Contacts of the helix formed by residues 673 - 699 (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 ASP 673 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A ALA* 1.3 83.2 - - - +
674A ALA* 1.3 62.3 + - - +
675A SER* 2.3 28.8 + - - -
676A THR* 2.5 36.2 + - - -
677A MET* 3.0 19.8 + - - +
737A ASN* 5.9 0.4 + - - -
194C GLU* 5.4 6.5 + - - +
195C VAL* 6.3 2.9 - - + -
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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
----------------------------------------------------------
673A ASP* 1.3 79.7 - - - +
675A SER* 1.3 65.8 + - - +
677A MET* 2.9 10.2 + - - +
678A LYS* 2.9 35.0 + - + +
722B THR* 5.1 9.1 - - + +
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Residues in contact with SER 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A ASP* 2.3 33.6 + - - -
674A ALA* 1.3 75.4 - - - +
676A THR* 1.3 70.0 + - - -
678A LYS* 2.9 24.5 + - - +
679A GLU* 3.0 16.2 + - - +
737A ASN* 4.8 2.4 + - - -
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Residues in contact with THR 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ALA* 3.9 19.7 - - + +
673A ASP* 2.5 23.9 + - - -
675A SER* 1.3 73.8 + - - +
677A MET* 1.3 56.4 + - - +
679A GLU* 3.2 10.3 + - - +
680A ILE* 2.9 55.0 + - + +
733A SER* 4.8 4.0 - - - -
734A ALA* 4.3 10.5 - - - +
737A ASN* 2.1 49.0 + - + +
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Residues in contact with MET 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ALA* 4.4 18.2 - - + +
673A ASP 3.0 20.2 - - - +
674A ALA 2.9 11.2 + - - +
676A THR* 1.3 76.8 - - - +
678A LYS* 1.3 64.9 + - - +
680A ILE* 4.4 14.4 - - + +
681A THR* 2.9 31.2 + - - +
763A SER 5.1 10.5 - - - +
764A ALA 6.1 0.7 - - - +
804A SER* 5.8 1.3 - - - +
807A ARG* 3.4 37.5 - - + +
722B THR* 3.8 30.7 - - + +
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Residues in contact with LYS 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A ALA* 2.9 28.3 + - + +
675A SER* 2.9 13.2 + - - +
677A MET* 1.3 76.4 - - + +
679A GLU* 1.3 64.2 + - + +
681A THR* 3.9 3.9 - - - -
682A HIS* 2.9 23.9 + - - +
722B THR* 6.0 3.8 - - + -
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Residues in contact with GLU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A SER 3.0 15.9 + - - +
676A THR* 3.6 12.2 - - - +
678A LYS* 1.3 77.8 - - + +
680A ILE* 1.3 60.5 + - + +
682A HIS* 3.1 6.7 + - - +
683A ALA* 2.9 29.0 + - - +
733A SER* 3.8 24.1 + - - +
737A ASN* 5.4 3.1 - - - +
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Residues in contact with ILE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ALA* 5.4 1.6 - - + -
676A THR* 2.9 38.8 + - + +
677A MET* 4.1 18.2 - - + +
679A GLU* 1.3 73.9 - - - +
681A THR* 1.3 66.5 + - - +
683A ALA* 3.2 5.6 + - - +
684A ILE* 3.1 29.2 + - + +
730A ALA* 3.5 32.8 - - + +
733A SER* 4.5 8.1 - - - -
734A ALA* 4.1 19.1 - - + -
763A SER* 5.5 1.3 - - - +
764A ALA* 4.1 27.1 - - + +
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Residues in contact with THR 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A MET* 2.9 20.1 + - - +
678A LYS* 3.9 4.3 - - - -
680A ILE* 1.3 78.6 - - - +
682A HIS* 1.3 52.0 + - - +
684A ILE* 3.5 4.4 + - - +
685A SER* 2.3 44.9 + - - +
807A ARG* 4.0 19.8 + - - -
720B ASN* 5.0 13.5 - - - +
722B THR* 5.7 1.9 - - - +
726B ILE* 6.1 4.2 - - + +
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Residues in contact with HIS 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A LYS 2.9 17.3 + - - +
