Contacts of the helix formed by residues 674 - 703 (chain J) in PDB entry 6ALH
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 THR 674 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668J PHE* 3.3 13.7 - - - -
673J VAL* 1.3 89.2 - - - +
675J ALA* 1.3 62.5 + - - +
676J GLY* 3.5 3.2 + - - -
677J GLU* 3.0 31.7 + - - +
678J ARG* 3.4 7.4 + - - +
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Residues in contact with ALA 675 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668J PHE* 3.6 20.7 - - + -
674J THR* 1.3 74.2 - - - +
676J GLY* 1.3 61.5 + - - +
678J ARG* 3.2 21.0 + - - +
679J TYR* 2.9 27.0 + - - +
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Residues in contact with GLY 676 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674J THR* 3.5 4.1 + - - -
675J ALA* 1.3 75.1 - - - +
677J GLU* 1.3 59.7 + - - +
679J TYR* 3.3 10.3 + - - +
680J ASN* 2.8 40.9 + - - -
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Residues in contact with GLU 677 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673J VAL* 3.4 35.3 - - + +
674J THR* 3.0 27.8 + - - +
676J GLY* 1.3 73.1 - - - +
678J ARG* 1.3 58.3 + - - +
680J ASN* 3.4 6.3 + - - +
681J LYS* 2.9 33.9 + - + +
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Residues in contact with ARG 678 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661J VAL 6.1 0.2 - - - -
664J ILE* 3.7 34.5 - - + +
665J GLN* 3.7 29.4 + - - +
668J PHE* 4.4 16.0 - - + -
673J VAL* 4.3 7.1 - - + +
674J THR 3.4 13.8 + - - +
675J ALA* 3.2 25.0 + - - +
677J GLU* 1.3 80.9 - - - +
679J TYR* 1.3 63.7 + - - +
681J LYS* 4.1 0.4 - - - +
682J VAL* 2.9 51.8 + - - +
756J GLU* 3.3 31.1 + - - +
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Residues in contact with TYR 679 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675J ALA 2.9 13.6 + - - +
676J GLY* 3.3 12.8 + - - +
678J ARG* 1.3 85.5 - - - +
680J ASN* 1.3 78.6 + - - +
682J VAL* 3.9 3.4 - - - +
683J ILE* 2.9 40.4 + - + +
753J SER* 4.2 6.6 - - - -
754J ILE* 2.3 53.4 + - + +
756J GLU* 3.7 38.1 - - + -
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Residues in contact with ASN 680 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676J GLY* 2.8 27.6 + - - +
677J GLU* 4.0 5.8 - - - +
679J TYR* 1.3 94.6 - - - +
681J LYS* 1.3 58.8 + - - +
683J ILE* 3.2 11.4 - - - +
684J ASP* 3.0 36.0 + - - +
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Residues in contact with LYS 681 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664J ILE* 4.4 28.5 - - + -
677J GLU* 2.9 21.9 + - + +
678J ARG* 4.1 3.4 - - - +
680J ASN* 1.3 77.1 - - - +
682J VAL* 1.3 57.2 + - - +
684J ASP* 3.3 9.9 + - + +
685J ILE* 3.0 47.7 + - + +
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Residues in contact with VAL 682 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661J VAL* 3.8 23.1 - - + +
664J ILE* 3.8 29.2 - - + -
678J ARG* 2.9 36.6 + - - +
679J TYR* 4.0 3.6 - - - +
681J LYS* 1.3 75.8 - - - +
683J ILE* 1.3 59.4 + - + +
685J ILE* 3.2 7.4 - - - +
686J TRP* 2.9 52.5 + - + +
756J GLU* 4.4 13.2 - - + +
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Residues in contact with ILE 683 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679J TYR* 2.9 29.9 + - + +
680J ASN* 3.2 23.8 - - + +
682J VAL* 1.3 78.1 - - + +
684J ASP* 1.3 62.2 + - - +
686J TRP* 3.5 5.9 + - + +
687J ALA* 3.0 27.2 + - - +
746J LEU* 3.7 21.4 - - + +
754J ILE* 3.7 52.5 - - + +
755J ILE 4.5 2.9 - - - +
756J GLU* 5.1 5.6 - - - +
758J PRO* 6.0 0.2 - - + -
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Residues in contact with ASP 684 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680J ASN* 3.0 25.6 + - - +
681J LYS* 3.7 11.7 - - + +
682J VAL 3.2 0.2 - - - -
683J ILE* 1.3 80.4 - - - +
685J ILE* 1.3 61.9 + - + +
687J ALA* 3.2 7.2 + - - +
688J ALA* 2.9 27.9 + - - +
