Contacts of the helix formed by residues 660 - 683 (chain A) in PDB entry 4EGA
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
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A PHE* 3.6 15.1 - - + -
655A TYR* 2.7 20.0 + - - +
656A TYR* 4.6 0.2 - - - +
658A ILE* 4.2 8.7 - - + -
659A PRO* 1.3 73.7 - - - +
661A ILE* 1.3 61.2 + - - +
662A GLN* 3.2 12.9 + - - +
663A LYS* 2.8 58.2 + - + +
664A ALA 3.2 9.4 + - - -
802A GOL 3.7 6.5 + - - -
801B GOL 2.8 31.6 + - - +
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Residues in contact with ILE 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 3.9 30.5 - - + +
268A VAL* 4.0 32.3 - - + -
269A ILE* 4.2 16.2 - - + -
582A LEU* 3.8 33.4 - - + -
656A TYR* 4.5 12.6 - - + -
659A PRO* 5.0 3.4 - - + -
660A ASP* 1.3 72.8 - - - +
662A GLN* 1.3 63.5 + - - +
664A ALA* 3.4 8.0 + - - +
665A ILE* 3.0 27.3 + - + +
716A ILE* 4.3 9.4 - - + -
802A GOL 3.8 20.0 + - - +
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Residues in contact with GLN 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU 3.6 13.7 - - - +
583A ARG* 2.6 38.5 + - - +
584A GLU 3.6 17.8 + - - -
585A SER 3.7 10.2 - - - +
586A GLY* 3.5 14.8 - - - +
660A ASP* 3.2 9.6 + - - +
661A ILE* 1.3 77.0 - - - +
663A LYS* 1.3 66.6 + - - +
665A ILE* 3.2 7.2 + - - +
666A ILE* 3.0 37.2 + - + +
801A GOL 4.9 4.9 + - - -
802A GOL 3.8 13.0 + - - +
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Residues in contact with LYS 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A TYR* 3.4 42.9 - - + +
658A ILE* 5.1 0.4 - - + -
660A ASP* 2.8 37.3 + - - +
662A GLN* 1.3 78.0 + - + +
664A ALA* 1.3 57.7 + - - +
666A ILE* 3.2 13.6 + - + +
667A ALA* 2.9 29.8 + - - +
637B GLU* 4.5 9.6 - - - -
677B ALA* 5.5 8.4 - - - +
681B ASP* 4.8 5.9 + - - -
801B GOL 3.5 20.6 - - - +
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Residues in contact with ALA 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ALA* 4.2 6.0 - - + +
655A TYR* 3.6 25.7 - - + +
656A TYR* 4.1 34.5 - - + +
660A ASP 3.2 8.1 + - - +
661A ILE* 3.7 11.4 - - - +
663A LYS* 1.3 77.2 - - - +
665A ILE* 1.3 61.4 + - + +
667A ALA* 3.3 3.5 + - - +
668A VAL* 3.1 29.5 + - - +
716A ILE* 5.8 0.7 - - - -
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Residues in contact with ILE 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A TYR* 3.5 28.9 - - + +
582A LEU* 3.7 30.1 - - + -
583A ARG* 3.8 28.0 - - + +
661A ILE* 3.0 17.2 + - + +
662A GLN 3.2 5.6 + - - +
664A ALA* 1.3 72.2 - - - +
666A ILE* 1.3 66.9 + - - +
668A VAL* 3.3 4.0 + - - -
669A PHE* 3.0 33.1 + - + -
713A LEU* 4.5 6.1 - - + -
716A ILE* 3.6 35.4 - - + -
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Residues in contact with ILE 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ARG* 3.6 42.8 - - - +
662A GLN* 3.0 31.6 + - + +
663A LYS* 3.2 13.4 + - + +
665A ILE* 1.3 76.3 - - - +
667A ALA* 1.3 58.9 + - - +
669A PHE* 3.4 4.4 + - - +
670A ASP* 2.9 50.1 + - - +
673A ARG* 4.9 4.3 - - - +
801A GOL 5.4 2.7 - - - +
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Residues in contact with ALA 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A LEU* 3.8 15.8 - - + +
651A THR* 3.9 27.8 - - + -
652A ALA* 5.1 1.6 - - - +
655A TYR* 4.2 8.7 - - + -
663A LYS 2.9 16.1 + - - +
664A ALA* 3.7 5.6 - - - +
665A ILE 3.2 0.2 - - - -
666A ILE* 1.3 78.1 - - - +
668A VAL* 1.3 62.5 + - - +
670A ASP* 3.4 20.3 - - - +
671A VAL* 3.4 6.4 + - - +
