Contacts of the helix formed by residues 686 - 709 (chain A) in PDB entry 6CNB
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 686 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A ILE 4.5 0.2 - - - +
682A LEU* 3.0 22.4 + - - +
684A ASP 3.5 2.4 + - - -
685A TYR* 1.3 84.9 - - - +
687A PRO* 1.3 77.3 - - - +
688A GLN 3.4 2.7 + - - -
689A GLU* 3.5 8.3 + - - +
690A ALA 3.6 5.7 + - - -
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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
----------------------------------------------------------
538A LYS* 3.0 39.9 - - + +
539A ASN* 3.1 26.9 - - - +
541A LEU* 5.3 1.1 - - + -
682A LEU* 3.2 19.0 - - + -
686A GLY* 1.3 81.7 - - - +
688A GLN* 1.3 62.1 + - + +
690A ALA* 2.5 27.6 + - + -
691A ALA* 3.0 12.3 + - - +
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Residues in contact with GLN 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A LYS* 3.3 34.3 - - + +
686A GLY 3.4 1.2 + - - -
687A PRO* 1.3 81.9 - - + +
689A GLU* 1.3 59.6 + - - +
691A ALA* 4.5 1.6 - - - +
692A ASN* 3.4 24.7 + - - +
695A ASN* 6.1 0.6 - - - +
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Residues in contact with GLU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ILE 4.7 1.2 - - - +
620A SER* 4.7 6.8 - - - -
621A PRO* 5.3 10.5 - - + +
622A VAL* 3.4 38.5 - - + +
681A ILE* 4.4 6.5 - - + -
685A TYR* 4.5 13.7 + - + +
686A GLY 3.5 8.8 + - - +
687A PRO 2.7 4.0 + - - -
688A GLN* 1.3 76.3 - - - +
690A ALA* 1.3 68.7 + - - +
692A ASN* 3.0 21.3 + - - +
693A ALA* 3.0 18.7 + - + +
696A ARG* 4.6 12.6 + - - -
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Residues in contact with ALA 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 4.3 11.7 - - + -
678A PHE* 4.4 8.0 - - - +
681A ILE* 3.8 14.0 - - + +
682A LEU* 3.7 37.7 - - + +
686A GLY 3.6 2.0 + - - -
687A PRO* 2.5 16.5 + - + +
689A GLU* 1.3 72.3 - - - +
691A ALA* 1.3 55.7 + - - +
693A ALA* 2.7 32.8 + - - +
694A MET* 3.2 9.8 + - + +
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Residues in contact with ALA 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 4.1 20.8 - - + +
390A ASP* 5.1 1.3 - - - +
537A VAL* 6.3 0.2 - - + -
538A LYS* 3.9 31.6 - - + -
541A LEU* 4.5 6.0 - - + +
687A PRO 3.0 7.6 + - - +
688A GLN* 4.8 1.8 - - - +
690A ALA* 1.3 76.5 - - - +
692A ASN* 1.3 57.2 + - - +
694A MET* 3.9 16.0 - - + +
695A ASN* 2.9 37.0 + - - +
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Residues in contact with ASN 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLU* 5.0 0.3 - - - +
688A GLN* 3.4 23.9 + - - +
689A GLU* 3.0 29.5 + - - +
690A ALA 3.0 0.6 - - - -
691A ALA* 1.3 74.2 - - - +
693A ALA* 1.3 67.0 + - - +
695A ASN* 3.1 14.0 + - - +
696A ARG* 3.1 50.2 + - - +
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Residues in contact with ALA 693 (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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613A LEU* 4.1 11.0 - - + +
614A ILE* 5.8 4.3 - - + +
678A PHE* 3.6 24.2 - - + -
681A ILE* 4.2 16.6 - - + -
689A GLU* 3.0 10.7 + - + +
690A ALA 2.7 15.5 + - - +
692A ASN* 1.3 69.1 - - - +
694A MET* 1.3 54.8 + - - +
696A ARG* 2.7 39.7 + - - +
697A MET 2.9 9.7 + - - -
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Residues in contact with MET 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 3.5 31.0 - - + -
501A ASN* 6.1 0.2 - - - -
503A CYS* 4.8 12.8 - - - -
541A LEU* 3.4 33.9 - - + -
551A ILE* 3.8 28.7 - - + +
552A ALA* 4.1 8.7 - - - -
678A PHE* 3.3 42.2 - - + -
690A ALA* 3.2 4.6 + - + +
691A ALA* 3.9 10.1 - - - +
693A ALA* 1.3 77.7 - - - +
695A ASN* 1.3 63.8 + - - +
697A MET* 3.1 10.3 + - + +
698A ALA* 2.9 24.1 + - - +
