Contacts of the helix formed by residues 547 - 578 (chain N) in PDB entry 1AIK
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 547 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C GLN* 3.5 12.2 - - - +
656C ASN* 3.0 34.1 + - - -
659C GLU* 4.9 7.9 + - - -
545N ACE 3.3 0.6 - - - -
546N SER* 1.3 81.7 + - - +
548N ILE* 1.3 52.0 + - - +
550N GLN* 3.3 6.9 - - - +
551N GLN 2.7 27.4 + - - -
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Residues in contact with ILE 548 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C ASN* 4.6 10.5 - - + +
660C LEU* 5.4 12.6 - - + -
545N ACE 3.3 23.1 - - + +
547N GLY* 1.3 75.1 - - - +
549N VAL* 1.3 61.6 + - + +
551N GLN* 3.3 7.6 + - + +
552N GLN* 2.9 46.8 + - + +
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Residues in contact with VAL 549 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545N ACE 3.0 16.3 + - - +
546N SER* 3.5 9.9 - - - +
548N ILE* 1.3 77.3 - - + +
550N GLN* 1.3 61.8 + - - +
552N GLN* 3.5 15.7 + - - +
553N ASN* 3.2 21.0 + - - +
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Residues in contact with GLN 550 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C GLU* 4.2 9.1 + - - +
652C GLN* 3.5 17.9 + - - +
546N SER* 2.8 22.1 + - - +
547N GLY* 3.3 11.4 - - - +
549N VAL* 1.3 72.7 - - - +
551N GLN* 1.3 57.5 + - - +
553N ASN* 3.1 19.2 + - - +
554N ASN* 2.8 54.8 + - - +
557N ARG* 5.2 2.7 + - - +
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Residues in contact with GLN 551 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C SER* 3.1 50.3 + - - +
652C GLN* 3.9 8.3 - - + +
653C GLN* 2.8 32.4 + - - +
656C ASN* 3.6 10.1 - - - +
547N GLY 2.7 22.0 + - - +
548N ILE* 3.6 7.6 - - - +
550N GLN* 1.3 70.5 - - - +
552N GLN* 1.3 52.8 + - + +
554N ASN* 3.0 10.6 + - - +
555N LEU* 2.8 54.2 + - + +
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Residues in contact with GLN 552 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548N ILE* 2.9 32.6 + - + +
549N VAL* 3.5 18.8 - - + +
551N GLN* 1.3 72.7 - - + +
553N ASN* 1.3 61.1 + - - +
555N LEU* 3.4 14.3 + - + +
556N LEU* 2.9 30.9 + - - +
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Residues in contact with ASN 553 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549N VAL 3.2 9.6 + - - +
550N GLN* 3.1 21.2 + - - +
552N GLN* 1.3 77.5 - - - +
554N ASN* 1.3 60.0 + - - +
556N LEU* 3.4 10.7 + - - +
557N ARG* 3.0 55.6 + - - +
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Residues in contact with ASN 554 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C LEU* 4.2 8.5 - - + +
648C GLU* 3.2 22.2 + - - +
649C SER* 3.2 24.2 + - - +
652C GLN* 4.1 10.3 + - - +
550N GLN* 2.8 40.8 + - - +
551N GLN* 3.0 14.3 + - - +
553N ASN* 1.3 78.3 - - - +
555N LEU* 1.3 61.4 + - - +
557N ARG* 2.8 37.5 + - - +
558N ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 555 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C SER* 4.1 18.2 - - - +
551N GLN* 2.8 40.3 + - + +
552N GLN* 3.7 16.8 - - + +
553N ASN 3.3 0.2 - - - -
554N ASN* 1.3 69.9 - - - +
556N LEU* 1.3 58.7 + - - +
558N ALA* 2.9 24.2 + - + +
559N ILE* 2.9 26.1 + - + +
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Residues in contact with LEU 556 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552N GLN 2.9 18.3 + - - +
553N ASN* 3.8 11.9 - - - +
555N LEU* 1.3 73.0 - - - +
557N ARG* 1.3 64.8 + - + +
559N ILE* 3.3 18.8 + - + +
560N GLU* 3.0 50.2 + - + +
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Residues in contact with ARG 557 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641C LEU* 5.6 1.1 - - - +
645C LEU* 3.4 40.0 - - + +
648C GLU* 3.6 14.8 + - - -
550N GLN* 5.2 3.8 + - - +
