Contacts of the helix formed by residues 530 - 555 (chain B) in PDB entry 3U44
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 ARG 530 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A LYS* 3.1 22.9 - - - +
704A PHE* 6.5 1.3 - - - -
708A HIS* 6.2 0.4 - - - -
524B ARG 4.2 6.9 + - - -
525B ALA* 2.8 42.3 + - - +
526B GLU 3.3 0.5 + - - -
528B ASP* 2.7 51.9 + - - +
529B GLY* 1.3 80.2 - - - +
531B ILE* 1.3 63.9 + - - +
532B ILE* 3.6 8.1 - - + -
533B GLU* 3.5 40.9 + - + +
534B ALA* 3.6 0.7 + - - +
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ARG* 5.9 1.1 - - - +
526B GLU* 4.5 29.2 - - + +
529B GLY* 3.6 23.3 + - - +
530B ARG* 1.3 72.8 - - - +
532B ILE* 1.3 75.2 + - + +
533B GLU 3.2 1.8 - - - -
534B ALA* 2.8 7.4 + - + +
535B GLN* 2.8 28.0 + - + +
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Residues in contact with ILE 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011A ARG* 4.3 18.6 - - - +
529B GLY 5.0 3.1 - - - +
530B ARG* 4.6 8.1 - - + -
531B ILE* 1.3 87.7 - - + +
533B GLU* 1.3 61.8 + - - +
535B GLN* 3.0 24.8 + - - +
536B GLN* 3.3 12.1 + - - +
581B ILE* 3.5 37.9 - - + -
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Residues in contact with GLU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ASN* 3.4 24.2 + - - +
708A HIS* 3.7 21.2 + - - -
521B GLU* 4.7 8.0 - - - +
525B ALA* 4.3 9.1 - - + +
530B ARG* 3.5 44.9 + - + +
531B ILE 3.2 0.4 - - - +
532B ILE* 1.3 80.4 - - - +
534B ALA* 1.3 51.6 + - - +
536B GLN* 2.9 36.7 - - - +
537B HIS* 2.7 33.7 + - + -
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Residues in contact with ALA 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ARG* 3.1 54.2 - - + +
525B ALA* 3.5 14.1 - - + -
526B GLU* 3.8 16.4 - - + +
530B ARG 3.6 6.1 + - - +
531B ILE* 2.8 12.7 + - + +
533B GLU* 1.3 78.6 - - - +
535B GLN* 1.3 60.2 + - - +
536B GLN 3.5 0.3 + - - -
537B HIS* 3.5 14.4 + - - +
538B GLN 4.7 0.7 + - - -
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Residues in contact with GLN 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011A ARG* 5.8 2.3 + - - -
522B ARG* 5.6 2.9 - - - +
531B ILE* 2.8 16.3 + - + +
532B ILE* 3.0 19.7 + - - +
534B ALA* 1.3 74.6 - - - +
536B GLN* 1.3 57.8 + - - +
537B HIS 3.1 6.0 + - - -
538B GLN 4.2 1.0 + - - -
539B GLN* 3.1 39.5 + - + +
579B SER* 5.3 7.4 - - - -
581B ILE* 5.9 1.6 - - - +
582B PRO* 5.8 5.5 - - - +
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Residues in contact with GLN 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ASN* 3.3 35.7 + - - +
708A HIS* 6.0 0.4 - - - -
381B HIS* 3.7 4.7 + - + -
532B ILE 3.3 5.6 + - - +
533B GLU* 2.9 36.9 + - - +
535B GLN* 1.3 77.5 - - - +
537B HIS* 1.3 62.4 + - - +
539B GLN* 3.7 13.2 - - - +
540B ALA* 2.9 29.3 + - - +
578B PHE* 3.0 46.6 - - + -