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Residues in contact with ILE 685 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657J ALA* 4.8 4.7 - - + +
660J GLU* 3.7 37.9 - - + +
661J VAL* 3.8 22.2 - - + -
664J ILE* 4.6 9.0 - - + -
681J LYS* 3.0 38.6 + - + +
682J VAL* 3.2 19.5 - - - +
684J ASP* 1.3 77.0 - - + +
686J TRP* 1.3 58.3 + - + +
688J ALA* 3.7 7.4 - - + +
689J ALA* 3.0 28.8 + - - +
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Residues in contact with TRP 686 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654J ILE* 5.1 9.2 - - + -
657J ALA* 4.5 26.2 - - + -
658J GLU* 5.3 2.5 - - + -
661J VAL* 3.4 31.4 - - + +
682J VAL* 2.9 41.9 + - + +
683J ILE* 3.7 7.4 - - - +
685J ILE* 1.3 77.5 - - + +
687J ALA* 1.3 57.9 + - - +
689J ALA* 3.3 6.2 + - + +
690J ASN* 2.9 27.8 + - - +
743J MET* 4.8 20.4 - - + +
746J LEU* 4.8 7.3 - - + +
756J GLU 4.4 2.8 + - - -
757J THR* 5.5 4.7 - - + +
758J PRO* 3.4 47.1 - - + +
760J THR* 3.6 31.4 - - + -
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Residues in contact with ALA 687 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683J ILE 3.0 17.4 + - - +
684J ASP* 3.2 9.6 + - - +
686J TRP* 1.3 76.3 - - - +
688J ALA* 1.3 58.4 + - - +
690J ASN* 3.2 9.5 + - - +
691J ASP* 3.0 33.8 + - - +
746J LEU* 5.2 8.2 - - + +
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Residues in contact with ALA 688 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684J ASP 2.9 16.6 + - - +
685J ILE* 3.7 8.3 - - - +
687J ALA* 1.3 78.3 - - - +
689J ALA* 1.3 57.0 + - - +
691J ASP* 3.3 9.2 + - - +
692J ARG* 3.0 33.4 + - + +
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Residues in contact with ALA 689 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653J ILE* 4.0 16.3 - - + +
657J ALA* 4.4 19.5 - - + -
685J ILE 3.0 17.6 + - - +
686J TRP* 3.3 8.9 + - + +
688J ALA* 1.3 75.7 - - - +
690J ASN* 1.3 57.1 + - - +
692J ARG* 3.2 15.2 + - - +
693J VAL* 2.9 33.5 + - - +
743J MET* 5.0 4.0 - - + -
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Residues in contact with ASN 690 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686J TRP 2.9 14.6 + - - +
687J ALA* 3.4 13.1 - - - +
688J ALA 3.2 0.2 - - - -
689J ALA* 1.3 77.4 - - - +
691J ASP* 1.3 60.5 + - - +
693J VAL* 3.3 4.0 + - - +
694J SER* 2.9 25.9 + - - -
738J ARG* 4.6 13.0 - - - +
743J MET* 3.4 39.0 + - - +
745J GLY* 3.4 25.1 - - - +
746J LEU* 5.0 5.9 - - + +
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Residues in contact with ASP 691 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687J ALA* 3.0 18.3 + - - +
688J ALA* 3.7 9.6 - - - +
690J ASN* 1.3 76.3 + - - +
692J ARG* 1.3 59.9 + - - +
694J SER* 3.4 10.6 - - - -
695J LYS* 2.9 38.4 + - + +
738J ARG* 5.9 0.3 + - - -
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Residues in contact with ARG 692 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649J LYS* 5.6 6.1 - - - +
653J ILE* 3.9 36.5 + - + +
656J GLU* 3.9 24.7 + - - +
688J ALA* 3.0 20.9 + - - +
689J ALA* 3.2 16.6 + - - +
691J ASP* 1.3 76.5 - - - +
693J VAL* 1.3 57.6 + - - +
695J LYS* 3.4 7.0 + - - +
696J ALA* 3.0 29.3 + - - +
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Residues in contact with VAL 693 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647J PRO* 5.0 4.7 - - + +
650J LYS* 3.6 33.2 - - + +
653J ILE* 3.7 28.7 - - + -
689J ALA 2.9 18.9 + - - +
690J ASN* 3.6 9.0 - - - +
692J ARG* 1.3 74.0 - - - +
694J SER* 1.3 58.9 + - - +
696J ALA* 3.3 6.8 + - - +
697J MET* 2.9 31.1 + - + +
738J ARG* 6.5 0.4 - - + -
742J GLY* 3.9 19.3 - - - -
743J MET* 3.8 21.5 - - + +
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Residues in contact with SER 694 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690J ASN* 2.9 14.3 + - - -
691J ASP* 3.4 17.9 + - - -
692J ARG 3.2 0.2 - - - -
