Contacts of the helix formed by residues 562 - 590 (chain A) in PDB entry 1Q2L
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 SER 562 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A MET 3.1 1.4 + - - -
561A ASP* 1.3 86.1 + - - +
563A ALA* 1.3 62.5 + - - +
564A ARG* 3.6 8.1 + - - +
565A ASN* 3.1 28.7 + - - +
566A GLN* 3.0 26.5 + - - +
670A PHE* 3.4 15.0 - - - -
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Residues in contact with ALA 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A SER* 1.3 73.7 - - - +
564A ARG* 1.3 58.4 + - - +
566A GLN* 3.3 4.2 + - - +
567A VAL* 2.9 35.5 + - - +
670A PHE* 3.5 30.4 - - + -
674A GLU* 3.6 26.2 + - + +
675A ARG* 4.1 12.8 - - + -
678A ILE* 4.0 14.1 - - + -
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Residues in contact with ARG 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A SER* 3.3 6.6 + - - +
563A ALA* 1.3 81.4 - - - +
565A ASN* 1.3 58.3 + - - +
567A VAL* 3.4 6.2 + - - +
568A MET* 2.9 54.7 + - + +
678A ILE* 3.4 30.5 - - + +
681A SER* 2.6 31.4 + - - -
682A ILE* 3.6 16.8 - - + +
686A GLU* 3.0 29.7 + - - -
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Residues in contact with ASN 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A LYS 3.4 8.3 - - - +
559A ALA* 3.2 21.6 - - - +
560A MET* 4.5 0.2 - - - -
561A ASP* 3.0 20.6 - - - +
562A SER* 3.1 24.0 + - - +
564A ARG* 1.3 78.0 - - - +
566A GLN* 1.3 58.0 + - - +
568A MET* 3.2 23.3 + - - +
569A PHE 2.9 23.4 + - - -
690A TYR* 3.5 24.5 + - + -
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Residues in contact with GLN 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A MET* 2.8 48.5 + - + +
562A SER 3.0 15.7 + - - +
563A ALA* 3.3 4.5 + - - +
565A ASN* 1.3 75.5 - - - +
567A VAL* 1.3 62.7 + - - +
569A PHE* 3.3 9.0 + - - +
570A ALA* 3.2 21.0 + - - +
641A TYR* 5.0 2.1 + - - +
668A PRO* 3.0 28.8 + - - +
669A TYR* 5.0 2.1 - - - -
670A PHE* 3.6 28.1 + - - +
675A ARG* 4.8 12.0 + - - -
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Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ALA 2.9 23.0 + - - +
564A ARG* 3.8 5.8 - - - +
566A GLN* 1.3 76.0 - - - +
568A MET* 1.3 63.5 + - - +
570A ALA* 3.3 2.3 + - - +
571A LEU* 3.0 26.6 + - + +
641A TYR* 3.9 22.4 - - + +
675A ARG* 3.6 37.9 - - + +
678A ILE* 5.7 1.3 - - + -
679A LEU* 3.9 23.8 - - + +
682A ILE* 3.4 24.5 - - + -
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Residues in contact with MET 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ARG* 2.9 36.0 + - + +
565A ASN* 3.3 33.4 - - - +
567A VAL* 1.3 73.6 - - - +
569A PHE* 1.3 61.7 + - - +
571A LEU* 3.9 7.7 - - - +
572A ASN* 2.9 31.4 + - - +
682A ILE* 4.0 22.4 - - + -
686A GLU* 3.7 41.1 - - + +
687A VAL* 4.3 6.0 - - + +
690A TYR* 3.8 23.8 - - + -
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Residues in contact with PHE 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A MET* 4.0 16.4 - - + -
565A ASN 2.9 9.0 + - - +
566A GLN 3.5 9.9 - - - +
567A VAL 3.2 0.4 - - - -
568A MET* 1.3 77.2 - - - +
570A ALA* 1.3 62.4 + - + +
572A ASN* 3.3 3.8 + - - +
573A ASP* 2.8 45.3 + - + +
597A ASN* 3.6 12.6 - - - -
598A ALA* 3.4 39.9 - - + -
601A GLY 4.2 3.6 - - - -
602A LEU* 3.9 32.1 - - + -
624A TYR* 4.1 3.6 - - - -
690A TYR* 3.4 35.0 - + - +
694A LEU* 4.0 17.5 - - + -
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Residues in contact with ALA 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLN 3.2 8.7 + - - +
567A VAL 3.3 6.0 + - - +
569A PHE* 1.3 86.4 - - + +
571A LEU* 1.3 56.9 + - - +
573A ASP* 3.4 5.3 + - - +
574A TYR* 3.0 29.1 + - - +
640A TRP* 3.9 12.4 - - + -
641A TYR* 3.5 35.9 - - + -
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Residues in contact with LEU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A VAL* 3.0 26.3 + - + +
568A MET* 3.9 4.3 - - - +
570A ALA* 1.3 75.6 - - - +
572A ASN* 1.3 65.0 - - - +
574A TYR* 3.1 7.1 + - - +
575A LEU* 3.0 28.1 + - + +
634A LEU* 4.6 5.2 - - + -
637A ALA* 4.3 21.3 - - + +
