Contacts of the helix formed by residues 696 - 721 (chain A) in PDB entry 1T65
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 SER 696 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A PRO 3.6 5.2 + - - -
695A ASP* 1.3 75.9 - - - +
697A PHE* 1.3 63.7 + - - +
698A ALA* 3.8 5.7 + - - +
699A ALA* 3.2 25.5 + - - +
700A LEU* 2.7 33.4 + - - +
777A LYS* 3.4 13.5 - - - +
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Residues in contact with PHE 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A SER* 1.3 73.5 - - - +
698A ALA* 1.3 67.7 + - - +
700A LEU* 3.9 2.4 - - - -
701A LEU* 3.0 44.3 + - + +
777A LYS* 3.3 33.7 - - - +
778A SER 3.3 20.6 - - - -
779A ARG* 3.5 57.7 - - + +
876A PHE* 4.5 5.8 - + - -
880A LEU* 4.0 18.4 - - + -
883A LYS* 6.0 2.5 - - - -
887A VAL* 4.0 20.4 - - + -
889A VAL* 3.9 18.2 - - + -
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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
----------------------------------------------------------
696A SER* 3.3 5.5 + - - +
697A PHE* 1.3 81.5 - - + +
699A ALA* 1.3 57.7 + - - +
701A LEU* 4.0 1.0 - - - +
702A SER* 2.8 34.8 + - - -
887A VAL 3.8 11.7 - - - +
888A SER* 3.6 24.9 - - - +
889A VAL* 4.2 11.9 - - - +
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Residues in contact with ALA 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A HIS* 4.1 14.1 - - + +
693A GLN* 6.4 1.6 - - + -
694A PRO 5.7 2.5 - - - +
696A SER* 3.2 19.5 + - - +
698A ALA* 1.3 75.4 - - - +
700A LEU* 1.3 69.6 + - + +
702A SER* 3.9 5.1 - - - -
703A SER* 3.1 29.3 + - - -
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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
----------------------------------------------------------
689A HIS* 4.1 22.4 - - + +
695A ASP* 3.9 14.8 - - + +
696A SER 2.7 44.5 + - - +
697A PHE* 3.9 3.6 - - - +
699A ALA* 1.3 82.4 - - + +
701A LEU* 1.3 63.9 + - + +
703A SER* 3.4 2.6 + - - -
704A LEU* 3.1 31.9 + - - +
768A LEU* 4.3 5.2 - - + +
770A PHE* 3.9 33.2 - - + -
774A ARG* 4.0 26.0 - - + +
777A LYS* 5.4 6.7 - - + -
778A SER* 5.4 3.4 - - - -
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Residues in contact with LEU 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A PHE* 3.0 49.7 + - + +
700A LEU* 1.3 78.4 - - + +
702A SER* 1.3 66.7 + - - +
704A LEU* 3.3 8.0 + - + +
705A ASN* 3.0 29.2 + - - -
778A SER* 3.7 24.0 - - - +
780A MET* 3.5 25.1 - - + -
876A PHE* 4.2 0.9 - - + -
880A LEU* 3.7 22.0 - - + -
889A VAL* 4.0 19.5 - - + -
931A DHT 4.0 15.3 - - + -
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Residues in contact with SER 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A ALA 2.8 24.1 + - - -
699A ALA* 3.9 5.8 - - - -
701A LEU* 1.3 76.3 - - - +
703A SER* 1.3 58.0 - - - +
705A ASN* 3.4 4.3 + - - +
706A GLU* 3.0 26.7 + - - +
888A SER 4.1 2.3 + - - -
889A VAL* 3.8 4.3 - - - +
890A ASP* 3.2 47.6 + - - +
892A PRO* 5.6 0.2 - - - +
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Residues in contact with SER 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ALA* 4.1 8.5 - - - +
688A GLY 5.0 0.9 - - - -
689A HIS* 2.7 49.8 + - - +
699A ALA 3.1 11.5 + - - -
700A LEU 3.7 4.0 - - - -
702A SER* 1.3 75.3 - - - +
704A LEU* 1.3 64.6 + - - +
706A GLU* 3.2 7.2 + - - +
707A LEU* 2.9 24.3 + - - +
768A LEU* 4.4 10.1 - - - -
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Residues in contact with LEU 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A LEU 3.1 21.4 + - - +
701A LEU* 3.3 13.9 + - + +
703A SER* 1.3 76.2 - - - +
705A ASN* 1.3 57.9 + - - +
707A LEU* 3.3 7.1 + - + +
708A GLY 2.9 23.0 + - - -
764A PHE* 3.8 36.8 - - + -
768A LEU* 3.7 22.2 - - + -
770A PHE* 3.9 21.5 - - + -
780A MET* 4.0 27.1 - - + -
