Contacts of the helix formed by residues 588 - 615 (chain A) in PDB entry 2O8B
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 TYR 588 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 6.2 0.7 - - + -
446A ASP 3.2 26.6 + - - -
447A PHE* 3.7 24.6 - + + -
449A LYS* 3.4 30.8 - - - +
450A PHE* 3.6 28.2 + + + -
584A ILE* 3.4 35.9 - - + -
585A SER* 3.1 18.4 + - - +
587A GLY* 1.3 81.6 - - - +
589A VAL* 1.3 58.9 + - - +
591A PRO* 3.3 24.3 - - + +
592A MET* 2.8 22.6 + - - +
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Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 5.6 5.4 - - - +
288A GLN* 5.5 7.0 - - - +
391A ALA* 4.3 20.6 - - + +
394A PHE* 4.3 15.5 - - + -
395A GLN* 4.8 21.1 - - + +
585A SER 5.0 0.2 - - - +
586A SER* 3.1 31.4 - - - +
587A GLY 3.3 3.6 + - - -
588A TYR* 1.3 74.9 - - - +
590A GLU* 1.3 69.8 + - + +
592A MET* 3.1 24.6 + - + +
593A GLN* 3.6 15.2 + - - +
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Residues in contact with GLU 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 5.4 9.9 - - - +
587A GLY 5.2 0.4 + - - -
589A VAL* 1.3 81.3 - - + +
591A PRO* 1.4 68.5 - - + +
592A MET 3.2 1.4 + - - -
593A GLN* 3.4 14.4 + - - +
594A THR* 3.4 20.5 + - + +
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Residues in contact with PRO 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 4.3 10.6 - - + +
446A ASP* 4.9 8.7 - - + +
447A PHE* 3.5 26.7 - - + -
587A GLY 5.0 2.2 - - - +
588A TYR* 3.3 33.9 - - + +
590A GLU* 1.4 92.4 - - + +
592A MET* 1.3 61.1 + - - -
594A THR* 3.2 22.2 + - + +
595A LEU* 3.2 16.5 + - - +
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Residues in contact with MET 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.6 21.6 - - + +
390A LEU* 3.7 31.6 - - + -
391A ALA* 4.1 18.4 - - + +
394A PHE* 4.8 6.1 - - + -
407A LEU* 3.7 42.2 - - + -
447A PHE* 4.3 11.0 - - - -
585A SER 5.3 3.6 - - - +
588A TYR* 2.8 27.7 + - - +
589A VAL* 3.1 18.3 + - + +
591A PRO* 1.3 77.0 - - - +
593A GLN* 1.3 58.5 + - - +
595A LEU* 3.3 6.1 + - - +
596A ASN* 2.8 27.8 + - - +
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Residues in contact with GLN 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE 4.7 6.7 + - - -
170A GLN* 5.3 4.0 - - - +
171A ARG* 2.8 58.3 + - - +
388A ASN* 3.5 20.5 + - - +
391A ALA* 4.2 19.9 - - + +
392A LYS* 6.0 3.0 - - - +
589A VAL* 3.6 13.0 + - - +
590A GLU* 3.4 9.1 + - - +
592A MET* 1.3 78.2 - - - +
594A THR* 1.3 60.8 + - + +
596A ASN* 3.4 8.5 - - - +
597A ASP* 2.9 40.1 + - - +
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Residues in contact with THR 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.6 18.3 - - - +
590A GLU* 3.4 16.7 + - + +
591A PRO* 3.2 17.8 + - + +
593A GLN* 1.3 75.6 - - + +
595A LEU* 1.3 63.3 + - - +
597A ASP* 3.5 6.0 + - - +
598A VAL* 3.1 35.9 + - - +
