Contacts of the helix formed by residues 660 - 681 (chain A) in PDB entry 1QXP
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 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A PHE* 3.3 4.3 - - - -
622A GLY 3.2 18.8 - - - +
623A SER* 4.9 1.6 - - - +
658A ILE* 5.7 1.8 - - + -
659A ILE* 1.4 60.0 - - - +
661A PHE* 1.4 55.1 + - - +
662A ASP* 2.8 9.4 + - - +
663A ASN* 2.6 36.3 + - - +
664A PHE* 2.7 36.6 + - - +
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Residues in contact with PHE 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A PHE 6.4 0.4 - - - -
606A ILE* 3.7 26.0 - - + -
609A TYR 4.0 4.3 - - - -
610A LEU* 3.5 48.5 - - + -
613A PHE* 3.2 30.7 - + + -
622A GLY 3.7 1.0 + - - -
660A ASP* 1.4 73.9 - - - +
662A ASP* 1.3 64.1 + - - +
664A PHE* 3.3 11.8 - + - +
665A VAL* 2.8 64.1 + - + +
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Residues in contact with ASP 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ASN* 6.6 0.4 - - + -
573A GLY* 5.6 1.6 - - - -
574A PHE* 4.0 25.2 - - - +
575A SER* 4.2 11.0 + - - -
578A SER* 2.6 31.7 + - - -
660A ASP* 2.8 10.3 + - - +
661A PHE* 1.3 88.0 - - - +
663A ASN* 1.3 67.7 + - - +
664A PHE 2.9 0.2 - - - -
665A VAL* 3.2 6.4 - - - +
666A ARG* 3.0 25.6 + - - +
767A ASP* 5.8 0.2 - - - +
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Residues in contact with ASN 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A ARG* 4.7 6.1 + - - +
652A PHE* 3.0 46.9 - - + +
659A ILE* 4.1 9.0 - - + -
660A ASP* 2.6 23.2 + - - +
662A ASP* 1.3 79.7 + - - +
664A PHE* 1.3 72.4 + - - +
666A ARG* 3.3 28.5 - - - +
667A CYS* 3.3 19.9 + - - +
766A ILE* 5.4 8.0 - - - +
767A ASP* 5.3 2.8 + - - -
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Residues in contact with PHE 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A TYR* 4.1 22.7 - - + -
612A ILE* 4.6 12.1 - - + -
613A PHE* 3.5 28.3 - + + -
624A MET* 4.1 9.2 - - + -
629A MET* 3.5 36.6 - - + -
632A ALA* 4.0 21.1 - - + -
659A ILE* 3.7 6.0 - - + +
660A ASP 2.7 23.5 + - - +
661A PHE* 3.3 17.9 - + - +
662A ASP 2.9 0.4 - - - -
663A ASN* 1.3 86.0 - - - +
665A VAL* 1.3 69.1 + - - +
667A CYS* 3.1 9.2 + - - +
668A LEU* 3.1 39.5 + - + +
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Residues in contact with VAL 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A SER* 4.7 11.4 - - - -
582A MET* 5.7 6.7 - - - -
606A ILE* 4.8 10.1 - - + -
609A TYR* 4.0 21.5 - - + -
661A PHE* 2.8 54.9 + - + +
662A ASP* 3.2 12.8 - - - +
664A PHE* 1.3 71.6 - - + +
666A ARG* 1.3 78.9 + - - +
668A LEU* 2.7 10.8 + - - -
669A VAL* 2.5 32.5 + - + +
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Residues in contact with ARG 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A GLU* 3.8 22.6 + - - +
578A SER* 3.8 34.8 + - - +
581A SER* 4.8 7.2 + - - -
651A ARG* 3.9 15.4 - - - +
652A PHE* 4.0 14.1 - - + -
662A ASP* 3.0 12.5 + - - +
663A ASN* 3.3 30.7 - - - +
665A VAL* 1.3 92.3 - - - +
667A CYS* 1.4 51.3 + - - +
669A VAL* 2.4 24.6 + - - +
670A ARG* 2.7 45.8 + - + +
767A ASP* 3.7 23.5 + - - -
771A SER* 6.3 0.4 - - - -
893A SER* 5.4 0.8 + - - -
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Residues in contact with CYS 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A MET* 3.4 31.6 - - + -