638A LYS* 4.5 9.0 - - + -
640A TRP* 5.4 0.9 - - + -
641A TYR* 4.0 31.2 - - + -
679A LEU* 4.2 11.9 - - + -
682A ILE* 4.0 38.6 - - + -
687A VAL* 4.4 13.0 - - + -
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Residues in contact with ASN 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A MET 2.9 20.3 + - - +
569A PHE* 3.7 4.2 - - - +
571A LEU* 1.3 75.6 - - - +
573A ASP* 1.3 58.1 + - - +
575A LEU* 3.3 1.6 + - - +
576A ALA* 2.9 27.7 + - - +
624A TYR* 3.5 26.5 + - - -
627A TYR* 2.7 33.9 + - - -
687A VAL* 3.8 12.5 - - + +
690A TYR* 4.7 6.1 - - + -
691A ARG* 3.2 40.2 - - - +
694A LEU* 4.3 8.1 - - - +
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Residues in contact with ASP 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A PHE* 2.8 32.3 + - + +
570A ALA* 3.6 6.9 - - - +
572A ASN* 1.3 78.8 + - - +
574A TYR* 1.3 57.6 + - - +
576A ALA* 3.8 1.9 - - - +
577A GLY* 3.0 23.4 + - - -
596A THR* 2.7 38.0 + - - +
597A ASN* 5.5 0.8 - - - -
624A TYR* 2.8 28.7 + - - +
640A TRP* 5.8 3.3 - - - -
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Residues in contact with TYR 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ALA 3.0 17.9 + - - +
571A LEU* 3.1 6.3 + - - +
573A ASP* 1.3 76.5 + - - +
575A LEU* 1.3 67.3 + - + +
577A GLY* 3.2 3.3 + - - -
578A LEU* 3.2 54.9 + - + +
636A GLN* 4.4 12.1 + - + +
637A ALA* 3.6 30.7 - - + -
640A TRP* 3.4 61.7 - + + +
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU 3.0 15.5 + - - +
574A TYR* 1.3 78.3 - - + +
576A ALA* 1.3 66.6 + - - +
578A LEU* 3.4 13.0 + - + +
579A ALA* 3.3 19.2 + - - +
627A TYR* 3.5 35.5 - - + +
629A ALA* 4.0 24.9 - - + -
633A GLN* 3.8 17.5 - - + +
634A LEU* 4.6 9.0 - - + -
637A ALA* 3.4 31.6 - - + -
684A LEU* 4.0 15.3 - - + -
687A VAL* 4.4 9.4 - - + -
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Residues in contact with ALA 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ASN 2.9 17.2 + - - +
573A ASP 3.8 1.1 - - - +
574A TYR 3.3 0.2 - - - -
575A LEU* 1.3 76.7 - - - +
577A GLY* 1.3 57.0 + - - +
579A ALA* 3.1 4.2 + - - +
580A LEU* 2.8 35.9 + - + +
624A TYR* 3.4 49.6 - - + +
627A TYR* 3.9 17.0 - - + -
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Residues in contact with GLY 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ASP 3.0 14.8 + - - -
574A TYR* 3.2 4.7 + - - -
575A LEU 3.2 0.4 - - - -
576A ALA* 1.3 78.1 - - - +
578A LEU* 1.3 60.7 + - - +
580A LEU* 3.2 8.3 + - - +
581A ASP* 3.0 22.9 + - - +
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Residues in contact with LEU 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A TYR* 3.2 51.2 + - + +
575A LEU* 3.6 13.0 - - + +
576A ALA 3.2 0.4 - - - -
577A GLY* 1.3 77.2 - - - +
579A ALA* 1.3 63.3 + - - +
580A LEU 3.4 0.3 + - - -
581A ASP* 3.4 17.5 + - - +
633A GLN* 4.3 36.3 - - + +
636A GLN* 4.8 5.4 - - - +
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Residues in contact with ALA 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LEU 3.3 5.2 + - - +
576A ALA* 3.1 8.1 + - - +
578A LEU* 1.3 79.9 - - - +
580A LEU* 1.3 62.8 + - - +
581A ASP 3.4 0.2 - - - -
582A GLN* 4.7 6.3 + - - +
583A LEU* 5.2 1.6 + - - +
623A GLY* 4.6 5.5 - - - +
627A TYR* 3.5 33.0 - - + -
628A THR 5.3 3.8 - - - +
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Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ALA* 2.8 21.5 + - + +
577A GLY* 3.2 7.4 + - - +
579A ALA* 1.3 77.9 - - - +
581A ASP* 1.3 58.9 + - - +
582A GLN 3.3 2.5 - - - -
583A LEU* 3.1 30.7 + - + +
584A SER* 2.8 29.3 + - - -
594A PHE* 4.1 11.6 - - + -
596A THR* 5.3 2.7 - - + -
619A ALA 4.3 0.7 - - - +
620A LEU* 3.6 39.5 - - + +
623A GLY* 3.9 20.2 - - - -
624A TYR* 4.0 25.1 - - + -
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Residues in contact with ASP 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG* 5.2 5.6 + - - -
325A ASP* 5.5 0.5 - - - +
328A GLN* 5.5 2.7 - - - +
329A LYS* 4.7 12.0 + - - -
577A GLY 3.0 10.0 + - - +
578A LEU* 3.5 17.3 - - - +
579A ALA 3.4 1.4 - - - -