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Residues in contact with LEU 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PHE* 6.0 1.8 - - + -
387A LEU* 3.6 20.6 - - + -
407A LEU* 5.8 0.7 - - + -
410A GLY 6.2 1.1 - - - -
411A ILE* 4.8 12.3 - - + -
414A LEU* 4.0 20.0 - - + -
440A LEU* 3.8 28.0 - - + -
443A LEU* 3.8 19.3 - - + -
447A PHE* 4.1 23.3 - - + -
591A PRO 3.2 14.6 + - - +
592A MET* 3.6 4.3 - - - +
594A THR* 1.3 78.9 + - - +
596A ASN* 1.3 66.7 + - - +
598A VAL* 4.6 0.9 - - - -
599A LEU* 3.0 44.3 + - + +
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Residues in contact with ASN 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLN* 5.0 2.4 - - - +
337A GLN* 3.0 38.1 + - - +
340A ARG* 4.5 4.0 - - - +
386A ASP* 3.8 0.2 - - - +
387A LEU* 3.2 32.0 + - + +
388A ASN* 3.3 33.9 + - - +
592A MET 2.8 16.8 + - - +
593A GLN* 3.4 11.9 - - - +
594A THR 3.2 0.2 - - - -
595A LEU* 1.3 78.4 - - - +
597A ASP* 1.3 64.3 + - - +
600A ALA* 3.0 32.5 + - - +
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Residues in contact with ASP 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLN* 3.4 28.4 + - - +
341A LEU* 4.5 0.9 - - - +
388A ASN* 5.1 1.0 + - - +
593A GLN* 2.9 25.7 + - - +
594A THR* 4.0 6.4 - - - +
596A ASN* 1.3 87.7 + - - +
598A VAL* 1.3 60.3 + - + +
600A ALA* 3.7 6.5 + - - +
601A GLN* 3.1 38.5 + - - +
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Residues in contact with VAL 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A VAL 4.9 8.7 - - - +
436A PHE* 4.2 15.6 - - + -
439A PRO* 4.7 17.5 - - + -
440A LEU* 3.8 31.0 - - + -
443A LEU* 4.9 5.2 - - + -
594A THR* 3.1 20.5 + - - +
595A LEU* 4.0 4.5 - - - +
597A ASP* 1.3 73.9 - - + +
599A LEU* 1.3 67.4 + - - +
601A GLN* 2.9 25.3 + - - +
602A LEU* 3.0 12.9 + - + +
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Residues in contact with LEU 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A THR* 5.4 3.4 - - + +
337A GLN* 3.8 11.9 - - - +
381A LEU* 5.0 9.7 - - + +
384A PHE* 3.7 54.7 - - + -
387A LEU* 3.9 13.7 - - + -
414A LEU* 4.8 2.0 - - + -
417A VAL* 6.0 2.2 - - + -
440A LEU* 4.4 21.8 - - + -
595A LEU* 3.0 42.6 + - + +
598A VAL* 1.3 77.2 - - + +
600A ALA* 1.3 52.8 + - - +
602A LEU* 3.7 9.2 - - + +
603A ASP* 2.8 35.6 + - - +
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Residues in contact with ALA 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A THR* 4.9 0.2 - - - -
337A GLN* 3.5 32.2 - - + +
338A GLY* 3.8 13.6 - - - +
341A LEU* 3.5 16.5 - - + +
596A ASN* 3.0 22.0 + - - +
597A ASP* 3.8 7.4 - - - +
599A LEU* 1.3 73.0 - - - +
601A GLN* 1.3 65.6 + - - +
603A ASP* 4.3 0.4 - - - -
604A ALA* 3.1 24.1 + - - +
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Residues in contact with GLN 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 3.7 16.4 - - + -
345A TRP* 4.5 10.9 - - + -
435A VAL* 5.2 8.5 - - - +
436A PHE* 4.1 21.4 - - + -
597A ASP* 3.1 25.0 + - - +
598A VAL* 2.9 16.7 + - - +
