Contacts of the helix formed by residues 832 - 859 (chain C) in PDB entry 1DQ8
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 832 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C ASP* 5.4 2.2 - - - -
652C GLY* 3.2 25.4 - - - -
653C ASP* 2.7 23.2 + - - -
704C LYS* 4.9 0.7 - - - -
831C PRO* 1.3 71.6 - - - +
833C GLU* 1.3 55.9 + - - +
835C ALA* 3.5 3.5 + - - +
836C ARG* 3.0 43.8 + - - +
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Residues in contact with GLU 833 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C LYS* 5.8 1.0 + - - -
827C CYS* 3.9 12.6 - - - -
830C ASN* 3.1 40.1 + - - +
831C PRO 3.3 0.4 - - - -
832C GLY* 1.3 75.0 - - - +
834C ASN* 1.3 63.1 + - - +
836C ARG* 2.7 43.4 + - - +
837C GLN* 3.0 36.8 + - + +
840C ARG* 5.0 8.9 + - - -
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Residues in contact with ASN 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C ASP* 2.8 14.5 + - - +
804C THR* 3.5 8.5 - - - +
822C GLY 4.0 6.3 + - - +
823C VAL* 3.4 36.4 + - - +
824C GLN 3.3 14.6 + - - -
825C GLY 2.8 21.0 + - - +
826C ALA 3.8 10.1 + - - -
827C CYS* 3.8 15.7 - - - +
833C GLU* 1.3 73.5 - - - +
835C ALA* 1.3 59.9 + - - +
837C GLN* 3.4 2.6 + - - +
838C LEU* 3.0 28.8 + - - +
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Residues in contact with ALA 835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C GLY 4.5 0.7 - - - +
653C ASP* 3.1 34.8 + - - +
704C LYS* 4.0 21.1 - - - +
802C ILE* 3.5 10.8 - - - +
803C GLY* 4.2 11.7 - - - -
804C THR* 3.9 10.0 - - - +
832C GLY 3.9 6.5 - - - +
834C ASN* 1.3 72.5 - - - +
836C ARG* 1.3 60.2 + - - +
838C LEU* 3.2 4.4 + - - +
839C ALA* 2.9 24.8 + - - +
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Residues in contact with ARG 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C VAL* 4.0 31.2 - - + +
586C ASP* 3.9 15.6 + - - +
650C ARG* 5.1 9.4 - - - +
704C LYS* 3.9 20.6 - - - +
830C ASN* 4.3 9.7 + - - +
831C PRO 2.9 27.5 + - - -
832C GLY* 3.0 22.5 + - - +
833C GLU* 2.7 48.0 + - - +
834C ASN 3.3 0.2 - - - -
835C ALA* 1.3 76.7 - - - +
837C GLN* 1.3 61.3 + - - +
839C ALA* 3.3 6.2 + - - +
840C ARG* 3.1 30.4 + - - +
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Residues in contact with GLN 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C LEU* 4.6 2.4 - - - +
547C ASP* 5.3 1.8 + - - +
549C LYS* 3.1 27.5 + - - +
551C PHE* 3.5 32.3 - - + -
823C VAL* 3.7 19.3 - - + -
833C GLU* 3.0 29.1 + - + +
834C ASN* 3.6 5.4 - - - +
836C ARG* 1.3 75.2 - - - +
838C LEU* 1.3 63.9 + - - +
840C ARG* 3.1 24.4 + - - +
841C ILE* 3.0 26.7 + - + +
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Residues in contact with LEU 838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760C ILE* 4.7 13.9 - - + -
764C CYS* 4.8 3.1 - - + -
766C GLN* 3.9 10.1 - - - +
802C ILE* 3.5 29.6 - - + -
803C GLY 4.1 1.1 - - - +
804C THR* 3.9 12.3 - - + -
818C LEU* 3.8 24.9 - - + -
821C LEU* 3.6 31.6 - - + -
823C VAL* 4.1 9.2 - - + +
834C ASN 3.0 14.5 + - - +
835C ALA 3.5 8.5 - - - +
837C GLN* 1.3 78.4 - - - +
839C ALA* 1.3 61.7 + - - +
