Contacts of the helix formed by residues 686 - 712 (chain A) in PDB entry 3IAY
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 ASP 686 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A GLU* 2.5 18.3 + - - +
685A LYS* 1.3 73.2 - - - +
687A PRO* 1.3 69.9 - - - +
688A PHE* 2.4 40.4 + - - +
689A LYS* 2.7 18.8 + - + +
690A ARG* 2.9 29.6 + - - +
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Residues in contact with PRO 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A LYS 3.2 7.8 - - - +
686A ASP* 1.3 91.6 - - - +
688A PHE* 1.3 63.7 + - + +
690A ARG* 3.6 10.7 + - + +
691A ASP* 3.1 23.7 + - - +
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Residues in contact with PHE 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A HIS 5.4 1.1 - - - -
486A PHE* 3.0 50.7 - + + -
530A LYS* 3.5 44.4 - - + -
531A LEU* 4.0 13.5 - - + -
686A ASP* 2.4 25.4 + - - +
687A PRO* 1.3 74.8 - - + +
689A LYS* 1.3 68.9 + - + -
691A ASP* 3.0 25.6 - - + +
692A VAL* 3.2 14.6 + - + +
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Residues in contact with LYS 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A MET* 6.0 1.3 - - - +
684A GLU* 3.7 26.0 - - + +
686A ASP* 2.7 22.6 + - + +
688A PHE* 1.3 80.7 - - + +
690A ARG* 1.3 57.9 + - - +
692A VAL* 3.1 8.6 + - - +
693A LEU* 2.8 34.0 + - + +
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Residues in contact with ARG 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 3.2 58.6 + - + +
682A ARG* 4.1 13.7 + - - +
684A GLU* 2.7 34.7 + - + +
685A LYS 3.8 12.8 - - - -
686A ASP 2.9 15.2 + - - +
687A PRO* 3.7 9.2 - - + +
688A PHE 3.3 0.2 - - - -
689A LYS* 1.3 76.3 - - - +
691A ASP* 1.3 51.5 + - - +
693A LEU* 3.2 1.7 + - - -
694A ASN* 2.7 33.3 + - - +
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Residues in contact with ASP 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A TYR* 4.1 19.6 + - - -
485A HIS* 5.8 2.7 + - - -
486A PHE* 5.3 6.6 - - + -
687A PRO 3.1 14.5 + - - +
688A PHE* 3.0 19.5 - - + +
690A ARG* 1.3 75.8 - - - +
692A VAL* 1.3 60.6 + - + +
694A ASN* 2.8 24.3 + - - +
695A GLY 3.1 10.0 + - - -
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Residues in contact with VAL 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A TYR* 3.8 20.5 + - - +
486A PHE* 6.1 0.7 - - + -
530A LYS 3.7 6.1 - - - +
531A LEU* 3.2 33.0 - - + +
532A MET* 3.4 24.7 - - + -
536A ASN* 4.2 3.7 + - - +
688A PHE* 3.3 40.8 - - + +
689A LYS* 3.1 8.0 + - - +
691A ASP* 1.3 75.4 - - + +
693A LEU* 1.3 62.6 + - - +
695A GLY* 3.1 4.0 + - - -
696A ARG* 3.1 19.2 + - - +
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A MET* 3.9 22.9 - - + -
677A ALA* 4.8 3.5 - - - +
680A ASP* 3.5 32.1 - - + +
681A LEU* 3.9 18.2 - - + +
684A GLU* 3.7 22.4 - - + +
689A LYS* 2.8 24.2 + - + +
690A ARG* 3.6 7.0 - - - +
692A VAL* 1.3 72.7 - - - +
694A ASN* 1.3 62.2 + - - +
696A ARG* 3.4 33.2 + - - +
697A GLN* 3.1 23.4 + - - +
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Residues in contact with ASN 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 3.7 16.8 - - + +
690A ARG 2.7 17.5 + - - +
691A ASP* 2.8 15.5 + - - +
693A LEU* 1.3 74.3 - - - +
695A GLY* 1.3 53.7 + - - +
697A GLN* 3.0 26.5 + - - +
698A LEU* 3.0 53.1 + - - +
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Residues in contact with GLY 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLU* 4.3 16.9 - - - +
472A TYR* 5.4 8.7 - - - -
691A ASP 3.1 10.3 + - - -
692A VAL* 3.1 4.2 + - - -
694A ASN* 1.3 73.2 - - - +
696A ARG* 1.3 55.4 + - - +
698A LEU* 3.2 10.4 + - - +
699A ALA* 2.7 37.5 + - - +
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Residues in contact with ARG 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A MET* 4.8 0.9 - - - +