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Residues in contact with HIS 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ASN* 3.6 26.7 + - - -
381B HIS* 3.5 17.8 + + - +
382B PRO* 6.0 3.3 - - + +
518B LEU* 4.0 24.3 - - + +
521B GLU* 3.1 43.5 + - + +
522B ARG* 3.9 16.4 - - + -
525B ALA* 5.0 2.4 - - + +
533B GLU* 2.7 38.6 + - + -
534B ALA* 3.6 14.1 + - - +
535B GLN 3.1 1.6 - - - -
536B GLN* 1.3 75.3 - - + +
538B GLN* 1.3 59.8 + - + +
539B GLN 3.0 3.1 - - - -
540B ALA* 2.9 26.2 + - - +
541B TRP* 3.2 4.2 + - - +
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Residues in contact with GLN 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A TYR* 3.3 35.6 - - - +
515B PRO* 4.0 19.6 + - - +
518B LEU* 4.3 7.5 - - + +
519B ASP* 4.0 29.9 + - - +
522B ARG* 5.3 10.0 - - - +
534B ALA 4.7 1.2 + - - -
535B GLN 4.2 2.0 + - - +
537B HIS* 1.3 76.9 - - - +
539B GLN* 1.3 61.8 + - - +
540B ALA 3.2 0.4 - - - -
541B TRP* 3.4 28.5 + - + +
542B ASP* 3.7 13.7 + - - +
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Residues in contact with GLN 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B MET* 4.7 1.0 - - - +
535B GLN* 3.1 46.2 + - + +
536B GLN* 3.7 10.9 - - - +
537B HIS 3.0 0.2 - - - -
538B GLN* 1.3 76.8 - - - +
540B ALA* 1.3 62.5 + - - +
541B TRP 3.2 0.6 + - - -
542B ASP* 3.7 7.2 + - - +
543B ALA* 3.6 17.2 + - - +
577B THR 4.8 1.7 - - - +
578B PHE* 3.6 18.0 - - + +
579B SER* 2.7 49.2 + - - +
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Residues in contact with ALA 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B MET* 3.3 26.8 - - + +
381B HIS* 3.6 26.7 - - + +
383B LEU* 3.7 6.3 - - + -
384B ILE* 5.3 0.7 - - + -
536B GLN 2.9 13.6 + - - +
537B HIS 2.9 13.8 + - - +
539B GLN* 1.3 77.3 - - - +
541B TRP* 1.3 60.3 + - - +
543B ALA* 3.4 10.4 + - - +
544B VAL* 3.4 19.8 + - - +
578B PHE* 4.2 0.6 - - + -
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Residues in contact with TRP 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A TYR* 3.6 27.5 - + - -
1045A ARG 3.2 9.9 + - - -
383B LEU* 3.6 19.2 - - + +
506B TYR* 4.3 20.0 - + - -
509B LEU* 4.2 30.1 - - + -
510B GLU* 5.2 2.2 - - + -
514B VAL* 3.7 23.6 - - + -
515B PRO* 3.5 31.0 - - + -
518B LEU* 3.7 19.3 - - + -
537B HIS 3.2 4.8 + - - +
538B GLN* 3.4 26.9 - - + +
539B GLN 3.2 0.2 - - - -
540B ALA* 1.3 77.7 - - - +
542B ASP* 1.3 67.7 + - - +
544B VAL* 2.9 25.7 - - + +
545B ILE* 3.0 40.1 - - + +
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Residues in contact with ASP 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A TYR 5.3 0.5 + - - -
1045A ARG* 3.8 32.9 + - - +
538B GLN* 3.7 11.5 + - - +
539B GLN* 3.7 8.9 + - - +
540B ALA 3.3 0.2 - - - -
541B TRP* 1.3 83.5 - - - +
543B ALA* 1.3 67.8 + - - +
545B ILE* 3.0 7.3 + - - +
546B GLN* 2.8 28.4 + - + +
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Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B MET* 3.7 27.1 - - + -