679A GLU* 3.1 6.9 + - - +
681A THR* 1.3 79.3 - - - +
683A ALA* 1.3 65.1 + - - +
685A SER* 3.1 11.8 - - - -
686A SER* 2.9 31.5 + - - -
689A GLU* 5.9 2.2 + - - -
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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 GLU 2.9 13.1 + - - +
680A ILE* 3.2 10.9 + - - +
682A HIS* 1.3 77.2 + - - +
684A ILE* 1.3 65.2 + - + +
686A SER* 2.6 27.8 + - - -
687A ALA* 3.0 6.0 + - - +
726A ALA* 5.0 5.4 - - + +
729A SER* 4.2 21.5 - - - +
730A ALA* 4.9 12.3 - - + +
733A SER* 6.0 1.6 - - - +
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Residues in contact with ILE 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A ILE* 3.1 24.2 + - + +
681A THR* 4.2 3.4 - - - +
683A ALA* 1.3 78.6 - - + +
685A SER* 1.3 67.0 + - - +
687A ALA* 3.0 9.1 + - + +
688A LYS* 3.0 23.1 + - + +
726A ALA* 5.2 9.0 - - + +
727A ARG* 5.5 1.6 - - - +
730A ALA* 4.8 9.2 - - + -
764A ALA 4.7 1.1 - - - +
765A CYS* 3.6 38.8 - - + -
800A PHE* 3.8 30.1 - - + -
802A GLU* 4.2 22.7 - - + +
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Residues in contact with SER 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A THR* 2.3 34.5 + - - +
682A HIS* 3.1 17.6 - - - -
684A ILE* 1.3 80.9 - - - +
686A SER* 1.3 63.9 + - - +
688A LYS* 3.0 5.9 + - - +
689A GLU* 3.0 33.7 + - - +
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Residues in contact with SER 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A HIS* 2.9 22.1 + - - -
683A ALA* 2.6 24.6 + - - -
685A SER* 1.3 75.6 - - - +
687A ALA* 1.3 62.2 + - - +
689A GLU* 3.3 20.4 + - - +
690A GLN* 2.9 35.5 + - - +
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Residues in contact with ALA 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A ALA 3.0 6.6 + - - +
684A ILE* 3.2 17.0 - - + +
685A SER 3.0 0.2 + - - -
686A SER* 1.3 77.0 + - - +
688A LYS* 1.3 64.7 + - + +
690A GLN* 3.0 22.5 + - - +
691A VAL* 3.0 16.1 + - - +
722A THR* 4.4 3.7 - - + +
723A LEU* 4.4 13.0 - - + -
726A ALA* 3.4 31.9 - - + -
800A PHE* 5.1 2.9 - - + -
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Residues in contact with LYS 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A ILE* 3.0 11.6 + - + +
685A SER* 3.0 8.7 + - - +
687A ALA* 1.3 79.9 - - + +
689A GLU* 1.3 62.5 + - + +
691A VAL* 3.1 8.8 + - - +
692A GLN* 3.0 28.7 + - + +
723A LEU* 5.7 0.7 - - + -
794A SER* 6.0 0.9 - - - -
795A PRO* 4.6 16.3 - - + +
796A GLU* 4.5 28.8 + - - +
800A PHE* 4.6 25.6 - - + -
802A GLU* 4.4 21.9 + - - +
726B ILE* 5.9 1.0 - - - +
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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
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682A HIS* 5.9 2.3 + - - -
685A SER* 3.0 24.4 + - - +
686A SER* 3.3 22.6 + - - +
688A LYS* 1.3 77.1 - - + +
690A GLN* 1.3 64.8 + - + +
692A GLN* 3.1 9.2 + - - +
693A GLU* 3.0 33.9 + - + +
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Residues in contact with GLN 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A SER* 2.9 27.9 + - - +
687A ALA* 3.0 7.7 + - - +
689A GLU* 1.3 75.9 - - + +
691A VAL* 1.3 57.9 + - - +
693A GLU* 3.1 15.7 + - - +
694A ILE* 2.8 39.6 + - + +
722A THR* 3.4 24.8 + - + +
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Residues in contact with VAL 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ALA 3.0 14.2 + - - +
688A LYS 3.1 6.5 + - - +
690A GLN* 1.3 78.0 - - - +
692A GLN* 1.3 63.1 + - - +
694A ILE* 3.1 6.4 + - + +
695A ILE* 3.0 36.1 + - + +
719A VAL* 4.4 25.1 - - + -
