Contacts of the helix formed by residues 697 - 721 (chain A) in PDB entry 2RD0
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 MET 697 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PRO* 3.9 32.1 - - + +
299A MET* 3.4 50.6 - - + +
301A CYS* 5.0 12.1 - - + -
696A GLY* 1.3 72.3 - - - +
698A TYR* 1.3 66.7 + - - +
700A LYS* 2.9 33.4 + - - +
701A HIS* 3.7 15.3 + - + -
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Residues in contact with TYR 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A MET* 4.8 0.8 - - - +
661A GLN* 3.2 47.3 + - + +
665A HIS* 2.7 47.9 + - + +
691A TYR* 3.9 12.8 - - - -
695A CYS* 4.2 12.7 + - + +
696A GLY* 3.0 1.6 - - - -
697A MET* 1.3 80.0 - - - +
699A LEU* 1.3 64.1 + - - +
701A HIS* 3.1 33.9 + + + -
702A LEU* 2.9 54.7 + - + +
705A GLN* 3.9 6.9 + - - -
752A LEU* 4.4 11.0 - - + -
757A PRO* 3.9 11.3 - - + +
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Residues in contact with LEU 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 4.3 8.5 - - - +
116A GLU* 4.1 19.7 - - - +
117A ILE* 3.7 22.9 - - + +
120A ALA* 4.1 10.1 - - + -
692A CYS* 3.6 42.2 - - + +
695A CYS* 3.7 14.9 - - - -
696A GLY 3.2 14.8 + - - +
697A MET 2.9 1.2 + - - -
698A TYR* 1.3 77.9 - - - +
700A LYS* 1.3 62.1 + - - +
702A LEU* 3.1 11.1 + - + +
703A ASN* 3.0 41.8 + - - +
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Residues in contact with LYS 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 4.6 16.1 + - - +
697A MET* 2.9 23.7 + - - +
699A LEU* 1.3 79.3 - - - +
701A HIS* 1.3 63.4 + - + +
703A ASN* 3.3 29.3 + - + +
704A ARG* 3.3 37.3 + - - +
707A GLU* 3.6 15.0 + - - -
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Residues in contact with HIS 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A GLN* 5.5 1.0 + - - -
697A MET* 3.7 12.9 + - + -
698A TYR* 3.1 40.8 + + + +
700A LYS* 1.3 78.1 - - + +
702A LEU* 1.3 62.8 + - - +
704A ARG* 2.8 52.5 + - - +
705A GLN* 3.1 20.0 + - - +
751A PHE* 5.4 0.5 - - - +
752A LEU* 4.6 20.5 + - + +
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Residues in contact with LEU 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 5.4 1.1 - - + -
665A HIS* 4.3 1.1 - - - +
668A PHE* 3.7 53.4 - - + -
669A TRP* 3.7 18.8 - - + +
691A TYR* 4.1 14.6 - - + -
695A CYS* 5.0 1.1 - - - -
698A TYR* 2.9 49.6 + - + +
699A LEU* 3.5 18.6 - - + +
701A HIS* 1.3 73.2 - - - +
703A ASN* 1.3 59.1 + - - +
705A GLN* 3.1 16.0 - - - +
706A VAL* 2.8 30.1 + - - +
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Residues in contact with ASN 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 4.9 14.4 - - - +
117A ILE 5.0 0.5 + - - +
119A PHE* 2.9 32.4 - - + +
120A ALA* 3.2 17.6 + - - +
699A LEU* 3.0 50.5 + - - +
700A LYS* 3.3 22.3 + - - +
701A HIS 3.2 0.4 - - - -
702A LEU* 1.3 73.5 - - - +
704A ARG* 1.3 58.4 + - - +
706A VAL* 2.9 4.3 + - - +
707A GLU* 2.6 45.5 + - - +
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Residues in contact with ARG 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A LYS* 3.3 42.3 + - - +
701A HIS* 2.8 48.4 + - - +
703A ASN* 1.3 78.3 - - - +
705A GLN* 1.3 62.1 + - - +
707A GLU* 3.4 11.5 + - - +
708A ALA* 2.9 27.0 + - - +
747A ALA 4.3 4.7 - - - +
750A GLY 3.3 23.2 + - - -
751A PHE* 4.0 15.3 - - + +
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Residues in contact with GLN 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A HIS* 2.8 35.5 + - - -
669A TRP* 3.2 15.5 + - + -
698A TYR* 4.0 10.3 + - - -
701A HIS* 3.1 26.7 + - - +
702A LEU* 3.1 16.5 - - - +