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Residues in contact with VAL 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A LEU* 4.0 19.5 - - + -
652A ALA* 4.4 5.6 - - + -
656A TYR* 6.1 0.9 - - + -
664A ALA 3.1 17.5 + - - +
665A ILE 3.9 3.4 - - - +
667A ALA* 1.3 76.4 - - - +
669A PHE* 1.3 57.3 + - - +
671A VAL* 2.9 20.4 + - - +
672A LEU* 3.0 12.5 + - + +
709A THR* 3.6 38.1 - - + +
712A LEU* 4.0 25.8 - - + +
713A LEU* 3.6 26.5 - - + -
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Residues in contact with PHE 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A TYR* 3.5 32.1 - + - -
583A ARG* 6.2 1.3 - - - +
605A GLU* 3.4 44.0 - - + -
606A LEU* 4.2 11.9 - - + -
609A THR* 4.1 13.2 - - + -
610A LEU* 4.4 5.2 - - + -
665A ILE* 3.0 29.5 + - + +
666A ILE* 4.0 4.0 - - - +
668A VAL* 1.3 73.3 - - - +
670A ASP* 1.3 59.8 + - - +
672A LEU* 3.5 24.4 - - + +
673A ARG* 2.8 50.4 + - - +
713A LEU* 3.8 28.7 - - + -
717A LEU* 5.4 0.2 - - + -
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Residues in contact with ASP 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU* 5.6 0.2 - - - +
666A ILE* 2.9 32.3 + - - +
667A ALA* 3.4 14.0 - - - +
668A VAL 3.2 0.4 - - - -
669A PHE* 1.3 76.2 - - - +
671A VAL* 1.3 62.8 + - + +
673A ARG* 2.7 37.9 + - - +
674A ALA* 3.3 19.8 + - - +
670B ASP* 5.3 5.7 - - - +
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Residues in contact with VAL 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 5.0 1.3 - - + -
644A LEU* 4.0 31.9 - - + +
645A ILE* 4.2 19.5 - - + +
648A LEU* 3.9 20.4 - - + -
667A ALA 3.4 10.5 + - - +
668A VAL 2.9 9.8 + - - +
670A ASP* 1.3 76.3 - - + +
672A LEU* 1.3 60.3 + - - +
674A ALA* 3.2 6.2 + - - +
675A ILE* 2.9 43.5 + - + +
709A THR* 3.9 11.7 - - + -
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Residues in contact with LEU 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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609A THR* 3.6 13.0 - - + -
610A LEU* 4.0 31.4 - - + -
613A LEU* 3.8 22.1 - - + +
668A VAL* 3.0 13.0 + - + +
669A PHE* 3.1 45.0 + - + +
671A VAL* 1.3 77.0 - - - +
673A ARG* 1.3 62.5 + - - +
675A ILE* 3.2 8.8 + - + +
676A ASN* 3.1 27.2 + - - -
706A VAL* 5.0 2.2 - - - -
709A THR* 3.2 30.5 - - + +
713A LEU* 4.2 9.9 - - + -
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Residues in contact with ARG 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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605A GLU* 4.9 9.9 - - - +
609A THR* 4.4 18.3 + - + +
666A ILE* 4.1 7.1 + - - +
669A PHE* 2.8 33.9 + - - +
670A ASP* 2.7 42.9 + - - +
672A LEU* 1.3 76.5 - - - +
674A ALA* 1.3 61.2 + - - +
676A ASN* 3.2 8.2 + - - +
677A ALA* 3.0 21.9 + - - +
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Residues in contact with ALA 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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641A LEU* 4.1 8.0 - - + +
644A LEU* 3.7 29.8 - - + -
670A ASP 3.3 9.1 + - - +
671A VAL 3.2 10.0 + - - +
673A ARG* 1.3 78.4 - - - +
675A ILE* 1.3 56.3 + - - +
677A ALA* 3.1 9.1 + - - +
678A TYR* 2.8 29.8 + - - +
655B TYR* 5.7 0.7 - - - +
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Residues in contact with ILE 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 3.4 22.7 - - + -
641A LEU* 3.8 28.7 - - + -
645A ILE* 4.8 0.9 - - + -
671A VAL* 2.9 36.8 + - + +
672A LEU* 3.2 19.2 + - + +
674A ALA* 1.3 75.5 - - - +
676A ASN* 1.3 56.8 + - - +
678A TYR* 3.2 4.0 + - - +
679A VAL* 2.9 29.1 + - + +
702A THR* 4.4 25.4 - - + +
705A GLY* 3.8 33.9 - - - +
