3 85.3 - - - +
440A PHE* 1.3 55.6 + - - +
442A LYS* 3.4 4.8 + - + +
443A PHE* 2.9 28.1 + - - +
753A TYR* 3.9 25.7 - - + +
754A PHE* 3.6 21.1 - - + -
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Residues in contact with PHE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TRP* 3.4 47.0 + + - +
392A TYR* 3.7 20.2 - + + -
395A LEU* 3.6 26.2 - - + +
398A LEU* 4.1 24.5 - - + -
406A LYS* 4.2 28.7 - - + -
409A VAL* 5.6 0.9 - - + -
438A GLY 3.4 0.8 - - - -
439A PRO* 1.3 76.6 - - - +
441A MET* 1.3 61.2 + - - +
443A PHE* 3.3 8.7 + + - +
444A VAL* 2.9 48.8 + - + +
1004A Y01 3.6 24.7 - - + -
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Residues in contact with MET 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 3.8 25.2 - - + +
398A LEU* 4.5 15.9 - - - -
409A VAL* 5.4 6.3 - - + -
413A VAL* 4.4 24.7 - - + -
420A LEU* 5.9 2.7 - - + -
432A MET* 6.2 3.8 - - + -
435A ILE* 3.5 39.5 - - + +
436A MET* 4.1 23.1 - - + -
438A GLY* 3.8 3.7 + - - +
439A PRO 3.4 0.4 - - - -
440A PHE* 1.3 74.3 - - - +
442A LYS* 1.3 59.8 + - - +
444A VAL* 3.7 13.2 - - + +
445A ALA* 2.9 30.0 + - + +
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A MET 4.6 4.2 + - - +
437A ARG* 4.0 15.7 + - - +
438A GLY 3.2 20.5 + - - +
439A PRO* 3.5 5.6 - - + +
441A MET* 1.3 76.7 - - - +
443A PHE* 1.3 56.4 + - - +
445A ALA* 3.4 4.6 + - - +
446A HIS* 3.0 41.4 + - + -
753A TYR* 3.3 28.1 + - + -
754A PHE 5.1 0.6 - - - -
755A GLU 3.4 18.0 + - - -
756A GLU* 5.0 1.2 - - - +
757A GLY 4.8 5.7 - - - +
758A ARG 3.6 17.0 + - - +
759A THR* 4.1 29.3 + - + +
1001A R0G 3.5 24.0 + - - +
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Residues in contact with PHE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TRP* 3.7 25.6 - + + -
439A PRO 2.9 17.4 + - - +
440A PHE* 3.3 17.2 + + - +
442A LYS* 1.3 75.8 - - - +
444A VAL* 1.3 61.5 + - + +
446A HIS* 3.4 1.9 + - + -
447A ALA* 2.9 29.4 + - + +
612A TYR 4.6 2.5 - - - -
613A ILE* 3.8 42.2 - - + -
616A ALA* 3.7 29.6 - - + -
749A LEU* 4.6 3.8 - - + -
753A TYR* 3.5 33.8 - + + -
1004A Y01 4.3 31.0 - - + -
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 6.2 0.2 - - + -
409A VAL* 4.2 10.3 - - + +
410A VAL* 4.0 34.8 - - + +
413A VAL* 3.9 27.4 - - + -
440A PHE* 2.9 49.3 + - + +
441A MET* 3.7 16.4 - - + +
442A LYS 3.3 0.2 - - - -
443A PHE* 1.3 79.3 - - + +
445A ALA* 1.3 58.8 + - - +
447A ALA* 3.4 2.6 + - - +
448A ALA* 2.9 27.7 + - - +
1004A Y01 6.0 0.7 - - + -
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A VAL* 4.2 19.1 - - + -
417A LEU* 4.5 3.7 - - + +
441A MET* 2.9 18.4 + - + +
442A LYS* 3.7 6.7 - - - +
444A VAL* 1.3 78.3 - - - +
446A HIS* 1.3 57.5 + - + +
448A ALA* 3.3 2.0 + - - +
449A SER* 3.0 30.0 + - - -
759A THR 4.9 5.4 - - - +
761A PRO* 3.7 24.1 - - + +
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Residues in contact with HIS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LYS* 3.0 37.4 + - + +
443A PHE 3.9 3.6 - - - +
445A ALA* 1.3 77.2 - - - +
447A ALA* 1.3 60.3 + - - +
449A SER* 3.9 3.2 + - - -
450A PHE* 3.7 13.7 + - - +
753A TYR* 4.5 5.8 - + - +
758A ARG* 3.5 26.0 + - + -
759A THR 4.4 5.0 + - - -
760A LEU 4.4 3.7 + - - -