693J VAL* 1.3 77.1 - - - +
695J LYS* 1.3 59.6 + - - +
697J MET* 3.3 11.7 - - - +
698J MET* 3.0 33.0 + - - +
738J ARG* 3.2 40.5 + - - +
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Residues in contact with LYS 695 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691J ASP* 2.9 24.1 + - + +
692J ARG* 3.8 6.3 - - - +
694J SER* 1.3 75.9 - - - +
696J ALA* 1.3 58.3 + - - +
698J MET* 3.4 4.6 + - + +
699J ASP* 3.0 39.9 + - - +
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Residues in contact with ALA 696 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647J PRO* 4.3 16.4 - - + -
649J LYS* 4.9 15.9 - - + -
653J ILE* 5.0 3.8 - - + -
692J ARG 3.0 17.7 + - - +
693J VAL* 3.6 8.3 - - - +
695J LYS* 1.3 77.4 - - - +
697J MET* 1.3 58.1 + - - +
699J ASP* 3.8 4.6 - - - +
700J ASN* 3.0 30.5 + - - +
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Residues in contact with MET 697 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645J VAL 5.2 2.2 - - - +
647J PRO* 3.7 24.3 - - + +
693J VAL* 2.9 20.7 + - + +
694J SER* 3.3 9.2 - - - +
696J ALA* 1.3 76.8 - - - +
698J MET* 1.3 68.4 + - + +
700J ASN* 3.8 1.5 - - - +
701J LEU* 2.9 55.3 + - + +
737J ILE* 3.3 30.1 - - + +
738J ARG* 3.7 20.6 - - - +
741J ALA* 3.7 12.3 - - + -
742J GLY* 3.5 28.9 - - - +
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Residues in contact with MET 698 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694J SER* 3.0 22.3 + - - +
695J LYS* 3.9 5.8 - - + +
696J ALA 3.3 0.2 - - - -
697J MET* 1.3 81.0 - - + +
699J ASP* 1.3 60.2 + - - +
701J LEU* 3.9 6.2 - - - +
702J GLN* 2.9 55.5 + - - +
723J TYR* 4.6 17.3 - - - -
734J ALA* 4.2 25.4 - - + +
737J ILE* 4.7 15.3 - - + -
738J ARG* 5.3 4.0 - - - +
----------------------------------------------------------
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Residues in contact with ASP 699 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695J LYS* 3.0 24.6 + - - +
696J ALA* 3.8 4.8 - - - +
698J MET* 1.3 76.8 - - - +
700J ASN* 1.3 63.0 + - - +
702J GLN* 3.2 15.3 + - - +
703J THR* 3.0 41.3 + - + +
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Residues in contact with ASN 700 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645J VAL* 3.7 25.8 - - + +
646J ILE 4.6 0.4 + - - -
647J PRO* 4.2 20.4 - - + +
648J GLU 5.2 1.2 - - - +
696J ALA 3.0 18.9 + - - +
697J MET* 4.2 5.2 - - - +
699J ASP* 1.3 75.9 - - - +
701J LEU* 1.3 62.9 + - - +
703J THR* 5.3 1.3 - - - -
704J GLU* 2.9 33.8 - - - +
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Residues in contact with LEU 701 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643J ASP 4.7 3.1 - - - +
645J VAL* 4.6 24.0 - - + +
697J MET* 2.9 37.2 + - + +
698J MET* 3.9 7.4 - - - +
700J ASN* 1.3 79.1 - - + +
702J GLN* 1.3 61.3 + - - +
704J GLU* 2.9 27.9 + - + +
718J SER* 3.3 8.4 + - - -
720J ASN* 3.5 29.3 - - + +
722J ILE* 4.7 6.5 - - + -
723J TYR* 4.5 19.9 - - + +
737J ILE* 3.9 30.1 - - + -
741J ALA* 5.4 4.3 - - + -
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Residues in contact with GLN 702 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698J MET* 2.9 38.9 + - - +
699J ASP* 4.2 17.3 + - - +
701J LEU* 1.3 72.2 - - - +
703J THR* 1.3 61.1 + - + +
704J GLU 3.6 0.2 - - - -
716J GLN 3.8 0.3 - - - +
717J VAL* 3.7 26.5 - - + +
718J SER 4.4 2.5 - - - -
723J TYR* 3.4 46.1 + - + +
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Residues in contact with THR 703 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699J ASP* 3.0 27.6 + - + +
700J ASN* 4.6 1.3 - - - -
702J GLN* 1.3 82.4 - - + +
704J GLU* 1.3 61.3 + - - +
705J THR 3.4 2.2 - - - -
706J VAL* 4.3 9.0 - - - +
715J LYS* 3.3 48.5 - - - +
716J GLN 3.8 9.5 + - - -
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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