Contacts of the helix formed by residues 634 - 663 (chain A) in PDB entry 1N54
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 ARG 634 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 5.0 2.0 - - - +
450A ARG* 5.8 7.1 - - - +
451A GLU* 3.1 16.1 + - - +
454A GLU* 3.0 28.4 + - - -
595A ARG 5.7 2.0 + - - -
598A PRO* 3.8 18.2 - - - +
630A ARG 4.4 4.0 - - - -
631A ASP* 2.5 50.3 + - - +
633A THR* 1.3 78.0 - - - +
635A LEU* 1.3 66.4 + - - +
636A PHE* 3.4 28.3 - - + -
637A VAL* 3.1 22.2 + - - +
638A TRP* 3.7 3.6 - - - -
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A THR* 6.0 0.4 - - + -
411A ASP* 3.2 42.3 - - + +
414A ILE* 4.2 31.0 - - + -
415A ASN* 4.7 3.8 - - - +
447A LYS* 4.8 5.4 - - - +
451A GLU* 3.0 34.4 + - + +
454A GLU* 5.4 0.7 - - - +
455A LYS* 4.1 26.0 - - + +
633A THR 4.9 0.4 - - - +
634A ARG* 1.3 66.8 - - - +
636A PHE* 1.3 70.1 + - - +
637A VAL 2.8 1.6 + - - -
638A TRP* 3.0 15.9 + - - +
639A GLU* 3.1 12.0 + - + +
746A ARG* 3.6 15.4 + - - +
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Residues in contact with PHE 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLU* 4.8 0.8 + - - -
454A GLU* 4.4 5.0 + - - +
458A ARG* 4.3 11.6 - - - +
591A PHE* 5.1 10.3 - + - -
598A PRO* 3.7 32.5 - - + -
601A ILE* 4.3 20.2 - - + -
602A ALA* 5.8 2.5 - - + -
622A TRP* 5.6 4.3 - + - -
628A LEU* 6.4 2.0 - - + -
631A ASP* 4.1 12.6 - - + -
634A ARG* 3.4 45.5 - - + -
635A LEU* 1.3 77.7 - - - +
637A VAL* 1.3 103.3 + - + +
639A GLU* 3.0 18.6 + - - +
640A ILE* 3.0 40.3 + - + +
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Residues in contact with VAL 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ILE* 3.7 39.1 - - + +
628A LEU* 5.0 11.0 - - + +
631A ASP* 3.3 29.8 - - + +
632A PHE* 4.5 7.2 - - + +
634A ARG 3.2 10.3 - - - +
635A LEU 2.8 1.6 + - - -
636A PHE* 1.3 115.7 - - + +
638A TRP* 1.3 73.7 - - + +
640A ILE* 3.1 14.5 + - - +
641A LEU 3.2 8.7 + - - -
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Residues in contact with TRP 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ILE* 4.8 4.0 - - + -
624A PHE* 4.2 4.3 - + - -
632A PHE* 2.8 62.8 + + - -
633A THR* 4.2 3.6 - - - +
634A ARG 3.7 13.2 + - - -
635A LEU 3.0 5.0 + - - +
637A VAL* 1.3 73.8 - - + +
639A GLU* 1.3 56.4 + - - +
641A LEU* 3.5 27.7 - - + +
642A HIS* 2.8 50.3 + - + -
717A PHE* 3.5 39.0 - + - -
742A ASN* 6.1 1.0 - - + +
743A CYS* 5.4 2.0 - - - -
746A ARG* 3.2 64.0 - - + +
750A ILE* 5.2 6.7 - - + -
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Residues in contact with GLU 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A LYS* 3.2 27.7 + - - +
458A ARG* 3.4 18.7 + - - -
602A ALA* 4.2 8.8 - - - +
635A LEU* 3.1 12.8 + - + +
636A PHE* 3.0 21.7 + - - +
638A TRP* 1.3 76.7 - - - +
640A ILE* 1.3 55.3 + - - +
642A HIS* 3.2 8.2 + - - +
643A SER* 2.8 29.8 + - - -
646A ARG* 5.5 0.5 + - - -
1555B GOL 2.9 35.0 + - - +
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Residues in contact with ILE 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ILE* 4.1 7.9 - - + +
602A ALA* 3.7 41.7 - - + +
605A VAL* 3.9 27.1 - - + -
619A VAL* 4.2 4.0 - - + -
622A TRP* 4.1 26.9 - - + -