706A VAL 4.2 0.9 - - - +
709A THR* 4.3 0.2 - - + -
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Residues in contact with ASN 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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608A ASP 4.2 3.5 - - - +
609A THR* 3.0 37.6 + - - +
612A ASN* 3.2 14.0 - - - +
613A LEU* 3.3 15.9 - - - +
616A ARG* 3.2 22.7 + - - +
672A LEU 3.1 23.2 + - - -
673A ARG* 3.5 9.2 - - - +
675A ILE* 1.3 75.6 - - - +
677A ALA* 1.3 57.0 + - - +
679A VAL* 3.1 3.9 + - - +
680A THR* 2.9 33.0 + - - -
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Residues in contact with ALA 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A ARG 3.0 11.7 + - - +
674A ALA* 3.3 12.6 - - - +
676A ASN* 1.3 73.2 - - - +
678A TYR* 1.3 68.5 + - - +
680A THR* 3.2 7.2 + - - -
681A ASP* 3.0 31.6 + - - +
663B LYS* 5.8 8.5 - - - +
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Residues in contact with TYR 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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637A GLU* 4.0 24.0 - - + -
638A ASP* 2.4 46.9 + - - -
641A LEU* 3.3 34.1 - - + -
674A ALA 2.8 13.2 + - - +
675A ILE* 3.3 9.4 - - + +
677A ALA* 1.3 77.2 - - - +
679A VAL* 1.3 65.5 + - + +
681A ASP* 3.2 5.1 + - - +
682A MET* 3.0 47.1 + - + +
698A VAL* 3.5 39.3 - - + +
701A ILE* 3.6 20.3 - - + +
702A THR* 4.4 2.9 - - - -
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Residues in contact with VAL 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 4.5 4.3 - - + -
616A ARG* 3.8 37.0 - - + +
675A ILE* 2.9 22.6 + - + +
676A ASN* 3.1 6.0 + - - +
678A TYR* 1.3 78.9 - - + +
680A THR* 1.3 58.9 + - - +
682A MET* 4.7 1.8 - - - -
683A ALA* 2.8 26.5 + - - -
684A PRO* 3.2 24.3 - - + +
685A TRP* 4.1 2.7 - - + -
698A VAL* 5.2 3.6 - - + -
702A THR* 3.4 35.0 - - + +
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Residues in contact with THR 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ARG* 4.1 15.8 + - - -
676A ASN* 2.9 15.4 + - - +
677A ALA* 3.6 9.9 - - - +
679A VAL* 1.3 73.4 - - - +
681A ASP* 1.3 71.0 + - - +
682A MET 3.3 0.3 + - - -
683A ALA* 3.4 13.7 + - - +
685A TRP* 4.3 14.3 - - + -
434B ARG* 5.1 1.6 + - - -
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Residues in contact with ASP 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU* 3.1 28.9 - - - +
677A ALA* 3.0 19.2 + - - +
678A TYR 3.4 9.0 - - - +
680A THR* 1.3 79.9 - - - +
682A MET* 1.3 66.0 + - + +
429B PRO* 5.8 3.5 - - - +
430B GLU* 3.4 14.2 + - + +
431B PHE* 4.8 1.6 + - - +
434B ARG* 3.0 24.8 + - - -
587B PHE* 6.0 2.3 - - - -
663B LYS* 4.6 8.7 + - - -
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Residues in contact with MET 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU* 3.4 44.4 - - + +
678A TYR* 3.0 32.5 + - + +
679A VAL 4.1 2.5 - - - +
681A ASP* 1.3 86.6 - - + +
683A ALA* 1.3 72.5 + - - +
684A PRO* 3.1 1.5 - - + -
687A LEU* 3.4 17.5 - - + +
694A ARG* 3.8 25.1 - - - +
698A VAL* 3.9 28.7 - - + -
430B GLU* 3.9 33.1 - - + +
434B ARG* 4.3 5.6 + - - -
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Residues in contact with ALA 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A VAL 2.8 12.6 + - - -
680A THR 3.4 6.6 + - - +
682A MET* 1.3 80.0 - - - +
684A PRO* 1.3 58.2 - - - +
685A TRP* 3.1 32.1 - - + +
686A LYS* 2.8 34.3 + - + +
687A LEU* 3.3 6.4 + - - +
434B ARG* 4.0 23.8 - - - +
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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