761A PRO* 4.1 30.0 - - + +
762A VAL* 4.9 5.2 + - + +
1001A R0G 3.4 65.8 - + + -
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A VAL* 4.8 5.8 - - + -
443A PHE* 2.9 18.6 + - + +
444A VAL* 3.9 5.6 - - - +
445A ALA 3.3 0.2 - - - -
446A HIS* 1.3 77.0 - - - +
448A ALA* 1.3 59.3 + - - +
450A PHE* 3.2 8.7 + - - +
451A THR* 3.0 31.2 + - - +
613A ILE* 4.2 22.7 - - + -
1001A R0G 4.5 0.4 - - - -
1004A Y01 4.1 28.0 - - + +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A VAL* 3.6 27.1 - - - +
413A VAL* 3.9 10.8 - - + +
414A ALA* 3.6 16.8 - - - +
417A LEU* 4.8 2.5 - - + -
444A VAL 2.9 17.4 + - - +
445A ALA 3.3 4.5 + - - +
447A ALA* 1.3 75.5 - - - +
449A SER* 1.3 58.1 + - - +
450A PHE 3.1 0.4 - - - -
451A THR* 3.3 9.0 + - - -
452A ILE* 3.0 35.7 + - - +
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 4.1 14.7 - - - +
445A ALA 3.0 15.9 + - - -
446A HIS* 4.2 5.2 - - - -
447A ALA 3.3 0.4 - - - -
448A ALA* 1.3 76.2 - - - +
450A PHE* 1.3 57.2 + - - +
452A ILE* 4.1 6.3 - - - -
453A PHE* 3.8 5.2 + - - +
501A TRP* 3.1 21.0 + - - -
761A PRO* 3.6 19.3 - - - -
762A VAL* 3.4 13.0 - - - +
763A PRO* 3.3 24.1 - - - +
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Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A HIS 3.7 11.4 + - - +
447A ALA* 3.2 8.4 + - - +
448A ALA 3.1 0.6 - - - -
449A SER* 1.3 74.8 - - - +
451A THR* 1.3 62.3 + - - +
452A ILE 3.2 1.3 - - - -
453A PHE* 3.3 14.7 + + - +
454A LEU* 3.0 62.9 + - + +
505A MET* 6.2 1.6 - - + -
606A SER 3.5 25.8 - - - -
607A PHE* 4.7 0.9 - - - -
609A ARG* 3.7 34.1 - - + -
610A ILE* 3.7 29.4 - - + -
613A ILE* 4.5 17.0 - - + -
1001A R0G 4.5 12.6 - + + -
1004A Y01 5.1 4.9 - - + -
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Residues in contact with THR 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A VAL* 4.4 6.2 - - - +
411A LEU* 4.3 19.3 - - + -
414A ALA* 4.8 8.3 - - + -
447A ALA 3.0 15.1 + - - -
448A ALA* 3.6 12.1 - - - -
450A PHE* 1.3 79.3 - - - +
452A ILE* 1.3 56.1 + - - +
454A LEU* 3.5 6.6 + - - +
455A GLY* 2.9 25.3 + - - -
1004A Y01 3.5 48.8 - - + +
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Residues in contact with ILE 452 (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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414A ALA* 3.3 34.5 - - + +
417A LEU* 3.8 29.6 - - + -
448A ALA 3.0 21.2 + - - +
449A SER* 4.4 2.7 - - - +
451A THR* 1.3 75.7 - - + +
453A PHE* 1.3 57.6 + - - +
455A GLY* 3.2 2.1 + - - -
456A LEU* 2.9 37.7 + - + +
501A TRP* 3.6 31.9 - - + -
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Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A SER 3.8 6.3 + - - +
450A PHE* 3.3 23.9 + + + +
452A ILE* 1.3 77.8 - - - +
454A LEU* 1.3 62.4 + - + +
456A LEU* 3.3 11.3 + - + +
457A LEU* 3.0 47.3 + - + +
498A ILE* 3.9 22.7 - - + -
501A TRP* 3.8 46.2 - + + +
502A VAL* 4.3 8.5 - - + -
505A MET* 4.3 19.5 - - + -
533A MET* 5.4 0.7 - - + -
537A PHE* 4.1 25.6 - + - -
606A SER* 4.2 15.0 - - - -
609A ARG* 6.3 1.1 - - - -
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Residues in contact with LEU 454 (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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450A PHE* 3.0 59.3 + - + +