633A ILE* 4.5 2.7 - - - -
648A ILE* 3.6 20.4 - - - -
652A PHE* 2.4 48.4 - - + -
663A ASN 3.3 2.3 + - - +
664A PHE 3.1 7.7 + - - +
665A VAL 3.0 0.2 + - - -
666A ARG* 1.4 76.7 - - - +
668A LEU* 1.3 70.5 + - - +
670A ARG* 3.7 3.8 - - - +
671A LEU* 3.1 26.2 + - - +
891A MET* 4.5 2.9 - - - +
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A TYR* 3.9 28.8 + - + -
612A ILE* 6.3 0.2 - - + -
629A MET* 4.9 0.2 - - + -
632A ALA 5.5 0.2 - - - +
633A ILE* 4.3 19.3 - - + -
636A ALA* 4.2 22.0 - - + -
638A PHE* 3.9 28.7 - - + -
664A PHE* 3.1 51.5 + - + +
665A VAL* 2.7 14.9 + - - +
667A CYS* 1.3 86.8 - - - +
669A VAL* 1.4 53.5 + - - -
671A LEU* 5.0 0.7 - - + -
672A GLU* 3.2 28.8 + - - +
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Residues in contact with VAL 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A SER* 3.1 44.0 - - - +
582A MET* 3.8 20.4 - - + +
585A LEU* 4.4 14.5 - - + +
602A LEU* 6.1 0.2 - - + -
605A ARG* 6.1 2.7 - - - -
609A TYR* 4.3 13.0 - - + -
665A VAL* 2.5 41.1 + - + +
666A ARG* 2.4 19.3 + - - +
668A LEU* 1.4 51.1 - - - +
670A ARG* 1.2 68.3 + - - +
671A LEU 3.1 0.9 - - - -
672A GLU* 2.9 10.4 - - - +
673A ILE* 2.8 18.2 + - + +
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Residues in contact with ARG 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A SER* 4.2 10.0 + - - +
651A ARG* 4.7 0.2 - - - +
652A PHE* 3.9 18.4 - - - -
666A ARG* 2.7 53.6 + - + +
667A CYS* 3.7 8.7 - - - +
669A VAL* 1.2 80.7 - - - +
671A LEU* 1.3 53.9 + - - +
673A ILE* 2.5 28.4 + - - +
674A LEU* 2.8 27.8 + - + +
702A LEU* 5.0 28.1 - - + +
890A THR 4.1 8.7 + - - -
891A MET* 3.3 45.4 + - - -
893A SER* 3.7 18.5 + - - -
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Residues in contact with LEU 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A PHE* 4.1 22.4 - - + -
640A LEU* 5.3 10.8 - - + -
648A ILE* 6.0 2.0 - - + -
667A CYS* 3.1 17.6 + - - +
668A LEU* 5.0 0.9 - - + -
670A ARG* 1.3 85.4 - - - +
672A GLU* 1.3 66.5 + - - +
674A LEU* 4.4 3.6 - - - +
675A PHE* 3.2 37.7 + - + -
887A LEU* 5.6 2.9 - - + -
891A MET* 4.3 16.8 - - + -
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Residues in contact with GLU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A ASN 5.3 4.3 - - - +
585A LEU* 4.1 11.9 - - + +
605A ARG* 3.0 32.8 + - - +
609A TYR* 3.4 24.7 - - - +
638A PHE* 3.6 21.3 - - + -
668A LEU 3.2 12.9 + - - +
669A VAL* 2.9 16.8 - - - +
671A LEU* 1.3 79.1 - - - +
673A ILE* 1.4 60.2 + - - +
674A LEU 3.3 0.3 + - - -
675A PHE* 4.0 3.9 + - - +
676A LYS* 3.4 18.4 + - - +
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Residues in contact with ILE 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A SER* 5.1 7.4 - - - +
584A ASN* 5.6 4.0 - - + -
585A LEU* 5.1 23.3 - - + +
588A ARG* 4.9 8.2 + - - +
669A VAL 2.8 9.7 + - - +
670A ARG* 2.5 22.6 + - - +
672A GLU* 1.4 70.2 - - - +
674A LEU* 1.4 57.4 + - + -
676A LYS* 3.2 9.6 + - - +
677A ILE* 3.0 33.0 + - + +
702A LEU* 5.8 9.4 - - + -
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ARG* 2.8 44.0 + - + +
671A LEU* 4.0 1.8 - - - +
672A GLU 3.2 0.2 - - - -
673A ILE* 1.4 72.1 - - + +
675A PHE* 1.3 76.4 + - - +
676A LYS 3.1 0.4 - - - -
677A ILE* 3.3 9.7 + - + +
678A PHE* 3.2 10.0 + - - +
