Contacts of the helix formed by residues 639 - 662 (chain A) in PDB entry 6A5T
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 639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A MET* 2.9 32.3 + - - +
636A ARG 4.5 2.0 + - - -
637A GLU 3.9 0.4 - - - -
638A LYS* 1.3 82.5 - - - +
640A PRO* 1.3 76.1 - - - +
643A CYS* 3.7 8.0 + - - +
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Residues in contact with PRO 640 (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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509A PRO* 3.4 39.4 - - + +
510A LEU* 3.9 18.4 - - + -
635A MET* 3.4 18.6 - - + -
638A LYS 4.6 0.4 - - - +
639A GLY* 1.3 82.1 - - - +
641A LYS* 1.3 65.4 + - + +
642A ILE 3.1 2.0 - - - -
643A CYS* 2.4 30.3 + - - +
644A ALA 2.8 9.3 + - - -
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Residues in contact with LYS 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PRO* 4.9 4.0 - - - -
638A LYS 5.2 0.4 + - - +
639A GLY 3.7 0.2 - - - -
640A PRO* 1.3 83.5 - - + +
642A ILE* 1.3 70.7 + - + +
644A ALA* 3.1 23.7 - - + +
645A GLU* 3.1 21.4 + - + +
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Residues in contact with ILE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PRO* 4.0 30.7 - - + -
634A VAL* 4.7 2.9 - - + -
638A LYS* 3.7 42.4 + - + +
639A GLY 4.3 0.4 + - - -
640A PRO 3.1 0.6 - - - -
641A LYS* 1.3 84.2 - - + +
643A CYS* 1.3 66.7 + - - +
645A GLU* 3.2 14.1 + - + +
646A LEU* 2.9 21.0 + - - +
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Residues in contact with CYS 643 (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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512A ILE* 3.5 22.2 - - + -
631A ILE* 3.6 40.2 - - - -
634A VAL* 5.0 6.4 - - - +
635A MET* 3.6 28.9 - - - +
639A GLY 3.7 3.8 + - - +
640A PRO 2.4 23.8 + - - +
642A ILE* 1.3 72.6 - - - +
644A ALA* 1.3 61.2 + - - +
646A LEU* 3.4 13.7 - - - +
647A PHE* 3.2 16.4 - - - -
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Residues in contact with ALA 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLU* 4.9 2.8 - - - +
362A LEU* 4.5 20.2 - - + +
363A ASP* 5.5 6.7 - - - +
509A PRO* 4.0 26.0 - - + -
512A ILE* 5.0 1.9 - - - +
640A PRO 2.8 5.1 + - - -
641A LYS* 3.1 14.4 - - + +
643A CYS* 1.3 76.3 - - - +
645A GLU* 1.3 68.8 + - + +
646A LEU 2.8 1.9 + - - -
647A PHE* 2.9 21.4 + - - +
648A GLY 3.6 5.4 + - - -
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Residues in contact with GLU 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLU* 4.4 18.6 - - - +
555A PRO* 5.7 6.6 - - + +
556A SER* 3.9 22.0 - - - -
641A LYS* 3.1 22.8 + - + +
642A ILE* 3.2 14.9 + - + +
644A ALA* 1.3 81.2 - - + +
646A LEU* 1.3 66.4 + - - +
648A GLY* 3.3 3.6 + - - +
649A ASN* 3.0 33.0 + - - +
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Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA* 4.7 4.0 - - + +
583A ILE* 4.4 14.6 - - + +
584A PRO* 4.1 26.0 - - + -
630A LEU* 4.7 12.8 - - + -
631A ILE* 4.1 31.6 - - + -
634A VAL* 5.2 10.8 - - + -
642A ILE 2.9 13.4 + - - +
643A CYS* 3.4 16.6 - - - +
644A ALA 2.8 1.2 + - - -
645A GLU* 1.3 74.4 - - - +
647A PHE* 1.3 67.5 + - + +
649A ASN* 2.8 18.2 + - - +
650A ILE* 3.0 40.2 + - + +
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Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 3.6 29.8 - - + -
472A ASN* 5.3 2.2 - - - +
474A SER* 2.9 29.4 - - - +
512A ILE* 5.0 8.3 - - + -
522A MET* 3.1 22.2 - - + -
523A GLY 3.1 24.2 - - - -
524A ILE* 3.5 15.9 - - + -
631A ILE* 3.6 32.3 - - + -
643A CYS* 3.2 30.3 - - - -
644A ALA 2.9 7.3 + - - +
646A LEU* 1.3 80.8 - - + +
648A GLY* 1.3 63.0 + - - +
650A ILE* 4.7 4.7 - - - +
651A GLN* 2.9 30.8 + - - +