600A ALA* 1.3 78.4 - - - +
602A LEU* 1.3 61.8 + - - +
604A ALA* 3.4 3.6 + - - +
605A VAL* 3.1 29.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PHE* 4.8 8.5 - - + -
376A LEU* 3.8 15.3 - - + -
381A LEU* 3.8 24.0 - - + -
417A VAL* 5.2 4.0 - - + -
421A LEU* 4.3 28.5 - - + -
436A PHE* 3.6 32.9 - - + -
440A LEU* 4.3 13.5 - - + -
598A VAL* 3.0 10.1 + - + +
599A LEU* 3.8 12.3 - - + +
601A GLN* 1.3 75.6 - - - +
603A ASP* 1.3 64.4 + - - +
605A VAL* 3.5 4.4 + - - +
606A VAL* 3.0 46.1 + - + +
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Residues in contact with ASP 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A CYS* 3.3 17.6 - - - +
334A LYS* 3.4 14.0 + - - +
335A THR* 2.6 48.4 + - + +
338A GLY* 3.6 2.8 - - - -
381A LEU* 3.7 27.0 - - + +
599A LEU 2.8 21.9 + - - +
600A ALA 3.8 4.7 - - - +
601A GLN 3.3 0.2 - - - -
602A LEU* 1.3 74.8 - - - +
604A ALA* 1.3 64.2 - - - +
606A VAL* 3.4 2.4 + - - +
607A SER* 3.1 17.7 + - - -
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Residues in contact with ALA 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A CYS* 3.6 14.3 - - - -
338A GLY 4.5 2.7 - - - +
341A LEU* 4.5 5.2 - - + -
342A VAL* 3.9 15.9 - - + -
345A TRP* 3.7 25.4 - - + -
600A ALA 3.1 16.0 + - - +
601A GLN 3.6 4.5 - - - +
603A ASP* 1.3 76.8 - - - +
605A VAL* 1.3 64.9 + - - +
607A SER* 2.7 22.4 + - - -
608A PHE* 3.0 11.4 + - - -
----------------------------------------------------------
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Residues in contact with VAL 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TRP* 4.4 14.4 - - + -
359A ARG* 5.0 3.1 - - + +
362A LEU* 3.2 60.6 - - + +
363A VAL* 4.1 8.9 - - + +
366A PHE* 3.8 16.6 - - + -
436A PHE* 4.7 4.9 - - + -
601A GLN* 3.1 19.9 + - + +
602A LEU* 3.8 5.6 - - - +
604A ALA* 1.3 78.3 - - - +
606A VAL* 1.3 63.8 + - - +
608A PHE* 3.3 11.2 + - - +
609A ALA* 3.1 21.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PHE* 3.9 31.0 - - + -
373A ARG* 4.8 12.5 - - + +
376A LEU* 4.2 5.4 - - + -
377A GLN* 4.1 24.9 - - + +
381A LEU* 3.8 20.4 - - + -
602A LEU* 3.0 39.2 + - + +
603A ASP 3.7 3.4 - - - +
605A VAL* 1.3 75.6 - - - +
607A SER* 1.3 58.0 + - - +
609A ALA* 3.3 7.9 + - - +
610A HIS* 2.9 25.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU 3.8 8.3 + - - -
332A LYS* 3.8 15.5 - - - -
333A CYS* 3.3 38.6 - - - -
342A VAL* 4.2 1.4 - - - +
377A GLN* 5.8 2.0 - - - -
603A ASP* 3.1 9.1 + - - -
604A ALA* 2.7 25.6 + - - -
606A VAL* 1.3 71.6 - - - +
608A PHE* 1.3 66.5 + - - -
610A HIS* 3.0 6.6 + - - +
611A VAL* 2.9 30.7 + - - +
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Residues in contact with PHE 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.5 21.5 - - + -
342A VAL* 3.7 34.5 - - + -
345A TRP* 3.6 36.3 - + - -
363A VAL* 4.4 19.8 - - + +
604A ALA 3.0 28.2 + - - -
605A VAL* 3.6 9.6 - - - +
607A SER* 1.3 77.7 + - - +
609A ALA* 1.3 52.5 + - - +