931A DHT 3.4 34.7 - - + +
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Residues in contact with ASN 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A LEU 3.0 12.0 + - - -
702A SER 3.6 4.7 - - - +
703A SER 3.2 0.2 - - - -
704A LEU* 1.3 77.0 - - - +
706A GLU* 1.3 56.9 + - - +
708A GLY* 3.2 2.1 + - - -
709A GLU* 3.1 23.0 + - - +
880A LEU* 4.9 0.4 - - - +
889A VAL* 3.4 23.6 - - - +
890A ASP 2.9 29.3 + - - +
891A PHE* 3.6 24.6 - - - -
892A PRO* 3.8 11.5 - - + +
895A MET* 3.8 13.4 - - + +
931A DHT 2.8 36.1 + - - +
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Residues in contact with GLU 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ALA 3.8 12.8 - - - +
702A SER 3.0 16.5 + - - +
703A SER* 3.7 7.0 - - - +
705A ASN* 1.3 72.9 - - - +
707A LEU* 1.3 66.5 + - - +
709A GLU* 3.2 6.9 + - - +
710A ARG* 2.8 70.8 + - - +
892A PRO* 3.8 21.0 - - + +
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 4.0 28.3 - - + +
686A CYS 4.1 11.0 - - - +
687A ALA* 3.9 11.4 + - + +
703A SER 2.9 16.8 + - - +
704A LEU* 3.6 6.1 - - + +
706A GLU* 1.3 77.1 - - - +
708A GLY* 1.3 57.6 + - - +
710A ARG* 3.3 3.5 + - - -
711A GLN* 2.8 59.0 + - + +
764A PHE* 3.5 39.7 - - + +
765A ALA* 4.1 4.5 - - + -
768A LEU* 4.3 7.9 - - + -
931A DHT 4.0 14.8 - - + -
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Residues in contact with GLY 708 (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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704A LEU 2.9 14.3 + - - -
705A ASN 3.2 4.2 + - - -
706A GLU 3.1 0.4 - - - -
707A LEU* 1.3 78.6 - - - +
709A GLU* 1.3 55.8 + - - +
711A GLN* 3.3 5.2 + - - +
712A LEU* 2.9 29.8 + - - +
745A MET* 3.9 9.1 - - - +
895A MET* 4.0 19.5 - - - +
931A DHT 4.2 13.9 - - - +
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Residues in contact with GLU 709 (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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705A ASN 3.1 12.9 + - - +
706A GLU* 3.2 14.8 + - - +
708A GLY* 1.3 76.2 - - - +
710A ARG* 1.3 61.6 + - + +
712A LEU* 3.4 17.1 + - - +
713A VAL* 3.5 13.0 + - + +
892A PRO* 3.3 25.2 - - + +
893A GLU* 3.8 5.0 + - - +
894A MET* 3.1 41.0 + - + +
895A MET* 3.0 35.1 + - - +
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Residues in contact with ARG 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 3.9 12.8 - - + -
686A CYS* 2.9 33.7 + - - +
687A ALA 3.6 18.8 + - - -
688A GLY* 3.7 9.1 - - - +
706A GLU* 2.8 50.1 + - - +
707A LEU* 3.8 4.3 - - - +
709A GLU* 1.3 74.5 - - + +
711A GLN* 1.3 64.3 + - - +
713A VAL* 3.3 15.1 + - - +
714A HIS* 3.1 23.6 + - + -
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Residues in contact with GLN 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 4.1 16.3 - - + +
707A LEU* 2.8 38.7 + - + +
708A GLY 3.9 2.9 - - - +
710A ARG* 1.3 73.3 - - - +
712A LEU* 1.3 61.3 + - - +
714A HIS* 3.1 9.3 + - - +
715A VAL* 2.9 33.3 + - + +
745A MET* 3.5 30.8 + - + +
748A ALA* 5.9 1.0 - - - +
752A ARG* 3.5 28.4 + - - +
764A PHE 3.9 1.4 - - - +
931A DHT 3.3 29.1 + - - +
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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
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708A GLY 2.9 17.6 + - - +
709A GLU* 3.5 9.2 - - - +
710A ARG 3.2 0.2 - - - -
711A GLN* 1.3 78.3 - - - +
713A VAL* 1.3 62.1 + - - +
715A VAL* 3.4 4.6 + - + +
716A VAL* 3.1 35.2 + - + +
737A ILE* 4.7 14.1 - - + -
741A TRP* 4.1 22.2 - - + -
745A MET* 3.7 17.4 - - + +
894A MET* 3.7 37.7 - - + -
895A MET* 5.3 6.3 - - - +
898A ILE* 3.8 28.3 - - + -
923B LEU* 4.8 4.5 - - + -
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Residues in contact with VAL 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A GLU* 3.6 15.0 - - + +