704A ARG* 1.3 76.5 - - - +
706A VAL* 1.3 58.0 + - - +
708A ALA* 3.5 2.6 - - - +
709A MET* 3.0 34.2 + - - +
751A PHE* 4.3 9.3 - - + +
752A LEU* 3.7 32.7 + - - +
754A PRO* 3.5 24.3 - - + +
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Residues in contact with VAL 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.4 38.8 - - + +
120A ALA* 4.3 3.1 - - - +
668A PHE* 3.9 19.1 - - + -
669A TRP* 3.6 28.5 - - + -
672A LYS* 4.1 15.5 - - - +
702A LEU 2.8 20.1 + - - +
703A ASN* 2.9 6.0 + - - +
705A GLN* 1.3 74.4 - - - +
707A GLU* 1.3 58.5 + - - +
709A MET* 3.2 4.2 + - - +
710A GLU* 2.9 37.5 + - + +
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Residues in contact with GLU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 5.7 1.0 - - - +
119A PHE* 3.6 26.7 - - + -
700A LYS* 3.6 22.0 + - - -
703A ASN* 2.6 27.7 + - - +
704A ARG* 3.7 10.1 + - - +
706A VAL* 1.3 71.1 - - - +
708A ALA* 1.3 63.3 + - - +
710A GLU* 3.0 16.1 + - - +
711A LYS* 3.0 18.7 + - - +
747A ALA* 4.8 16.4 - - + +
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Residues in contact with ALA 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ARG 2.9 18.2 + - - +
705A GLN 3.5 5.6 - - - +
707A GLU* 1.3 76.5 - - - +
709A MET* 1.3 63.3 + - + +
711A LYS* 3.3 5.2 + - - +
712A LEU* 3.2 21.1 + - - +
747A ALA* 3.6 23.3 + - - +
748A LEU* 3.8 13.2 - - + +
751A PHE* 3.8 31.6 - - + -
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Residues in contact with MET 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A TRP* 4.1 16.4 - - + -
705A GLN 3.0 19.6 + - - +
706A VAL* 3.2 5.4 + - - +
708A ALA* 1.3 76.7 - - - +
710A GLU* 1.3 66.0 - - - +
712A LEU* 3.8 9.5 - - - +
713A ILE* 2.8 33.6 + - - +
751A PHE* 5.4 5.2 - - - -
754A PRO* 4.6 7.6 - - + -
801A PHE* 3.6 15.0 - - + -
841A ILE* 3.3 44.9 - - + -
847A LEU* 3.4 45.3 - - + -
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Residues in contact with GLU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 6.4 1.1 - - - -
119A PHE* 4.8 9.6 - - + -
672A LYS* 5.3 4.0 + - - -
706A VAL* 2.9 30.4 + - + +
707A GLU* 3.0 13.2 + - - +
709A MET* 1.3 80.3 - - - +
711A LYS* 1.3 62.6 + - + +
713A ILE* 3.3 17.9 + - - +
714A ASN* 3.1 22.9 + - - +
841A ILE* 6.0 0.2 - - - +
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Residues in contact with LYS 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY* 3.2 27.3 - - - +
90A CYS 4.5 0.6 + - - -
91A ASP* 2.8 31.2 + - - +
707A GLU* 3.0 15.0 + - + +
708A ALA 3.6 8.1 - - - +
709A MET 3.3 0.2 - - - -
710A GLU* 1.3 73.0 - - + +
712A LEU* 1.3 66.5 - - - +
714A ASN* 3.1 7.5 + - - +
715A LEU* 2.9 24.7 + - - +
743A ASP* 3.5 28.6 + - - -
744A PHE* 3.9 37.9 - - + -
747A ALA* 3.8 17.5 - - + -
748A LEU* 4.3 7.4 - - + -
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Residues in contact with LEU 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A ALA 3.2 5.8 + - - +
709A MET* 3.8 14.4 - - - +
711A LYS* 1.3 79.1 - - - +
713A ILE* 1.3 61.3 + - - +
715A LEU* 4.5 3.6 - - + -
716A THR* 2.8 31.4 + - - +
739A MET* 5.9 1.8 - - + -
744A PHE* 4.9 4.5 - - + -
748A LEU* 3.7 39.3 - - + -
751A PHE* 6.0 1.3 - - + -
779A LEU* 4.5 12.1 - - + -
781A LEU* 3.7 30.3 - - + -
783A TRP* 5.5 1.3 - - + -
801A PHE* 3.5 44.2 - - + -
847A LEU* 5.2 2.2 - - + -
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Residues in contact with ILE 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A MET 2.8 25.7 + - - +
710A GLU* 3.9 18.2 - - - +
711A LYS 3.3 0.4 - - - -
712A LEU* 1.3 74.5 - - - +
714A ASN* 1.3 58.1 + - - +
716A THR* 3.3 6.0 + - - -