611A VAL* 3.9 4.4 + - - +
612A SER* 2.6 33.8 + - - -
691A ILE* 3.7 26.0 - - + -
692A GLY 4.8 1.8 - - - -
693A CYS* 3.5 40.7 - - + -
694A PHE* 5.5 0.5 - - - +
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Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 4.0 6.7 - - + +
366A PHE* 3.7 30.5 - - + -
367A VAL* 4.0 18.2 - - + -
373A ARG* 4.1 5.6 - - - -
605A VAL 3.1 11.8 + - - +
606A VAL 3.5 8.7 - - - +
607A SER 3.1 0.6 - - - -
608A PHE* 1.3 77.0 - - - +
610A HIS* 1.3 60.3 + - - +
612A SER* 2.8 17.2 + - - -
613A ASN* 2.9 20.8 - - - +
----------------------------------------------------------
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Residues in contact with HIS 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS* 4.7 18.9 - - + +
373A ARG* 3.9 21.4 + - - +
377A GLN* 3.0 44.9 + - - +
606A VAL* 2.9 17.8 + - + +
607A SER* 3.0 6.3 + - - +
609A ALA* 1.3 75.0 - - - +
611A VAL* 1.3 71.8 + - + +
613A ASN* 3.2 13.2 + - - +
614A GLY* 3.4 13.0 + - - -
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Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 3.3 42.6 - - + +
330A LEU* 3.5 38.1 - - + +
332A LYS* 4.3 16.6 - - + -
607A SER 2.9 18.9 + - - +
608A PHE* 4.2 3.6 - - - +
610A HIS* 1.3 78.5 - - + +
612A SER* 1.3 64.2 + - - +
613A ASN 3.2 1.2 + - - -
614A GLY* 3.3 11.8 + - - -
615A ALA* 3.5 11.5 + - + +
619A TYR* 5.0 7.2 - - + +
----------------------------------------------------------
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Residues in contact with SER 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 4.1 7.1 - - - +
608A PHE 2.6 24.1 + - - -
609A ALA* 2.8 16.5 + - - -
611A VAL* 1.3 79.0 - - - +
613A ASN* 1.3 58.8 + - - -
615A ALA* 4.0 2.2 - - - +
618A PRO* 3.3 8.8 - - - +
619A TYR* 3.1 63.2 + - - -
693A CYS* 5.7 0.7 - - - -
694A PHE* 4.1 12.8 - - - +
----------------------------------------------------------
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Residues in contact with ASN 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 3.8 31.5 + - - +
370A ALA* 5.5 0.4 - - - +
373A ARG* 3.3 34.9 - - - +
609A ALA 2.9 16.2 - - - +
610A HIS 3.2 8.5 + - - +
612A SER* 1.3 76.8 + - - +
614A GLY* 1.3 58.0 + - - +
615A ALA 3.1 16.8 + - - +
618A PRO* 4.0 17.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A HIS* 3.4 9.9 + - - -
611A VAL* 3.3 9.3 + - - -
613A ASN* 1.3 76.8 - - - +
615A ALA* 1.3 62.6 + - - +
616A PRO* 3.8 3.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A VAL 3.5 6.6 + - - +
612A SER 4.0 4.9 - - - +
613A ASN 3.1 8.8 - - - +
614A GLY* 1.3 79.0 - - - +
616A PRO* 1.3 69.5 - - + +
617A VAL 2.8 19.0 + - - +
618A PRO* 3.6 2.1 - - - +
619A TYR* 3.2 42.8 - - + +
643A GLU* 4.5 3.8 - - - +
644A VAL* 5.9 3.6 - - + -
----------------------------------------------------------
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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