553N ASN* 3.0 45.0 + - - +
554N ASN* 2.8 28.9 + - - +
556N LEU* 1.3 77.1 - - + +
558N ALA* 1.3 57.3 + - - +
560N GLU* 3.2 16.8 + - - +
561N ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 558 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C ILE* 4.4 4.7 - - + +
645C LEU* 3.5 21.3 - - + +
646C ILE* 5.2 12.3 - - + -
649C SER* 5.5 1.6 - - - +
554N ASN 3.1 13.7 + - - +
555N LEU* 2.9 17.6 + - + +
557N ARG* 1.3 76.5 - - - +
559N ILE* 1.3 55.5 + - + +
561N ALA* 3.3 4.7 + - - +
562N GLN* 2.9 38.0 + - - +
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Residues in contact with ILE 559 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555N LEU* 2.9 27.1 + - + +
556N LEU* 3.6 18.6 - - + +
558N ALA* 1.3 74.9 - - + +
560N GLU* 1.3 62.2 + - + +
562N GLN* 3.2 15.2 + - + +
563N GLN* 2.8 30.3 + - + +
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Residues in contact with GLU 560 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556N LEU* 3.0 49.4 + - + +
557N ARG* 3.6 13.8 - - - +
559N ILE* 1.3 77.7 - - + +
561N ALA* 1.3 63.1 + - - +
563N GLN* 3.1 9.8 + - - +
564N HIS* 3.1 33.4 + - + +
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Residues in contact with ALA 561 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C TYR* 4.3 8.7 - - + +
641C LEU* 4.3 22.7 - - + -
642C ILE* 3.3 33.3 - - + +
645C LEU* 4.6 1.3 - - + -
557N ARG 2.9 17.0 + - - +
558N ALA* 3.5 5.2 - - - +
559N ILE 3.2 0.2 - - - -
560N GLU* 1.3 75.1 - - - +
562N GLN* 1.3 64.1 + - - +
564N HIS* 3.1 21.2 + - - +
565N LEU* 3.2 9.7 + - - +
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Residues in contact with GLN 562 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C ILE* 3.6 32.5 - - + +
646C ILE* 5.1 4.9 - - - +
558N ALA* 2.9 25.3 + - - +
559N ILE* 3.2 15.0 + - - +
561N ALA* 1.3 75.1 - - - +
563N GLN* 1.3 55.4 + - - +
565N LEU* 3.2 7.3 + - + +
566N LEU* 2.8 42.0 + - + +
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Residues in contact with GLN 563 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559N ILE* 2.8 15.9 + - + +
560N GLU* 3.3 13.2 - - - +
562N GLN* 1.3 78.0 - - - +
564N HIS* 1.3 66.4 + - + +
566N LEU* 3.1 28.1 + - - +
567N GLN* 3.0 53.6 + - + +
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Residues in contact with HIS 564 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C TYR* 2.9 52.7 + + + -
560N GLU* 3.1 20.3 + - + +
561N ALA* 3.1 10.2 + - - +
563N GLN* 1.3 80.6 - - + +
565N LEU* 1.3 60.9 + - - +
567N GLN* 3.2 11.6 + - + +
568N LEU* 2.9 31.1 + - + +
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Residues in contact with LEU 565 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635C ILE* 3.7 38.6 - - + +
638C TYR* 3.7 20.8 - - + +
639C THR* 3.9 11.2 - - + +
642C ILE* 3.7 29.4 - - + -
561N ALA 3.2 4.3 + - - +
562N GLN* 3.3 11.4 - - + +
564N HIS* 1.3 78.8 - - - +
566N LEU* 1.3 61.8 + - - +
568N LEU* 3.1 6.1 + - + +
569N THR* 3.0 32.8 + - + +
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Residues in contact with LEU 566 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562N GLN* 2.8 24.2 + - + +
563N GLN* 3.1 36.8 + - - +
565N LEU* 1.3 69.9 - - - +
567N GLN* 1.3 62.5 + - - +
569N THR* 2.6 25.7 + - - +
570N VAL* 3.1 20.1 + - + +
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Residues in contact with GLN 567 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563N GLN* 3.0 44.6 + - + +
564N HIS* 3.2 13.4 + - + +
566N LEU* 1.3 72.1 - - - +
568N LEU* 1.3 65.2 + - + +
570N VAL* 3.2 14.6 + - - +
571N TRP* 2.9 28.8 + - - +
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Residues in contact with LEU 568 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631C TRP* 2.8 29.6 + - + +