841C ILE* 3.1 11.9 + - + +
842C VAL* 2.9 22.4 + - + +
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Residues in contact with ALA 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704C LYS* 3.7 34.3 - - + -
706C VAL* 4.0 9.6 - - + +
800C ILE* 3.7 22.3 - - + +
802C ILE* 4.2 3.9 - - + +
835C ALA 2.9 13.1 + - - +
836C ARG 3.3 9.6 + - - +
838C LEU* 1.3 76.6 - - - +
840C ARG* 1.3 56.6 + - - +
842C VAL* 3.3 5.3 + - - +
843C CYS* 3.0 27.5 + - - +
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Residues in contact with ARG 840 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C LEU* 3.5 12.2 - - + +
547C ASP* 3.5 20.4 + - - +
549C LYS* 4.2 16.6 - - - +
581C SER* 2.8 49.1 + - - +
582C ARG* 4.1 14.8 - - - +
583C VAL* 3.9 21.9 - - + +
706C VAL* 4.2 11.2 - - + -
833C GLU* 5.0 8.9 + - - -
836C ARG* 3.1 21.3 + - - +
837C GLN* 3.1 25.5 + - - +
839C ALA* 1.3 73.4 - - - +
841C ILE* 1.3 60.3 + - - +
843C CYS* 3.3 2.3 + - - +
844C GLY* 2.8 25.1 + - - -
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Residues in contact with ILE 841 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C LEU* 3.9 3.7 - - + +
546C LEU* 3.8 7.2 - - - -
551C PHE* 3.9 39.3 - - + -
553C VAL* 4.0 21.1 - - + -
760C ILE* 5.0 2.0 - - + -
821C LEU* 4.0 35.9 - - + +
823C VAL* 4.4 1.3 - - + -
837C GLN* 3.0 32.8 + - + +
838C LEU* 3.4 15.5 - - + +
840C ARG* 1.3 74.3 - - - +
842C VAL* 1.3 57.9 + - - +
844C GLY* 3.8 0.3 - - - -
845C THR* 2.7 46.8 + - - +
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Residues in contact with VAL 842 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756C ILE* 4.4 0.5 - - - +
757C VAL* 4.0 29.6 - - + -
760C ILE* 4.1 32.5 - - + -
761C TYR* 4.3 6.3 - - + -
797C MET* 4.4 0.2 - - + -
800C ILE* 4.0 20.0 - - + -
802C ILE* 3.7 23.1 - - + -
838C LEU* 2.9 18.3 + - + +
839C ALA* 3.5 9.4 - - - +
841C ILE* 1.3 76.8 - - - +
843C CYS* 1.3 57.5 + - - +
845C THR* 3.3 1.9 + - - -
846C VAL* 2.8 32.7 + - + +
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Residues in contact with CYS 843 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706C VAL* 3.6 39.7 - - + -
708C CYS* 3.3 19.2 - - + -
795C CYS* 3.5 25.4 - - - +
797C MET* 3.8 32.1 - - - -
800C ILE* 4.3 0.9 - - + -
839C ALA 3.0 11.3 + - - +
840C ARG 3.7 2.2 - - - +
842C VAL* 1.3 76.4 - - - +
844C GLY* 1.3 63.2 + - - +
846C VAL* 3.3 4.0 + - - +
847C MET* 3.0 18.2 + - - +
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Residues in contact with GLY 844 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C LEU* 3.8 23.8 - - - +
546C LEU* 4.7 7.6 - - - -
573C ILE* 4.3 2.4 - - - +
579C ALA* 5.5 0.4 - - - -
708C CYS* 3.7 16.5 - - - -
840C ARG 2.8 15.6 + - - -
841C ILE 3.8 0.9 - - - -
843C CYS* 1.3 75.7 - - - +
845C THR* 1.3 60.6 + - - +
847C MET* 3.3 7.3 + - - +
848C ALA* 3.1 17.0 + - - +
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Residues in contact with THR 845 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C ALA* 5.5 0.2 - - + -
544C LEU* 3.5 14.3 - - - +
553C VAL* 3.6 26.1 - - + +
555C MET* 4.7 2.0 - - - -
566C THR* 3.4 23.7 - - + +