717A ASP* 2.9 38.6 + - - +
801A PHE* 3.6 11.9 - - + -
803A ASN* 3.9 17.5 - - - +
841A ILE* 3.9 16.6 - - + +
842A GLY* 6.0 1.6 - - - -
845A VAL* 3.5 29.6 - - + -
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Residues in contact with ASN 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 3.7 16.1 + - - +
9A GLU* 3.4 24.3 + - + +
14A HIS* 2.9 50.1 + - - +
15A LEU* 5.0 2.1 - - - +
710A GLU 3.1 13.8 + - - +
711A LYS* 3.1 7.6 + - - +
713A ILE* 1.3 77.0 - - - +
715A LEU* 1.3 65.4 + - - +
717A ASP* 3.4 6.2 + - - +
718A ILE* 3.3 26.7 + - - +
744A PHE* 6.4 0.2 - - + -
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Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LYS 2.9 15.7 + - - +
712A LEU* 3.8 7.0 - - + +
714A ASN* 1.3 74.4 + - - +
716A THR* 1.3 66.9 + - + +
718A ILE* 2.9 29.0 + - + +
719A LEU* 3.3 19.8 + - + +
734A PHE* 3.8 27.4 - - + -
735A LEU* 3.8 25.8 - - + +
738A GLN* 4.6 8.3 - - + -
739A MET* 4.2 11.9 - - + -
744A PHE* 3.6 34.5 - - + -
779A LEU* 4.4 10.8 - - + -
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Residues in contact with THR 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A LEU 2.8 20.3 + - - +
713A ILE 3.3 1.6 + - - -
715A LEU* 1.3 78.7 - - - +
717A ASP* 1.3 55.3 + - - +
719A LEU* 3.5 10.6 + - - +
720A LYS* 3.0 32.9 + - - +
777A ARG* 4.0 14.3 - - - +
779A LEU* 3.6 36.3 - - + -
801A PHE* 3.5 17.0 - - + +
803A ASN* 2.9 37.3 + - + +
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Residues in contact with ASP 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.7 23.6 - - + -
713A ILE* 2.9 26.8 + - - +
714A ASN* 3.4 15.0 + - - +
715A LEU 3.0 0.2 + - - -
716A THR* 1.3 74.6 + - - +
718A ILE* 1.3 56.7 + - - +
720A LYS* 2.9 7.6 + - - +
721A GLN* 2.7 47.8 + - - +
803A ASN* 2.9 20.2 + - - +
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Residues in contact with ILE 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.8 24.7 + - + -
15A LEU* 3.8 29.4 - - + -
714A ASN* 3.3 26.7 - - - +
715A LEU* 2.9 16.0 + - + +
717A ASP* 1.3 77.6 - - - +
719A LEU* 1.3 63.5 + - - +
721A GLN 3.2 19.2 + - - +
722A GLU* 3.6 25.0 - - + +
724A LYS* 3.3 22.7 - - + +
734A PHE* 3.6 29.2 - - + -
738A GLN* 5.8 0.4 - - + -
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Residues in contact with LEU 719 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LEU* 3.3 24.7 + - + +
716A THR* 3.8 13.0 - - - +
717A ASP 3.2 0.6 - - - -
718A ILE* 1.3 75.4 - - - +
720A LYS* 1.3 62.3 + - - +
724A LYS* 3.6 26.1 - - + +
725A ASP* 3.7 7.6 - - - +
731A GLN* 3.8 35.0 + - + +
734A PHE* 3.5 32.5 - - + -
735A LEU* 4.3 7.0 - - + +
771A ILE* 3.8 28.0 - - + -
777A ARG* 4.2 15.5 - - + +
779A LEU* 4.3 7.2 - - + -
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Residues in contact with LYS 720 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A THR* 3.0 22.8 + - - +
717A ASP* 2.9 8.5 + - - +
719A LEU* 1.3 76.8 - - - +
721A GLN* 1.3 66.1 + - + +
725A ASP* 3.6 15.7 - - - +
776A LYS* 3.1 29.0 - - + +
777A ARG* 4.0 21.8 - - + +
803A ASN* 2.9 40.2 + - + +
804A GLY* 3.4 11.7 - - - -
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Residues in contact with GLN 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.5 23.7 + - - +
717A ASP* 2.7 20.8 + - - +
718A ILE 3.2 4.0 - - - +
719A LEU 4.1 0.2 - - - +
720A LYS* 1.3 89.1 - - + +
722A GLU* 1.3 73.4 + - + +
723A LYS* 2.5 6.6 + - - -
724A LYS 2.7 12.6 + - - -
725A ASP* 4.3 4.2 + - - +
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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