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Residues in contact with GLY 648 (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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360A LEU 4.9 3.8 - - - -
361A GLU* 4.4 16.5 + - - -
362A LEU* 5.6 1.2 - - - +
472A ASN* 5.6 2.1 - - - +
555A PRO* 5.0 2.0 - - - -
644A ALA 3.6 4.8 + - - -
645A GLU* 3.3 6.2 + - - -
646A LEU 3.2 1.0 - - - -
647A PHE* 1.3 78.3 - - - +
649A ASN* 1.3 63.7 + - - +
651A GLN* 4.2 3.0 - - - +
652A LYS* 3.0 46.1 + - - +
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Residues in contact with ASN 649 (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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554A VAL* 3.6 8.7 - - + +
555A PRO* 3.0 30.8 - - - +
556A SER* 3.0 32.2 + - - -
582A ALA* 3.5 30.1 + - + -
584A PRO* 6.1 0.4 - - - +
645A GLU* 3.0 22.5 + - - +
646A LEU* 2.8 14.4 + - - +
648A GLY* 1.3 72.7 - - - +
650A ILE* 1.3 64.0 + - - +
652A LYS* 4.1 0.9 - - - +
653A VAL* 3.0 29.9 + - - +
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Residues in contact with ILE 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ILE* 5.1 18.4 - - + -
528A THR* 4.4 11.9 - - + -
532A VAL* 4.9 7.2 - - + -
579A LEU* 4.7 17.0 - - + -
582A ALA* 4.4 16.2 - - + -
583A ILE* 5.4 4.3 - - + -
623A VAL* 5.2 18.4 - - + -
630A LEU* 5.4 4.0 - - + -
631A ILE* 5.8 0.9 - - + -
646A LEU* 3.0 45.0 + - + +
647A PHE* 4.2 4.5 - - - +
649A ASN* 1.3 75.0 - - - +
651A GLN* 1.3 65.1 + - + +
653A VAL* 4.7 2.7 - - - -
654A VAL* 3.0 37.5 + - + +
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Residues in contact with GLN 651 (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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358A PRO* 4.4 16.7 - - - +
472A ASN* 3.0 24.6 + - - +
473A LEU* 3.7 13.8 + - - +
474A SER* 3.2 34.2 + - - +
524A ILE* 4.8 14.0 - - + +
525A VAL* 5.0 3.0 - - - +
528A THR* 3.8 27.9 + - + +
647A PHE 2.9 19.7 + - - +
648A GLY* 4.2 1.9 - - - +
650A ILE* 1.3 73.8 - - - +
652A LYS* 1.3 68.1 + - + +
655A ASN* 2.6 39.7 + - - +
835B GLN* 5.6 0.4 + - - -
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Residues in contact with LYS 652 (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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358A PRO 4.7 9.7 + - - +
359A ASN* 4.9 15.3 - - - +
360A LEU 3.4 24.8 + - - -
361A GLU* 4.0 10.7 + - - -
553A TRP* 3.7 56.3 - - + +
555A PRO* 4.1 15.9 - - + +
648A GLY* 3.0 27.0 + - - +
649A ASN* 4.1 2.2 - - - +
651A GLN* 1.3 76.7 - - + +
653A VAL* 1.3 68.0 + - + +
655A ASN* 3.8 4.0 - - - +
656A TYR* 3.0 22.0 + - - +
62K LYS* 6.2 1.8 - - - +
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Residues in contact with VAL 653 (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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535A MET* 4.7 9.4 - - + -
550A MET* 4.2 34.0 - - + +
553A TRP* 5.2 3.8 - - + -
554A VAL* 3.4 31.2 - - + +
578A LEU* 5.1 12.3 - - + +
579A LEU* 5.4 5.8 - - + +
581A ILE* 6.4 0.2 - - + -
582A ALA* 5.4 4.0 - - + -
649A ASN 3.0 22.7 + - - +
650A ILE* 3.9 3.8 - - - +
652A LYS* 1.3 80.7 - - + +
654A VAL* 1.3 74.1 + - + +
656A TYR* 2.8 12.6 + - - +
657A TRP* 3.0 10.4 + - - +
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Residues in contact with VAL 654 (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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528A THR* 3.6 18.2 - - + +
531A GLY* 3.8 9.6 - - - -
532A VAL* 3.3 55.4 - - + +
535A MET* 4.6 13.2 - - + -
579A LEU* 4.8 2.7 - - + -
650A ILE* 3.0 21.9 + - + +
653A VAL* 1.3 86.0 - - + +
655A ASN* 1.3 57.9 + - - +
657A TRP* 4.1 6.2 - - + +
658A LEU* 2.8 27.8 + - + +
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Residues in contact with ASN 655 (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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358A PRO* 4.0 19.1 - - + +