451A THR* 3.9 4.0 - - - +
453A PHE* 1.3 79.3 - - + +
455A GLY* 1.3 57.6 + - - +
457A LEU* 3.3 8.5 + - + +
458A VAL* 3.0 32.7 + - - +
606A SER* 4.3 10.5 - - - +
607A PHE* 3.9 41.3 - - + -
610A ILE* 4.8 3.8 - - + -
1004A Y01 3.9 40.2 - - + -
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Residues in contact with GLY 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A THR 2.9 15.5 + - - -
452A ILE* 3.7 4.0 - - - -
454A LEU* 1.3 76.1 - - - +
456A LEU* 1.3 58.0 + - - +
458A VAL* 3.4 2.8 + - - +
459A MET* 2.9 37.3 + - - +
1004A Y01 4.3 12.9 - - - +
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Residues in contact with LEU 456 (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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452A ILE* 2.9 25.9 + - + +
453A PHE* 3.6 9.2 - - + +
454A LEU 3.3 0.2 - - - -
455A GLY* 1.3 76.0 - - - +
457A LEU* 1.3 57.3 + - - +
459A MET* 6.0 0.4 - - + -
460A ASN* 2.9 33.3 + - - +
493A TRP* 6.1 2.9 - - + -
494A MET* 3.8 27.5 - - + +
497A LEU* 3.8 35.7 - - + -
498A ILE* 4.2 17.5 - - + +
501A TRP* 4.1 25.1 - - + -
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Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE* 3.0 36.9 + - + +
454A LEU* 3.3 13.4 + - + +
456A LEU* 1.3 76.4 - - - +
458A VAL* 1.3 63.9 + - + +
460A ASN* 4.0 8.1 + - - +
461A ALA* 4.6 1.4 + - - +
498A ILE* 4.1 15.3 - - + -
537A PHE* 4.2 10.8 - - + -
599A TYR* 3.3 27.1 + - + +
603A VAL* 3.8 28.0 - - + +
606A SER* 3.3 26.7 - - - +
607A PHE* 4.9 5.4 - - + -
650B ILE* 4.4 5.7 - - + +
654B ASN* 4.3 16.3 + - - +
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU 3.0 21.4 + - - +
455A GLY* 3.8 5.6 - - - +
457A LEU* 1.3 79.1 - - - +
459A MET* 1.3 75.3 + - + +
460A ASN 3.2 2.1 + - - -
461A ALA* 3.7 8.7 + - - +
465A PHE* 3.9 30.2 - - + -
607A PHE* 5.0 2.5 - - + -
1004A Y01 3.8 23.8 - - + -
650B ILE* 3.7 35.2 - - + -
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Residues in contact with MET 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLY* 2.9 21.0 + - - +
456A LEU* 6.0 0.4 - - + -
458A VAL* 1.3 85.4 - - + +
460A ASN* 1.3 64.0 + - - +
461A ALA 3.4 0.2 - - - -
462A ALA* 3.3 30.0 - - - +
465A PHE* 4.6 13.7 - - + -
494A MET* 3.3 29.1 - - + +
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Residues in contact with ASN 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU 2.9 17.6 + - - +
457A LEU 4.1 6.7 - - - +
458A VAL 3.2 1.0 - - - -
459A MET* 1.3 79.8 - - - +
461A ALA* 1.3 59.5 + - - +
462A ALA 3.2 4.7 + - - -
463A ASP* 4.9 1.0 + - - +
464A ARG* 5.1 1.9 + - - -
492A SER* 5.5 3.5 - - - -
494A MET* 3.7 20.1 - - - +
495A GLU* 4.5 13.2 + - - +
498A ILE* 4.1 16.2 - - + +
599A TYR* 3.1 29.9 + - - +
654B ASN* 6.2 0.2 - - - +
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Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LEU 4.6 1.4 + - - +
458A VAL 3.7 5.9 + - - +
460A ASN* 1.3 79.3 - - + +
462A ALA* 1.3 57.1 + - - +
463A ASP 3.5 2.9 + - - +
464A ARG* 3.4 43.3 + - - +
465A PHE* 3.2 22.9 - - - -
653B PHE* 3.6 12.4 - - + -
654B ASN* 3.6 22.4 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il