539B GLN 3.6 7.5 + - - +
540B ALA 3.4 10.0 + - - +
542B ASP* 1.3 78.4 - - - +
544B VAL* 1.3 61.9 + - - +
546B GLN* 3.8 9.9 + - - +
547B LEU* 3.2 22.2 + - - +
576B LEU* 3.8 25.3 - - + +
577B THR 5.1 2.5 - - - +
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Residues in contact with VAL 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 4.0 14.1 - - + -
384B ILE* 3.6 27.6 - - + -
387B ILE* 3.9 26.7 - - + -
509B LEU* 4.9 8.7 - - + -
540B ALA 3.4 12.6 - - - +
541B TRP* 2.9 28.0 - - + +
543B ALA* 1.3 75.7 - - - +
545B ILE* 1.3 64.8 + - + +
547B LEU* 3.2 11.6 - - + +
548B LEU* 3.1 33.9 + - + +
576B LEU* 4.4 4.5 - - + -
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Residues in contact with ILE 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A ARG* 2.8 62.6 - - + +
1046A ARG 4.6 0.4 - - - -
1047A PRO* 4.1 16.6 - - + -
506B TYR* 4.8 14.6 - - + -
509B LEU* 6.3 0.9 - - + -
541B TRP* 3.0 41.7 - - + +
542B ASP* 3.0 7.9 + - - +
544B VAL* 1.3 83.1 - - + +
546B GLN* 1.3 53.0 + - - +
547B LEU 3.0 1.3 - - - -
548B LEU* 2.7 14.4 + - + +
549B GLU* 2.7 42.7 + - + +
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Residues in contact with GLN 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A ARG* 4.3 5.3 - - - +
86B PHE* 5.7 4.8 + - - -
88B THR* 2.9 30.3 + - - +
542B ASP* 2.8 18.3 + - + +
543B ALA* 4.1 8.6 - - - +
545B ILE* 1.3 75.5 - - - +
547B LEU* 1.3 58.2 - - - +
549B GLU* 3.6 13.4 - - - +
550B GLU* 2.9 40.8 + - + +
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Residues in contact with LEU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 4.6 13.9 - - + +
94B MET* 3.5 30.0 - - + +
543B ALA 3.2 13.7 + - - +
544B VAL* 3.2 13.7 - - + +
545B ILE 3.0 0.2 - - - -
546B GLN* 1.3 79.5 - - - +
548B LEU* 1.3 56.7 + - + +
550B GLU* 3.9 6.1 - - + +
551B PHE* 2.9 30.5 + - + +
569B ILE* 4.3 28.5 - - + +
572B GLY* 4.0 35.7 - - - +
573B ALA* 4.5 0.9 - - - +
575B SER* 5.6 0.2 - - - +
576B LEU* 4.9 13.7 - - + -
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Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A PRO* 5.1 1.8 - - + -
1049A PHE* 4.0 17.7 - - + -
502B ALA* 3.7 36.8 - - + +
505B LEU* 4.1 22.7 - - + -
506B TYR* 4.3 24.9 - - + -
509B LEU* 5.3 5.4 - - + -
544B VAL* 3.1 20.0 + - + +
545B ILE* 2.7 18.4 + - + +
547B LEU* 1.3 72.5 - - + +
549B GLU* 1.3 56.1 + - - +
551B PHE* 3.1 6.9 + - + +
552B VAL* 2.8 35.4 + - - +
565B PHE* 5.5 0.4 - - + -
569B ILE* 4.2 17.9 - - + -
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Residues in contact with GLU 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A ARG* 2.8 47.9 + - - -
1046A ARG 4.0 0.2 - - - +
1047A PRO* 3.5 5.4 - - + +
1048A ALA* 2.7 40.9 + - + +
1049A PHE* 4.0 4.4 - - + -
545B ILE* 2.7 25.3 + - + +
546B GLN* 3.6 10.9 - - + +
548B LEU* 1.3 72.5 - - - +
550B GLU* 1.3 58.9 + - + +