623A ILE* 4.5 1.6 - - + -
636A PHE* 3.0 32.6 + - + +
637A VAL* 3.3 8.3 - - - +
639A GLU* 1.3 73.6 - - + +
641A LEU* 1.3 69.1 + - - +
643A SER* 2.6 23.6 + - - -
644A THR* 2.8 18.2 + - - +
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Residues in contact with LEU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A VAL* 5.0 1.6 - - + +
620A ALA* 5.0 10.3 - - - -
623A ILE* 4.0 30.2 - - + +
624A PHE* 4.0 12.3 - - + -
637A VAL 3.2 4.4 + - - +
638A TRP* 3.2 45.3 + - + +
640A ILE* 1.3 79.6 - - - +
642A HIS* 1.3 60.2 + - + +
644A THR* 3.4 11.2 - - + -
645A ILE* 2.8 47.4 + - + +
709A LEU* 5.3 3.1 - - + -
713A ILE* 4.3 23.3 - - + -
750A ILE* 5.2 4.9 - - + -
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Residues in contact with HIS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TRP* 2.8 40.4 + - + +
639A GLU* 3.6 6.5 - - - +
640A ILE 2.7 2.8 + - - -
641A LEU* 1.3 70.3 - - + +
643A SER* 1.3 66.9 + - - +
644A THR 3.1 1.3 - - - -
645A ILE* 2.9 9.0 + - + +
646A ARG* 2.7 40.7 + - - +
746A ARG* 5.2 0.2 - - - -
749A GLN* 3.5 34.3 + - + -
750A ILE* 3.5 29.7 - - + +
753A GLN* 3.6 27.6 + - - +
754A HIS* 3.8 14.2 + + - +
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Residues in contact with SER 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ASP* 3.7 8.2 + - - +
639A GLU* 2.8 14.1 + - - -
640A ILE* 2.6 19.7 + - - -
642A HIS* 1.3 74.1 - - - +
644A THR* 1.3 63.7 + - - -
646A ARG* 3.0 19.2 + - - +
647A LYS* 2.4 53.7 + - - +
65B ASP* 4.3 7.5 + - - -
1555B GOL 5.5 3.5 + - - -
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Residues in contact with THR 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A VAL* 4.6 1.6 - - - +
609A ILE* 3.7 24.5 - - + +
616A CYS* 3.8 27.6 - - + +
619A VAL* 3.5 28.5 - - + +
640A ILE* 2.8 16.6 + - - +
641A LEU* 3.4 14.1 - - + -
643A SER* 1.3 77.3 - - - +
645A ILE* 1.3 61.6 + - + +
647A LYS* 3.7 13.6 + - - +
648A MET* 3.3 19.6 + - - +
709A LEU* 5.1 4.5 - - + -
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Residues in contact with ILE 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 2.8 36.8 - - + +
642A HIS* 2.9 14.9 + - + +
644A THR* 1.3 76.7 - - - +
646A ARG* 1.3 53.0 + - - +
648A MET* 2.9 8.7 + - - +
649A ASN* 2.6 36.9 + - - +
709A LEU* 4.0 17.0 - - + -
710A PHE* 3.9 19.3 - - + -
713A ILE* 3.9 20.6 - - + -
750A ILE* 5.0 5.8 - - + -
754A HIS* 3.4 39.9 - - + +
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Residues in contact with ARG 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A GLU 5.5 0.6 + - - -
642A HIS* 2.7 35.4 + - - +
643A SER* 3.6 17.6 + - - +
645A ILE* 1.3 70.9 - - - +
647A LYS* 1.3 53.2 + - + +
649A ASN* 2.7 13.9 + - + +
650A LYS* 2.6 53.1 + - + +
753A GLN* 5.2 4.6 + - - -
754A HIS* 4.6 13.5 - - + -
1558A GOL 3.8 39.3 + - - -
65B ASP* 3.6 28.0 + - - +
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Residues in contact with LYS 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A VAL 5.6 0.2 - - - -
606A ASP* 3.0 38.0 + - - +
609A ILE* 5.0 17.5 - - + -
610A ARG* 3.8 39.9 - - + +
643A SER* 2.4 55.8 + - - +
644A THR* 3.7 12.0 - - - +
646A ARG* 1.3 77.4 - - + +
648A MET* 1.3 60.1 + - - +