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Residues in contact with ASN 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER* 2.3 33.2 + - - +
389A ILE* 2.5 33.9 + - - +
501A ASN* 4.4 1.4 + - - +
688A GLN* 6.1 0.8 - - - +
691A ALA* 2.9 25.1 + - - +
692A ASN* 3.3 14.2 + - - +
694A MET* 1.3 74.1 - - - +
696A ARG* 1.3 65.5 + - + +
698A ALA* 3.3 6.2 + - - +
699A LYS* 3.0 33.5 + - + +
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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
----------------------------------------------------------
583A MET* 3.4 30.5 - - + +
584A SER* 4.6 5.8 - - - -
588A GLU* 2.8 32.1 + - - -
613A LEU* 3.3 30.6 + - + -
614A ILE 4.3 2.4 + - - -
616A PRO* 3.1 42.2 - - - +
617A ASN* 5.7 2.2 - - - +
620A SER* 5.7 1.6 - - - -
689A GLU* 4.6 10.3 + - - -
692A ASN* 3.4 37.6 + - - +
693A ALA* 2.7 17.2 + - - +
695A ASN* 1.3 70.6 - - + +
697A MET* 1.3 65.5 + - - +
699A LYS* 3.3 1.4 + - - -
700A LEU* 2.9 25.6 + - - +
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Residues in contact with MET 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A CYS* 5.9 1.6 - - - -
553A ALA* 4.7 12.1 - - + -
557A PHE* 4.6 11.2 - - + +
561A SER* 3.0 23.3 - - - +
610A PHE* 3.4 37.7 - - + -
613A LEU* 3.7 12.0 - - + +
669A LEU* 3.6 16.6 - - + -
678A PHE* 3.7 33.2 - - + -
693A ALA 2.9 6.1 + - - -
694A MET* 3.2 10.1 - - + +
696A ARG* 1.3 73.8 - - - +
698A ALA* 1.3 65.1 + - - +
700A LEU* 2.9 8.0 + - - +
701A CYS* 2.9 29.7 + - - +
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Residues in contact with ALA 698 (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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385A PRO* 4.0 19.5 - - - +
501A ASN* 4.1 12.1 - - - +
503A CYS* 5.1 1.3 - - - -
557A PHE* 3.4 34.8 - - + -
694A MET 2.9 14.3 + - - +
695A ASN* 3.5 7.6 - - - +
697A MET* 1.3 75.1 - - - +
699A LYS* 1.3 59.9 + - - +
700A LEU 2.8 7.1 + - - -
702A ALA* 3.0 27.0 + - - +
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Residues in contact with LYS 699 (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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385A PRO 4.5 2.5 - - - +
386A ASN* 3.7 46.8 + - - +
387A LEU 5.7 0.2 - - - +
388A SER* 5.9 1.8 - - - +
582A MET 3.1 18.5 - - - +
583A MET* 3.9 12.3 - - - +
584A SER* 4.6 1.8 - - - +
585A ASP* 3.2 51.0 + - - +
695A ASN* 3.0 30.1 + - + +
696A ARG* 3.6 0.7 - - - -
698A ALA* 1.3 71.6 - - - +
700A LEU* 1.3 58.1 + - - +
702A ALA* 4.7 4.3 - - - -
703A ARG* 3.6 21.3 - - - +
93K ILE 6.1 0.2 - - - -
94K PRO* 5.2 5.6 + - - -
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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
----------------------------------------------------------
561A SER* 6.2 0.2 - - - +
564A ILE* 3.9 22.7 - - + -
579A LEU* 4.1 31.2 - - + +
582A MET* 4.7 3.8 - - + -
583A MET* 3.9 37.9 - - + +
609A VAL* 5.2 10.8 - - + +
610A PHE* 5.1 15.5 - - + -
613A LEU* 5.5 2.0 - - + -
696A ARG 2.9 17.8 + - - +
697A MET* 2.9 6.3 + - - +
698A ALA 2.8 0.8 + - - -
699A LYS* 1.3 76.9 - - - +
701A CYS* 1.3 69.0 + - + +
702A ALA 3.0 1.4 + - - -
703A ARG* 3.2 2.9 + - - +
704A PHE* 2.9 27.0 + - + +
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Residues in contact with CYS 701 (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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556A ASP* 3.2 30.1 - - - -
557A PHE* 3.4 27.6 - - + +
560A GLY* 3.4 23.3 - - - -
561A SER* 3.6 10.3 - - - +
564A ILE* 5.5 1.6 - - + -
697A MET* 2.9 18.8 + - - +
700A LEU* 1.3 77.2 - - + +
702A ALA* 1.3 67.6 + - - +
704A PHE* 4.7 5.8 - - - -
705A LEU* 2.9 29.9 + - - +
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Residues in contact with ALA 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PRO* 3.9 18.6 - - + -
386A ASN* 5.6 1.8 - - - +