710A ARG* 3.3 11.2 + - - +
711A GLN 3.2 0.6 - - - -
712A LEU* 1.3 77.8 - - - +
714A HIS* 1.3 68.6 + - + +
716A VAL* 3.4 5.7 + - - +
717A LYS* 3.3 47.1 + - + +
894A MET* 4.1 15.0 - - + -
925B ARG* 5.1 10.5 - - - +
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Residues in contact with HIS 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A PRO* 4.2 27.7 - - + +
683A GLY 5.0 6.1 - - - -
684A VAL 5.1 3.2 + - - -
685A VAL* 3.7 32.2 - - + +
710A ARG* 3.1 24.5 + - + -
711A GLN* 3.1 9.0 + - - +
713A VAL* 1.3 82.7 - - + +
715A VAL* 1.3 61.8 + - + +
717A LYS* 3.4 11.9 + - + +
718A TRP* 2.9 30.9 + - - +
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Residues in contact with VAL 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A PRO* 5.6 2.0 - - + -
711A GLN* 2.9 23.5 + - + +
712A LEU* 3.7 9.6 - - + +
714A HIS* 1.3 78.2 - - + +
716A VAL* 1.3 56.6 + - - +
718A TRP* 3.6 14.8 - - + +
719A ALA* 2.9 30.5 + - + +
737A ILE* 4.6 18.6 - - + -
741A TRP* 5.4 2.9 - - + -
744A LEU* 4.2 27.8 - - + -
745A MET* 4.1 25.4 - - + -
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Residues in contact with VAL 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A LEU* 3.1 21.1 + - + +
713A VAL* 3.8 6.7 - - - +
714A HIS 3.3 0.2 - - - -
715A VAL* 1.3 78.5 - - - +
717A LYS* 1.3 63.3 + - + +
719A ALA* 3.9 1.2 - - - +
720A LYS* 3.0 33.7 + - + +
737A ILE* 4.3 24.7 - - + -
894A MET* 6.4 1.3 - - - -
923B LEU* 4.2 26.2 - - + -
925B ARG* 3.3 27.4 - - + +
926B LEU* 4.1 12.6 - - - -
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Residues in contact with LYS 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A VAL* 3.3 34.2 + - + +
714A HIS* 3.8 13.7 - - + +
716A VAL* 1.3 77.8 - - + +
718A TRP* 1.3 63.7 + - - +
720A LYS* 3.7 18.9 + - - +
721A ALA* 3.5 18.7 + - - +
925B ARG* 2.9 38.2 - - - +
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Residues in contact with TRP 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A LEU* 5.3 2.6 + - + +
680A ILE* 3.6 46.6 - - + +
681A GLU* 4.1 2.6 + - - -
682A PRO* 3.8 22.7 - - + -
714A HIS 2.9 18.7 + - - +
715A VAL* 3.6 17.9 - - + +
717A LYS* 1.3 75.1 - - - +
719A ALA* 1.3 77.5 + - + +
721A ALA* 3.0 17.4 + - - +
722A LEU* 3.4 34.8 + - + +
744A LEU* 4.0 26.9 - - + -
805A LEU 5.5 0.9 - - - -
808A LYS* 3.7 34.9 - - + +
809A ALA* 3.9 31.4 - - + -
812A LEU* 4.3 9.4 - - + -
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Residues in contact with ALA 719 (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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715A VAL* 2.9 19.0 + - + +
716A VAL 3.9 3.4 - - - +
718A TRP* 1.3 87.0 - - + +
720A LYS* 1.3 62.5 + - - +
721A ALA 3.1 1.4 + - - -
722A LEU* 3.1 18.9 + - - +
725A PHE* 3.1 23.3 - - + +
737A ILE* 4.1 22.2 - - + -
812A LEU* 4.0 22.0 - - + -
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Residues in contact with LYS 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A VAL* 3.0 28.8 + - + +
717A LYS* 3.9 18.7 - - - +
718A TRP 3.3 0.2 - - - -
719A ALA* 1.3 75.5 - - + +
721A ALA* 1.3 58.7 + - - +
722A LEU 3.4 1.1 + - - +
725A PHE* 3.8 24.6 - - + +
726A ARG* 4.6 22.8 + - - +
733A GLN* 5.1 3.6 - - - +
737A ILE* 5.7 1.3 - - + -
925B ARG* 3.4 23.6 + - - +
926B LEU 3.5 28.6 + - - -
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Residues in contact with ALA 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A VAL* 4.2 5.4 - - - +
680A ILE* 3.9 32.6 - - + +
717A LYS 3.5 10.7 + - - +
718A TRP* 3.0 11.6 + - - +
720A LYS* 1.3 76.4 - - - +
722A LEU* 1.3 63.9 + - - +
723A PRO* 3.7 3.5 - - - +
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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