650A LYS* 3.9 8.4 - - - +
651A HIS* 3.3 21.8 + - - +
65B ASP* 4.6 4.4 + - - +
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Residues in contact with MET 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A CYS* 3.9 20.2 - - - -
644A THR 3.3 12.7 + - - +
645A ILE* 2.9 12.0 + - - +
647A LYS* 1.3 77.6 - - - +
649A ASN* 1.3 66.7 + - - +
651A HIS* 3.1 37.0 + - + +
652A VAL* 3.1 16.1 + - + +
702A ALA 3.4 24.0 - - - +
705A GLU* 3.7 24.0 - - - +
706A GLN* 3.9 31.4 - - + -
709A LEU* 4.2 13.5 - - + -
710A PHE* 5.8 0.2 - - + -
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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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645A ILE* 2.6 20.2 + - - +
646A ARG* 2.7 11.7 + - + +
648A MET* 1.3 77.1 - - - +
650A LYS* 1.3 62.2 + - + +
652A VAL* 3.6 2.9 + - - +
653A LEU* 3.5 27.0 + - + +
706A GLN* 3.4 23.0 + - - +
710A PHE* 4.2 15.2 - - - -
754A HIS* 3.1 33.6 + - - -
757A ILE* 4.1 23.5 - - + +
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Residues in contact with LYS 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A ARG* 2.6 35.6 + - + +
647A LYS* 4.2 7.2 - - - +
649A ASN* 1.3 74.0 - - + +
651A HIS* 1.3 63.9 + - - +
653A LEU* 3.2 15.0 + - + +
654A LYS* 2.9 24.1 + - - +
1558A GOL 4.9 9.9 + - - -
65B ASP* 5.6 4.9 + - - +
89B TYR* 6.4 1.8 - - - -
90B SER* 5.0 12.1 - - - -
93B ASP* 5.0 14.2 + - - -
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Residues in contact with HIS 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A LYS 3.3 13.4 + - - +
648A MET* 3.1 30.8 + - + +
650A LYS* 1.3 77.1 - - - +
652A VAL* 1.3 65.6 + - - +
654A LYS* 3.2 19.0 + - + +
655A ILE* 3.2 40.7 + - + +
698A LYS* 4.5 11.7 + - + -
702A ALA* 4.1 13.9 - - + +
705A GLU* 4.9 5.1 + - - -
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Residues in contact with VAL 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A MET* 3.1 15.4 + - + +
649A ASN 3.9 4.3 - - - +
651A HIS* 1.3 79.2 - - - +
653A LEU* 1.3 64.2 + - + +
655A ILE* 3.1 4.0 + - - +
656A GLN* 3.0 40.8 + - + +
699A VAL* 5.6 1.7 - - + +
702A ALA* 3.7 28.5 - - + +
703A GLN* 3.9 23.6 - - + +
706A GLN* 3.2 37.2 - - - +
757A ILE* 6.1 1.8 - - + -
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Residues in contact with LEU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ASN* 3.5 16.5 + - + +
650A LYS* 3.2 17.6 + - + +
652A VAL* 1.3 78.5 - - + +
654A LYS* 1.3 62.2 + - - +
656A GLN* 3.0 25.1 + - + +
657A LYS* 3.0 22.0 + - - +
757A ILE* 6.3 2.0 - - + -
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Residues in contact with LYS 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A LYS 2.9 12.9 + - - +
651A HIS* 3.2 15.5 + - + +
653A LEU* 1.3 76.5 - - - +
655A ILE* 1.3 56.5 + - + +
657A LYS* 2.9 33.4 + - - +
658A GLU* 2.8 57.5 + - + +
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Residues in contact with ILE 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A HIS* 3.5 37.2 - - + +
652A VAL 3.1 7.3 + - - +
654A LYS* 1.3 78.4 - - + +
656A GLN* 1.3 60.1 + - - +
658A GLU* 3.9 11.1 - - - +
659A LEU* 3.3 21.5 + - - +
695A LEU* 4.1 16.8 - - + +