536A ASN* 3.7 41.6 + - + +
539A GLU* 3.0 38.4 + - - +
676A ARG* 4.6 6.1 - - - +
677A ALA* 3.8 27.3 - - + +
680A ASP* 2.7 34.6 + - - +
692A VAL 3.1 8.9 + - - +
693A LEU* 3.5 31.3 - - - +
694A ASN 3.3 0.2 - - - -
695A GLY* 1.3 77.5 - - - +
697A GLN* 1.3 61.8 + - - +
699A ALA* 3.3 7.0 + - - +
700A LEU* 3.2 22.5 + - + +
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Residues in contact with GLN 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A ARG* 2.8 48.9 + - + +
677A ALA* 3.9 21.3 - - + +
678A LYS* 3.7 24.6 - - + +
681A LEU* 4.5 7.6 - - + -
693A LEU 3.1 12.9 + - - +
694A ASN* 3.0 27.6 + - - +
696A ARG* 1.3 79.4 - - - +
698A LEU* 1.3 94.1 + - - +
700A LEU* 3.2 2.7 + - - +
701A LYS* 3.0 17.5 + - - +
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Residues in contact with LEU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A ARG* 4.9 0.9 - - - +
694A ASN* 3.0 44.1 + - - +
695A GLY* 3.2 9.6 + - - +
697A GLN* 1.3 115.3 - - - +
699A ALA* 1.3 66.3 + - - +
701A LYS* 3.1 22.6 + - + +
702A ILE* 2.9 33.9 + - + +
986A DCP 5.8 0.2 - - - +
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Residues in contact with ALA 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLU* 3.8 22.0 - - - +
537A TYR* 6.1 1.8 - - + -
540A MET* 3.9 18.8 - - + +
556A GLN* 5.6 0.9 + - - -
559A LYS* 5.1 0.3 + - - -
695A GLY 2.7 21.3 + - - +
696A ARG* 3.3 7.6 + - - +
698A LEU* 1.3 73.4 - - - +
700A LEU* 1.3 57.8 + - - +
702A ILE* 3.4 11.0 + - - +
703A SER* 3.0 29.8 + - - -
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLU* 4.3 20.0 - - - +
540A MET* 4.1 27.1 - - + -
543A VAL* 4.8 14.1 - - + -
670A LEU* 4.5 14.4 - - + +
673A ALA* 3.8 22.2 - - + +
674A ARG* 3.8 37.4 - - + +
677A ALA* 4.4 8.3 - - + -
696A ARG* 3.2 13.6 + - + +
697A GLN 3.2 7.1 + - - +
698A LEU 3.1 0.8 - - - -
699A ALA* 1.3 75.2 - - - +
701A LYS* 1.3 60.2 + - - +
703A SER* 3.3 5.8 + - - +
704A ALA* 3.1 26.7 + - - +
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Residues in contact with LYS 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A ARG* 3.7 27.5 - - - +
697A GLN 3.0 13.5 + - - +
698A LEU* 3.4 22.8 - - + +
700A LEU* 1.3 75.3 - - - +
702A ILE* 1.3 69.5 + - + +
704A ALA* 3.1 7.8 + - - +
705A ASN* 2.9 38.0 + - - +
986A DCP 2.8 73.7 + - - +
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Residues in contact with ILE 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A TYR* 5.7 0.2 - - - +
556A GLN* 3.5 25.8 - - - +
698A LEU* 2.9 27.3 + - + +
699A ALA* 3.8 8.5 - - - +
701A LYS* 1.3 83.2 - - + +
703A SER* 1.3 53.5 + - - +
705A ASN* 3.7 6.3 - - - +
706A SER* 2.8 42.8 + - - +
986A DCP 4.5 14.8 - - - +
4T G 4.0 16.8 - - + +
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Residues in contact with SER 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A MET* 3.5 11.1 - - - +
544A THR* 5.2 1.1 - - - -
556A GLN* 4.1 9.9 - - - -
559A LYS* 3.0 29.1 + - - +
560A VAL* 5.0 1.9 - - - +
563A GLN* 5.7 1.4 + - - -
670A LEU* 3.9 19.7 - - - +
699A ALA 3.0 16.1 + - - -
700A LEU* 3.4 12.3 - - - -
701A LYS 3.1 0.2 - - - -
702A ILE* 1.3 76.2 - - - +
704A ALA* 1.3 61.9 + - - +
706A SER* 3.4 9.9 + - - -
707A VAL* 3.4 17.2 + - - +
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Residues in contact with ALA 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A PRO* 4.1 19.5 - - + +
667A LEU* 3.5 15.5 - - + +
670A LEU* 3.8 22.6 - - + +
671A ILE* 4.7 11.0 - - + +
674A ARG* 6.4 0.4 - - - -
700A LEU 3.1 13.2 + - - +
701A LYS* 3.1 9.8 + - - +
703A SER* 1.3 74.9 - - - +
705A ASN* 1.3 66.3 + - - +
707A VAL* 3.1 19.8 + - - +
708A TYR* 3.7 2.3 + - - +