528A THR* 3.5 20.9 + - - -
651A GLN* 2.6 39.8 + - - +
652A LYS* 3.8 4.4 - - - +
654A VAL* 1.3 78.5 - - - +
656A TYR* 1.3 58.3 + - - +
658A LEU* 3.0 11.2 + - - +
659A LEU* 2.8 30.9 + - - +
830B TYR 5.2 0.3 - - - +
831B SER* 4.9 11.0 - - - +
832B GLY* 4.1 9.8 + - - -
835B GLN* 3.5 21.2 + - - +
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Residues in contact with TYR 656 (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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546A GLN* 4.4 4.5 + - + +
549A ASN* 2.9 43.6 + - + +
550A MET* 3.1 35.4 - - + -
553A TRP* 3.3 39.0 - + + +
652A LYS 3.0 14.8 + - - +
653A VAL* 2.8 7.8 + - - +
655A ASN* 1.3 73.0 - - - +
657A TRP* 1.3 62.8 + - - +
659A LEU* 3.3 19.6 - - + +
660A HIS* 2.8 60.5 + + - -
61K TYR* 5.6 4.4 + + - -
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Residues in contact with TRP 657 (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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531A GLY 5.2 1.3 - - - -
534A LYS* 4.5 9.4 - - + -
535A MET* 3.5 54.7 - - + -
540A THR* 4.6 12.3 - - + -
542A ILE* 3.5 22.1 - - + +
546A GLN* 3.6 18.1 - - - +
550A MET* 3.3 41.7 - - + -
653A VAL 3.0 10.4 + - - +
654A VAL* 4.1 3.8 - - + +
656A TYR* 1.3 77.3 - - - +
658A LEU* 1.3 80.5 + - + +
660A HIS 3.3 0.9 + - - +
661A ASN* 2.9 57.2 + - + -
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Residues in contact with LEU 658 (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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527A ASP* 4.3 21.5 - - + +
528A THR* 5.9 0.7 - - - -
531A GLY* 4.2 24.5 - - - +
534A LYS* 5.6 4.0 - - + -
654A VAL* 2.8 26.2 + - + +
655A ASN* 3.0 11.4 + - - +
657A TRP* 1.3 84.5 - - + +
659A LEU* 1.3 53.7 + - - +
661A ASN* 5.5 0.2 - - - -
662A GLY* 2.4 43.2 + - - +
663A PHE* 4.1 24.7 - - + -
829B CYS* 4.1 28.3 - - + +
830B TYR 4.8 2.7 - - - +
831B SER* 6.3 0.2 - - - -
832B GLY 5.7 4.7 - - - +
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Residues in contact with LEU 659 (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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655A ASN 2.8 12.1 + - - +
656A TYR* 3.3 31.0 - - + +
658A LEU* 1.3 79.3 - - - +
660A HIS* 1.3 75.2 + - + +
662A GLY* 2.9 9.2 + - - -
830B TYR* 3.0 55.1 + - + +
831B SER* 4.2 16.8 - - - +
1074B ASN* 4.8 9.9 - - - +
1076B HIS* 4.9 14.8 - - + +
1081B LEU* 3.2 15.0 - - + +
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Residues in contact with HIS 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLN* 3.5 31.0 - - + +
656A TYR* 2.8 65.6 + + - +
657A TRP 3.3 0.2 + - - -
659A LEU* 1.3 85.9 - - + +
661A ASN* 1.3 61.4 + - - +
1074B ASN* 3.3 26.5 + - - -
1076B HIS* 5.1 3.4 - - + -
1077B THR* 3.8 26.4 + - + +
1079B LYS* 5.3 16.4 - - + +
1080B LYS 4.2 9.9 - - - +
1081B LEU* 3.8 9.9 - - - +
1082B MET* 4.3 1.6 + - - +
61K TYR* 5.8 2.3 + - - -
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Residues in contact with ASN 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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534A LYS* 4.0 14.4 - - - +
546A GLN* 4.9 1.0 - - - +
657A TRP* 2.9 56.1 + - + +
658A LEU* 3.7 2.2 - - + +
659A LEU 3.3 0.7 - - - -
660A HIS* 1.3 78.7 - - - +
662A GLY* 1.3 82.6 + - - +
1081B LEU* 3.5 5.7 - - - +
1082B MET* 2.8 49.1 + - - +
1083B ALA* 3.6 8.3 + - - +
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Residues in contact with GLY 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LYS* 4.5 2.3 - - - -
658A LEU* 2.4 29.9 + - - +
659A LEU* 2.9 7.3 + - - -
661A ASN* 1.3 94.9 + - - +
663A PHE* 1.3 65.3 + - - +
829B CYS 4.7 7.9 - - - -
1081B LEU* 4.1 15.3 - - - -
1083B ALA* 4.0 5.9 - - - +
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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