634C GLU* 3.7 50.0 - - + +
635C ILE* 3.3 33.7 - - + -
638C TYR* 3.7 13.2 - - + -
564N HIS* 2.9 23.0 + - + +
565N LEU* 3.1 5.3 + - - +
567N GLN* 1.3 81.2 - - + +
569N THR* 1.3 57.9 + - - +
571N TRP* 3.2 7.8 + - + +
572N GLY 2.9 17.0 + - - -
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Residues in contact with THR 569 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631C TRP* 4.5 11.0 - - + +
635C ILE* 5.0 8.1 - - + -
565N LEU* 3.0 22.2 + - + +
566N LEU* 2.6 29.6 + - - +
568N LEU* 1.3 77.0 - - - +
570N VAL* 1.3 56.8 + - - +
572N GLY* 3.0 2.8 + - - +
573N ILE* 2.9 39.4 + - - +
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Residues in contact with VAL 570 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566N LEU* 3.1 22.0 + - + +
567N GLN* 3.2 17.0 + - - +
569N THR* 1.3 72.8 - - - +
571N TRP* 1.3 67.3 + - - +
573N ILE* 3.2 14.8 + - + +
574N LYS* 2.9 53.9 + - + +
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Residues in contact with TRP 571 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627C ACE 4.0 26.5 - - + -
628C TRP* 3.6 40.8 - + - -
631C TRP* 3.3 36.8 - + + -
567N GLN 2.9 13.5 + - - +
568N LEU* 3.3 13.5 - - + +
570N VAL* 1.3 77.3 - - - +
572N GLY* 1.3 63.0 + - - +
574N LYS* 4.0 7.3 - - + +
575N GLN* 3.0 63.7 + - + +
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Residues in contact with GLY 572 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628C TRP* 3.6 24.0 - - - -
631C TRP* 4.3 7.0 - - - -
568N LEU 2.9 13.3 + - - -
569N THR 3.0 4.6 + - - -
571N TRP* 1.3 80.8 - - - +
573N ILE* 1.3 63.2 + - - +
575N GLN* 3.4 2.1 + - - +
576N LEU* 3.0 31.0 + - - +
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Residues in contact with ILE 573 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569N THR* 2.9 29.3 + - - +
570N VAL* 3.6 14.8 - - + +
572N GLY* 1.3 75.7 - - - +
574N LYS* 1.3 61.2 + - + +
576N LEU* 3.2 7.9 + - - +
577N GLN* 2.8 31.4 + - + +
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Residues in contact with LYS 574 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570N VAL* 2.9 46.1 + - + +
571N TRP* 4.0 6.5 - - + +
573N ILE* 1.3 73.8 - - + +
575N GLN* 1.3 59.2 + - - +
577N GLN* 3.7 10.2 - - - +
578N ALA* 2.9 30.5 + - - +
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Residues in contact with GLN 575 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628C TRP* 3.8 13.6 + - + +
571N TRP* 3.0 67.7 + - + +
572N GLY 3.4 7.9 - - - +
574N LYS* 1.3 80.0 - - - +
576N LEU* 1.3 63.9 + - - +
578N ALA* 3.4 11.5 + - - +
579N ARG* 3.6 44.3 + - - +
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Residues in contact with LEU 576 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628C TRP* 3.9 25.6 - - + +
572N GLY 3.0 20.4 + - - +
573N ILE* 3.9 5.8 - - - +
575N GLN* 1.3 81.2 - - - +
577N GLN* 1.3 61.7 + - - +
579N ARG* 3.3 17.4 + - - +
580N ILE* 3.1 36.6 + - + +
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Residues in contact with GLN 577 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573N ILE* 2.8 24.8 + - + +
574N LYS* 3.7 9.9 - - - +
575N GLN 3.3 0.2 - - - -
576N LEU* 1.3 74.1 - - - +
578N ALA* 1.3 69.9 + - - +
580N ILE* 4.5 5.6 - - - +
581N LEU* 3.0 58.6 + - + +
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Residues in contact with ALA 578 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574N LYS 2.9 17.6 + - - +
575N GLN* 3.7 8.5 - - - +
576N LEU 3.3 0.4 - - - -
577N GLN* 1.3 83.4 + - - +
579N ARG* 1.3 63.4 + - + +
581N LEU 3.7 13.8 - - - +
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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