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Residues in contact with ASN 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A TYR* 4.5 0.2 - - - +
614A PRO* 3.3 28.3 - - - +
701A LYS* 2.9 33.3 + - - +
702A ILE* 4.0 4.9 - - - +
704A ALA* 1.3 76.6 - - - +
706A SER* 1.3 57.8 + - - +
708A TYR* 3.2 10.4 + - - +
709A GLY 2.9 20.8 + - - -
986A DCP 3.4 71.6 + - + +
4T G 3.2 11.5 + - - +
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Residues in contact with SER 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A GLN* 3.3 42.3 - - - +
560A VAL* 3.8 8.2 - - - +
702A ILE* 2.8 22.8 + - - +
703A SER 3.5 7.4 - - - -
704A ALA 3.1 0.4 - - - -
705A ASN* 1.3 76.5 - - - +
707A VAL* 1.3 58.1 + - - +
709A GLY 3.6 0.6 - - - -
710A PHE* 2.8 29.6 + - - +
4T G 3.5 26.4 + - - -
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Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A VAL* 4.1 24.2 - - + -
563A GLN* 5.1 2.0 - - - +
617A MET* 4.3 10.3 - - + -
663A LEU* 4.2 26.5 - - + -
666A ILE* 4.0 15.7 - - + -
667A LEU* 3.8 17.5 - - + -
670A LEU* 4.0 18.8 - - + -
703A SER 3.4 13.4 + - - +
704A ALA 3.1 10.2 + - - +
706A SER* 1.3 73.5 - - - +
708A TYR* 1.3 69.1 + - - +
710A PHE* 3.5 11.1 + - - +
711A THR* 3.5 14.0 + - - +
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Residues in contact with TYR 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TYR* 2.8 26.5 + - - -
613A TYR* 3.5 39.4 - + + -
614A PRO* 5.6 1.1 - - + -
617A MET* 3.9 22.0 - - - -
704A ALA 3.7 2.9 + - - +
705A ASN* 3.2 9.5 + - - +
707A VAL* 1.3 79.5 - - - +
709A GLY* 1.3 71.6 + - - +
711A THR* 2.7 26.8 + - - -
712A GLY 3.4 3.1 + - - -
724A SER* 3.6 27.8 - - - -
727A VAL* 3.9 22.0 - - + -
728A THR* 3.2 18.1 - - + +
986A DCP 3.8 5.2 - - + -
4T G 3.4 22.2 - - - -
5T G 3.9 18.5 + - - +
6T T 4.7 2.4 + - - -
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Residues in contact with GLY 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A ASN 2.9 11.7 + - - -
706A SER 3.4 0.6 + - - -
707A VAL 3.3 0.4 - - - -
708A TYR* 1.3 78.5 - - - +
710A PHE* 1.3 61.7 + - - +
712A GLY 2.9 13.2 + - - -
713A ALA* 3.0 14.9 + - - +
4T G 3.4 33.0 - - - -
5T G 3.5 16.5 - - - +
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Residues in contact with PHE 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A GLN* 3.6 39.0 - - + -
560A VAL* 3.7 27.8 - - + -
561A VAL* 3.9 22.9 - - + -
564A LEU* 4.2 17.5 - - + -
624A TYR* 3.2 29.4 - + - -
663A LEU* 6.4 0.4 - - + -
706A SER 2.8 21.9 + - - +
707A VAL 3.5 7.2 - - - +
708A TYR 3.2 0.2 - - - -
709A GLY* 1.3 71.6 - - - +
711A THR* 1.3 62.8 + - + +
713A ALA* 3.2 21.8 + - - +
718A LEU* 3.8 32.7 + - + +
1T T 4.0 15.5 - + + -
4T G 4.2 3.9 - - - +
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Residues in contact with THR 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A MET* 4.7 1.3 - - + -
624A TYR* 3.6 24.0 - - + +
663A LEU* 3.7 25.6 - - + -
707A VAL 3.6 12.8 - - - +
708A TYR* 2.7 18.9 + - - -
710A PHE* 1.3 78.5 - - + +
712A GLY* 1.3 56.8 + - - +
713A ALA 3.4 0.2 - - - -
719A PRO* 3.5 3.2 - - - +
720A CYS 2.8 44.8 + - - +
721A LEU* 3.7 2.1 - - - +
723A ILE* 3.7 15.2 - - + +
724A SER* 3.4 18.4 + - - -
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Residues in contact with GLY 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TYR* 3.8 19.9 - - - -
708A TYR 3.4 2.0 + - - -
709A GLY 2.9 10.6 + - - -
711A THR* 1.3 82.0 + - - +
713A ALA* 1.3 55.8 + - - +
714A THR* 3.4 8.8 + - - +
721A LEU* 4.0 7.4 - - - +
724A SER* 3.5 20.6 - - - -
5T G 3.5 15.4 - - - +
6T T 4.7 1.2 + - - -
----------------------------------------------------------
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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