722A THR* 4.2 10.3 - - + -
723A LEU* 3.6 28.7 - - + -
793A PHE 5.1 1.8 - - - +
794A SER* 4.7 2.0 - - - -
795A PRO* 3.8 30.3 - - + -
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Residues in contact with GLN 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A LYS* 3.0 15.9 + - + +
689A GLU* 3.1 10.3 + - - +
691A VAL* 1.3 78.3 - - - +
693A GLU* 1.3 58.4 + - + +
695A ILE* 3.5 10.4 + - - +
696A TYR* 2.9 28.6 + - - +
794A SER* 3.4 31.1 + - - -
795A PRO* 6.4 0.4 - - + -
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Residues in contact with GLU 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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689A GLU* 3.0 26.2 + - - +
690A GLN* 3.1 16.9 + - - +
692A GLN* 1.3 77.2 - - + +
694A ILE* 1.3 64.5 + - + +
696A TYR* 3.2 8.5 + - - +
697A LYS* 2.9 41.7 + - - +
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Residues in contact with ILE 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A GLN* 2.8 29.0 + - + +
691A VAL* 3.1 10.3 + - + +
693A GLU* 1.3 76.3 - - + +
695A ILE* 1.3 59.9 + - - +
697A LYS* 3.3 15.7 - - + +
698A ALA* 2.9 24.8 + - - +
703A LEU* 5.1 2.6 - - + +
715A PHE* 4.6 8.1 - - + -
718A GLU* 3.0 48.5 - - + +
719A VAL* 4.4 17.3 - - + -
722A THR* 3.3 28.5 - - + +
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Residues in contact with ILE 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A VAL* 3.0 27.9 + - + +
692A GLN* 4.0 9.2 - - - +
694A ILE* 1.3 73.1 - - + +
696A TYR* 1.3 64.3 + - - +
697A LYS 2.8 6.0 + - - -
698A ALA* 2.8 13.3 + - - +
699A GLN* 2.8 49.7 + - + +
715A PHE* 3.5 25.1 - - + -
719A VAL* 5.6 0.7 - - + -
793A PHE* 3.6 39.0 - - + +
794A SER* 4.2 6.5 - - - +
99I LEU* 5.7 0.7 - - + -
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Residues in contact with TYR 696 (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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692A GLN 2.9 18.6 + - - +
693A GLU* 3.2 9.2 + - - +
695A ILE* 1.3 76.2 - - - +
697A LYS* 1.3 60.2 + - + +
699A GLN* 5.6 0.4 - - - -
700A HIS* 2.6 73.4 + + + +
702A GLU* 4.4 8.0 - - - +
73I LYS* 5.4 8.2 - - - -
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Residues in contact with LYS 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A GLU* 2.9 34.8 + - - +
694A ILE* 3.3 16.1 - - + +
695A ILE 2.8 1.0 + - - -
696A TYR* 1.3 76.7 - - + +
698A ALA* 1.3 58.9 + - + +
700A HIS* 2.7 24.6 + - - +
701A ASN 3.1 0.5 + - - -
702A GLU* 3.1 46.2 + - + +
703A LEU* 4.6 17.7 - - + +
718A GLU* 5.8 1.1 - - - +
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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
----------------------------------------------------------
694A ILE 2.9 11.5 + - - +
695A ILE 2.8 6.8 + - - +
697A LYS* 1.3 76.1 - - - +
699A GLN* 1.3 57.7 + - + +
701A ASN* 2.8 21.5 + - - -
703A LEU* 3.8 28.7 - - + +
711A LEU* 4.8 18.6 - - + +
715A PHE* 3.8 29.2 - - + -
97I MET* 5.2 5.4 - - - +
98I THR* 5.4 1.7 - - - +
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Residues in contact with GLN 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A ILE* 2.8 40.1 + - + +
698A ALA* 1.3 72.9 - - + +
700A HIS* 1.3 59.1 + - - +
701A ASN 3.4 0.7 - - - -
715A PHE* 5.7 0.9 - - + -
791A ASP* 5.1 4.9 + - - +
793A PHE* 3.7 32.9 - - - -
85I PHE* 5.0 1.6 - - - -
87I GLN* 5.4 3.4 - - - +
97I MET* 3.4 40.4 + - + +
98I THR* 4.2 3.7 - - - -
99I LEU* 3.2 47.2 + - + +
112I ASP* 2.9 23.7 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il