552B VAL* 3.0 13.1 - - - +
553B GLU* 2.8 34.9 + - + +
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Residues in contact with GLU 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE 4.0 5.5 - - - +
87B LEU* 3.7 16.7 - - + +
88B THR* 2.7 52.3 + - - +
90B THR* 3.6 11.1 + - - -
91B GLY* 4.2 15.1 - - - -
94B MET* 4.4 4.0 - - - -
546B GLN* 2.9 37.7 + - + +
547B LEU* 4.0 5.7 - - + +
549B GLU* 1.3 74.1 - - + +
551B PHE* 1.3 64.0 + - - +
553B GLU* 3.2 9.5 + - + +
554B MET* 3.0 29.5 + - - +
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Residues in contact with PHE 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B MET* 3.7 25.7 - - + -
498B VAL* 3.9 26.0 - - + -
502B ALA* 5.2 0.7 - - + -
547B LEU 2.9 19.0 + - - +
548B LEU* 3.1 11.9 + - + +
550B GLU* 1.3 76.4 - - - +
552B VAL* 1.3 58.1 - - + +
553B GLU 3.2 0.3 + - - -
554B MET* 4.3 0.3 - - - +
555B MET* 3.0 55.4 + - + -
556B GLY 3.3 2.3 + - - -
560B ILE* 5.5 1.6 - - + -
565B PHE* 3.7 43.7 - + - -
568B MET* 4.0 25.4 - - + -
569B ILE* 4.2 20.2 - - + -
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Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A PHE* 3.2 43.7 - - + -
498B VAL* 4.5 0.9 - - + -
499B GLN* 3.9 22.2 - - + +
502B ALA* 3.7 27.6 - - + -
548B LEU 2.8 19.4 + - - +
549B GLU* 3.0 17.7 - - - +
551B PHE* 1.3 72.1 - - + +
553B GLU* 1.3 62.2 + - + +
556B GLY* 2.9 29.6 + - - -
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Residues in contact with GLU 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PRO* 6.1 0.3 - - - +
87B LEU* 5.9 2.5 - - + -
180B TYR* 2.6 36.5 + - + +
549B GLU* 2.8 25.1 + - + +
550B GLU* 3.3 11.7 - - + +
551B PHE 3.1 0.4 - - - -
552B VAL* 1.3 83.7 - - + +
554B MET* 1.3 70.9 - - + +
556B GLY 4.5 0.3 + - - -
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Residues in contact with MET 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.9 30.7 - - + -
91B GLY* 3.5 28.0 - - - +
94B MET* 4.7 5.4 - - + -
95B LEU* 3.6 38.8 - - + +
98B LYS* 4.2 11.0 + - - +
175B SER 5.4 2.7 - - - +
176B LEU* 4.5 8.1 - - + -
180B TYR* 4.3 26.0 - - + -
550B GLU 3.0 16.3 + - - +
551B PHE 4.3 0.7 - - - +
553B GLU* 1.3 82.0 - - + +
555B MET* 1.3 66.0 + - + +
556B GLY 3.6 0.4 + - - -
558B ASP* 4.0 4.5 - - - +
----------------------------------------------------------
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Residues in contact with MET 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B MET* 3.5 34.3 - - + +
95B LEU* 5.3 0.2 - - - -
97B ARG* 5.3 1.6 - - - -
98B LYS* 3.8 25.1 - - + -
498B VAL* 3.1 20.8 - - + +
551B PHE* 3.0 37.9 + - + +
554B MET* 1.3 82.0 - - + +
556B GLY* 1.3 65.1 + - - +
557B ASP 3.3 2.2 - - - -
558B ASP* 2.9 36.5 + - + +
560B ILE* 5.7 5.2 - - + -
568B MET* 3.5 25.6 - - + +
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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