580A LEU* 1.3 75.8 - - - +
582A GLN* 1.3 65.1 + - - +
584A SER* 3.1 10.2 + - - -
585A ASN* 2.9 41.8 + - - +
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Residues in contact with GLN 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG 5.9 1.6 - - - +
319A SER* 4.6 3.8 + - - -
320A PRO* 3.6 30.5 - - + +
502A GLU* 3.3 29.7 + - - +
578A LEU 5.0 0.2 + - - -
579A ALA 4.7 5.6 + - - +
580A LEU 3.3 0.8 - - - -
581A ASP* 1.3 81.4 + - - +
583A LEU* 1.3 63.6 + - - +
585A ASN* 3.1 9.3 + - - +
586A GLN* 2.9 45.9 + - + +
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Residues in contact with LEU 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A TYR* 3.5 37.2 - - + +
579A ALA 5.2 0.8 + - - +
580A LEU* 3.1 28.1 + - + +
582A GLN* 1.3 78.3 - - - +
584A SER* 1.3 56.6 + - - +
586A GLN* 3.4 9.3 + - - +
587A ALA* 2.9 29.6 + - - +
594A PHE* 4.1 7.4 - - + -
616A LEU* 3.7 20.0 - - + -
619A ALA* 3.9 7.9 - - + +
620A LEU* 3.5 38.8 - - + +
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Residues in contact with SER 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LEU 2.8 12.5 + - - -
581A ASP* 3.1 13.7 + - - -
583A LEU* 1.3 77.9 - - - +
585A ASN* 1.3 66.0 + - - +
587A ALA* 3.8 1.4 - - - +
588A SER* 3.0 31.8 + - - -
592A ILE 4.8 0.3 - - - +
594A PHE* 3.6 25.6 + - - -
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Residues in contact with ASN 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG* 3.8 58.3 + - + +
581A ASP* 2.9 36.5 + - - +
582A GLN* 3.5 10.3 - - + +
584A SER* 1.3 81.5 + - - +
586A GLN* 1.3 64.1 + - + +
588A SER* 3.4 12.1 + - - -
589A VAL* 3.5 18.8 + - - +
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Residues in contact with GLN 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 5.9 4.0 + - - -
502A GLU* 4.9 9.9 + - - +
503A LEU 3.9 9.3 + - - -
504A ASN* 3.0 39.6 + - + +
505A PRO* 3.9 20.0 - - - +
506A TYR* 3.8 23.6 - - + +
582A GLN* 2.9 43.6 + - + +
583A LEU* 3.8 11.6 - - - +
585A ASN* 1.3 76.7 - - + +
587A ALA* 1.3 65.3 + - - +
589A VAL* 3.2 12.6 - - - +
590A GLY 3.3 2.3 + - - -
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Residues in contact with ALA 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A TYR* 4.2 11.1 - - - +
583A LEU 2.9 17.5 + - - +
584A SER 3.8 3.1 - - - +
586A GLN* 1.3 77.2 - - - +
588A SER* 1.3 61.5 + - - +
590A GLY 2.9 10.7 + - - -
591A GLY 3.0 0.3 + - - -
592A ILE* 2.9 44.2 + - + +
594A PHE* 4.3 8.5 - - + -
616A LEU* 4.0 23.8 - - + -
----------------------------------------------------------
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Residues in contact with SER 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A SER* 3.0 23.6 + - - -
585A ASN* 3.7 9.0 + - - -
586A GLN 3.2 0.4 - - - -
587A ALA* 1.3 77.2 - - - +
589A VAL* 1.3 64.0 + - - +
591A GLY* 2.9 14.3 + - - +
592A ILE 3.4 9.6 + - - +
593A SER* 5.4 4.2 - - - -
----------------------------------------------------------
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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
----------------------------------------------------------
313A TYR* 5.3 9.9 - - + +
395A VAL* 4.5 14.9 - - + +
398A ILE* 4.3 10.2 - - - +
504A ASN* 2.7 29.8 - - - +
507A ILE* 3.7 18.4 - - + -
585A ASN 3.5 15.0 - - - +
586A GLN* 3.2 2.9 + - - +
588A SER* 1.3 78.6 - - - +
590A GLY* 1.3 61.5 + - - +
591A GLY 3.2 0.9 + - - -
----------------------------------------------------------
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Residues in contact with GLY 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 4.3 3.5 - - - +
506A TYR 3.3 25.0 - - - +
507A ILE* 4.1 3.4 - - - -
508A PRO* 3.5 24.4 - - - +
586A GLN 3.3 1.4 + - - -
587A ALA 2.9 8.9 + - - -
589A VAL* 1.3 86.6 - - - +
591A GLY* 1.3 60.0 + - - +
592A ILE* 3.5 3.7 - - - +
609A TYR* 3.5 13.2 - - - +
----------------------------------------------------------
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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