556A ASP* 6.5 1.1 - - - -
557A PHE* 4.2 7.0 - - + -
698A ALA 3.0 19.1 + - - +
699A LYS* 4.8 1.3 - - - -
700A LEU 3.0 0.2 + - - -
701A CYS* 1.3 82.0 - - - +
703A ARG* 1.3 68.3 + - + +
704A PHE 3.1 0.3 + - - -
705A LEU* 3.2 8.1 + - - +
706A GLY 3.8 6.1 + - - -
763B SER 2.8 16.8 - - - +
764B GLY* 3.5 26.4 + - - -
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Residues in contact with ARG 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASN* 2.7 45.7 + - - +
582A MET* 3.4 31.9 + - + +
699A LYS* 3.6 24.8 + - - +
700A LEU 3.2 2.4 + - - -
702A ALA* 1.3 81.9 - - + +
704A PHE* 1.3 59.8 + - - +
706A GLY 4.4 0.2 + - - -
707A ASN* 3.6 17.2 + - - +
763B SER 3.7 7.4 - - - +
1008B ILE* 5.2 6.7 - - + +
70K HIS* 5.2 9.3 + - - -
92K SER* 3.7 18.4 + - - +
93K ILE* 2.4 42.2 + - - +
94K PRO 3.8 4.6 + - - -
95K HIS* 4.1 2.6 - - - +
96K PRO* 4.5 6.3 - - - +
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Residues in contact with PHE 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLY 4.5 8.1 - - - -
563A LEU* 5.0 2.5 - - + -
564A ILE* 3.5 36.6 - - + -
571A TYR* 4.2 19.3 - + - -
575A THR* 6.2 1.6 - - + -
579A LEU* 3.5 35.0 - - + -
582A MET* 3.5 6.4 - - + +
700A LEU* 2.9 22.2 + - + +
701A CYS* 4.7 3.6 - - - -
703A ARG* 1.3 78.1 - - - +
705A LEU* 1.3 78.9 + - + +
707A ASN* 3.1 6.6 + - + -
708A ARG* 2.9 60.8 + - + -
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Residues in contact with LEU 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ASP* 3.9 31.6 - - + +
559A THR* 4.6 4.7 - - + -
560A GLY* 3.7 23.3 - - - +
563A LEU* 4.2 19.7 - - + -
701A CYS* 2.9 21.3 + - - +
702A ALA* 3.2 3.8 + - - +
704A PHE* 1.3 88.9 - - + +
706A GLY* 1.3 52.6 + - - +
708A ARG* 3.3 1.4 + - + +
709A GLY* 2.6 38.4 + - - +
710A PHE* 4.6 11.2 - - + -
761B SER* 3.5 32.5 - - - +
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Residues in contact with GLY 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ALA 3.8 7.1 + - - -
703A ARG 4.9 0.9 - - - -
704A PHE 3.3 0.2 - - - -
705A LEU* 1.3 80.3 - - - +
707A ASN* 1.3 61.9 + - - +
708A ARG 3.0 2.9 + - - -
709A GLY* 3.3 8.5 + - - -
760B MET* 4.6 4.9 - - - +
761B SER 3.0 24.0 + - - +
762B TYR* 3.9 20.9 - - - +
763B SER 4.8 0.7 - - - -
1006B SER* 4.2 4.4 + - - -
1013B LEU* 3.6 10.7 - - - +
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Residues in contact with ASN 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A GLN* 4.8 13.5 - - - +
582A MET* 5.0 9.0 - - + +
703A ARG 3.6 18.8 + - - +
704A PHE* 3.1 10.1 + - + +
706A GLY* 1.3 73.2 - - - +
708A ARG* 1.3 56.9 + - - +
1006B SER* 3.7 16.2 + - - +
1008B ILE* 4.3 22.0 - - + +
1009B THR* 2.4 37.4 + - - -
1011B GLU* 4.4 10.9 - - - +
1012B CYS 5.5 0.9 - - - +
1013B LEU* 3.8 9.9 - - - +
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Residues in contact with ARG 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LEU* 3.3 41.8 + - - +
571A TYR* 6.4 0.2 - - - -
704A PHE* 2.9 49.6 + - + +
705A LEU* 3.9 2.7 - - + +
706A GLY 3.5 1.3 - - - -
707A ASN* 1.3 79.1 - - - +
709A GLY* 1.3 70.8 + - - +
710A PHE* 5.1 2.2 - - - -
788A TRP* 3.4 33.5 - - - -
1013B LEU* 3.1 8.4 - - - +
1014B GLN* 3.0 78.9 + - + +
1015B ALA* 4.2 4.9 + - - +
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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
----------------------------------------------------------
563A LEU* 5.0 0.2 - - - +
705A LEU* 2.6 22.6 + - - +
706A GLY 3.3 7.1 + - - -
708A ARG* 1.3 96.6 + - - +
710A PHE* 1.3 64.2 + - - +
760B MET* 4.6 10.8 - - - -
761B SER 4.8 0.2 - - - -
1013B LEU* 4.4 6.7 - - - -
1015B ALA* 3.8 14.0 - - - +
1017B ILE* 5.3 1.8 - - - -
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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