699A PHE 5.5 3.6 - - - +
702A LEU* 5.9 8.3 - - + -
886A TRP* 3.1 39.7 + - + +
887A LEU* 3.8 10.3 - - + -
890A THR* 3.0 41.5 - - + +
891A MET* 3.6 16.6 - - - -
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Residues in contact with PHE 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A ILE* 3.6 21.3 - - + -
518A GLN 3.5 14.4 - - - -
519A ALA* 2.9 30.1 - - + -
522A PRO 5.7 5.2 - - - +
638A PHE* 3.4 24.9 - + + -
640A LEU* 3.7 11.0 - - + -
671A LEU* 3.2 34.3 + - + +
672A GLU* 4.4 4.3 - - - +
674A LEU* 1.3 83.6 - - - +
676A LYS* 1.3 66.2 + - - +
678A PHE* 4.5 4.7 - - - -
679A LYS* 2.6 27.9 + - + +
883A ILE* 3.6 32.3 - - + -
886A TRP* 5.1 0.4 - - - +
887A LEU* 4.2 12.9 - - + +
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Residues in contact with LYS 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A PRO 5.7 2.7 - - - -
585A LEU* 5.9 6.5 - - + -
588A ARG* 3.8 22.2 - - - +
672A GLU* 3.4 14.2 + - - +
673A ILE* 3.2 14.6 + - - +
674A LEU 3.1 1.0 - - - -
675A PHE* 1.3 77.2 - - - +
677A ILE* 1.3 67.7 + - - +
679A LYS* 2.9 11.2 + - - +
680A GLN* 3.0 13.0 + - - +
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Residues in contact with ILE 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A ARG* 5.2 16.6 - - - +
673A ILE* 3.0 24.8 + - + +
674A LEU* 3.3 10.7 + - + +
675A PHE 2.9 1.2 + - - -
676A LYS* 1.3 75.9 - - - +
678A PHE* 1.3 56.6 + - - +
679A LYS 2.5 12.8 + - - -
680A GLN* 2.6 18.5 + - + +
681A LEU* 3.0 45.0 + - + +
699A PHE* 5.2 14.4 - - + +
702A LEU* 5.9 8.1 - - - -
886A TRP* 4.1 25.1 - - + -
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Residues in contact with PHE 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A LEU 3.2 15.2 + - - +
675A PHE* 3.8 4.5 - - - +
677A ILE* 1.3 79.7 - - - +
679A LYS* 1.3 61.1 + - - +
681A LEU* 4.4 1.1 - - - +
682A ASP* 3.4 21.2 + - + +
685A ASN* 6.2 0.2 - - - -
687A GLY* 3.3 27.1 - - - -
688A THR 4.6 0.2 - - - -
689A ILE* 3.2 42.2 - - + -
881A VAL 3.3 13.9 - - - -
882A ASN 3.6 2.2 - - - -
883A ILE* 3.0 43.3 - - + -
886A TRP* 3.5 34.2 - + + +
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Residues in contact with LYS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A PRO 4.8 17.9 - - - +
675A PHE* 2.6 23.8 + - + +
676A LYS* 3.5 6.5 - - - +
677A ILE 2.5 6.5 + - - -
678A PHE* 1.3 70.8 - - - +
680A GLN* 1.3 54.7 + - - +
682A ASP 2.4 27.2 - - - +
683A PRO* 4.9 0.2 - - - +
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Residues in contact with GLN 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A ARG* 6.0 6.1 - - - +
676A LYS 3.0 10.5 + - - +
677A ILE* 2.6 17.1 + - + +
679A LYS* 1.3 71.1 - - - +
681A LEU* 1.3 53.3 + - + +
682A ASP 2.3 24.6 + - - -
683A PRO* 3.4 7.6 - - - +
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Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A ILE* 3.0 38.4 + - + +
678A PHE* 4.9 0.4 - - - -
680A GLN* 1.3 72.3 - - + +
682A ASP* 1.3 60.1 + - - +
683A PRO* 3.9 6.6 - - - +
688A THR 4.6 0.2 - - - +
689A ILE* 3.7 32.3 - - + +
690A GLN* 4.7 34.2 + - + +
691A LEU* 5.0 9.6 - - + -
695A SER* 6.5 0.4 - - - -
699A PHE* 5.9 3.6 - - + -
886A TRP* 5.4 2.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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