698A LYS* 3.8 31.9 - - + +
699A VAL* 3.5 33.6 - - + +
702A ALA* 3.8 20.2 - - + -
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Residues in contact with GLN 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A VAL* 3.0 28.9 + - + +
653A LEU* 3.1 42.1 + - + +
654A LYS 2.9 1.0 - - - -
655A ILE* 1.3 77.6 - - - +
657A LYS* 1.3 59.7 + - - +
659A LEU* 3.6 6.0 + - - +
660A GLU* 3.0 27.9 + - - +
699A VAL* 4.8 14.1 - - + +
703A GLN* 5.0 8.1 + - - -
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Residues in contact with LYS 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A LEU 3.0 8.3 + - - +
654A LYS* 2.9 42.6 + - - +
656A GLN* 1.3 75.4 - - - +
658A GLU* 1.3 72.7 + - - +
659A LEU 3.1 2.0 - - - -
660A GLU* 3.7 7.5 - - - +
661A GLU* 3.0 55.7 + - + +
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Residues in contact with GLU 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A LYS* 2.8 41.9 + - + +
655A ILE* 4.2 10.2 - - - +
656A GLN 3.4 0.2 - - - -
657A LYS* 1.3 93.7 + - - +
659A LEU* 1.3 56.4 + - - +
661A GLU* 4.2 5.9 - - - +
662A ALA* 3.2 25.3 + - - +
691A GLN* 5.0 2.8 + - - -
694A ARG* 5.8 0.2 + - - -
695A LEU* 3.5 32.1 - - + +
698A LYS* 5.9 0.7 + - - -
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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
----------------------------------------------------------
655A ILE 3.3 16.7 + - - +
656A GLN* 4.0 5.6 - - - +
657A LYS 3.1 0.2 - - - -
658A GLU* 1.3 78.1 - - - +
660A GLU* 1.3 58.3 + - - +
661A GLU 3.2 2.0 - - - -
662A ALA* 3.6 3.4 - - - +
663A LYS* 3.1 51.5 + - + +
692A ILE* 3.6 23.6 - - + +
695A LEU* 3.4 13.0 - - + +
696A GLN* 3.3 42.8 - - - +
699A VAL* 3.9 17.5 - - + -
----------------------------------------------------------
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A GLN 3.0 19.0 + - - +
657A LYS* 3.3 9.4 + - - +
659A LEU* 1.3 77.3 - - - +
661A GLU* 1.3 60.7 + - + +
663A LYS* 4.3 5.9 + - - +
664A GLU* 3.0 41.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LYS* 3.0 50.0 + - + +
658A GLU* 4.2 5.4 - - - +
660A GLU* 1.3 79.0 - - + +
662A ALA* 1.3 69.5 + - - +
664A GLU* 3.3 21.3 + - - +
665A LYS* 4.0 11.4 - - - +
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Residues in contact with ALA 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A GLU 3.2 18.5 + - - +
659A LEU* 3.4 9.4 + - - +
661A GLU* 1.3 80.2 - - - +
663A LYS* 1.3 65.7 + - - +
664A GLU 2.9 1.6 + - - -
665A LYS* 2.9 27.0 + - - +
689A GLU* 4.3 1.4 - - - +
691A GLN* 5.1 6.3 - - + -
692A ILE* 3.8 25.7 - - + +
695A LEU* 4.3 9.9 - - + -
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Residues in contact with LYS 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A LEU* 3.1 49.1 + - + +
660A GLU* 4.6 5.4 - - - +
661A GLU 3.4 0.2 - - - -
662A ALA* 1.3 78.4 - - - +
664A GLU* 1.3 63.9 + - - +
665A LYS 2.7 21.3 + - - +
689A GLU* 4.4 0.3 - - - +
692A ILE* 3.9 27.5 - - + +
696A GLN* 3.7 13.7 - - - +
----------------------------------------------------------
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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).
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