570C CYS* 5.4 2.5 - - - -
756C ILE* 3.4 23.1 - - + +
760C ILE* 3.9 10.8 - - + -
841C ILE 2.7 25.3 + - - -
842C VAL 3.8 1.6 - - - -
844C GLY* 1.3 73.4 - - - +
846C VAL* 1.3 66.5 + - - +
848C ALA* 3.1 7.2 + - + +
849C GLY* 2.9 19.9 + - - -
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Residues in contact with VAL 846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753C ALA* 3.6 34.5 - - + +
756C ILE* 3.9 26.7 - - + +
757C VAL* 4.1 5.8 - - + -
777C CYS* 4.1 8.7 - - - -
795C CYS* 4.4 2.2 - - - -
797C MET* 3.8 30.3 - - + -
842C VAL* 2.8 21.6 + - + +
843C CYS 3.5 5.4 - - - +
845C THR* 1.3 75.5 - - - +
847C MET* 1.3 52.7 + - - +
849C GLY* 3.0 3.1 + - - -
850C GLU* 2.7 47.4 + - + +
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Residues in contact with MET 847 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ILE* 3.9 13.5 - - + -
579C ALA* 3.5 32.8 - - + -
708C CYS* 3.6 23.6 - - - +
709C GLU* 3.6 27.1 - - - -
710C ALA* 3.7 9.0 - - + -
793C ILE* 3.7 35.8 - - + +
794C SER* 4.4 1.1 - - - -
795C CYS* 3.6 16.4 - - - -
843C CYS 3.0 13.8 + - - +
844C GLY 3.5 7.6 - - - +
845C THR 3.2 0.4 - - - -
846C VAL* 1.3 77.6 - - - +
848C ALA* 1.3 62.2 + - - +
850C GLU* 3.3 2.0 + - - +
851C LEU* 3.0 24.8 + - + +
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Residues in contact with ALA 848 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C LEU* 4.7 0.7 - - + -
566C THR* 3.8 8.5 - - + +
569C GLY* 3.3 15.7 - - - -
570C CYS* 3.7 35.9 - - - +
573C ILE* 3.7 18.8 - - + +
844C GLY 3.1 9.5 + - - +
845C THR* 3.1 11.5 + - - +
847C MET* 1.3 75.1 - - - +
849C GLY* 1.3 62.8 + - - +
851C LEU* 3.3 2.4 + - - +
852C SER* 3.2 18.7 + - - -
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Residues in contact with GLY 849 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C SER* 4.4 0.6 + - - -
566C THR* 4.4 11.8 - - - +
752C HIS* 2.9 31.1 - - - -
756C ILE* 4.3 13.2 - - - -
845C THR 2.9 13.8 + - - -
846C VAL 3.4 2.9 - - - -
848C ALA* 1.3 76.6 - - - +
850C GLU* 1.3 61.0 + - - +
851C LEU 3.5 0.2 + - - -
852C SER* 3.5 3.2 + - - -
853C LEU 3.1 14.7 + - - -
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Residues in contact with GLU 850 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736C ASN* 3.9 1.0 + - - -
750C ASN* 3.2 6.1 - - - +
751C ALA* 2.8 25.7 + - - +
752C HIS* 2.8 34.7 + - - -
753C ALA 3.5 5.5 + - - -
779C THR* 2.6 43.7 + - + +
781C MET* 4.8 0.9 - - - -
793C ILE* 4.4 2.0 - - + -
795C CYS* 4.0 4.5 - - - -
846C VAL* 2.7 33.9 + - + +
847C MET* 3.5 7.2 - - - +
849C GLY* 1.3 74.0 - - - +
851C LEU* 1.3 61.1 + - - +
853C LEU* 5.0 0.9 - - - -
854C MET* 2.9 34.0 + - + +
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Residues in contact with LEU 851 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C GLY* 4.1 10.3 - - - +
572C ALA* 4.5 6.3 - - + -
573C ILE* 3.6 35.7 - - + -
712C ILE* 3.7 19.5 - - + -
721C LEU* 4.5 9.0 - - + -
728C MET* 3.3 18.2 - - + +
791C LEU* 3.7 28.5 - - + -
793C ILE* 3.6 30.5 - - + +
847C MET 3.0 12.4 + - - +
848C ALA 3.5 7.6 - - - +
850C GLU* 1.3 76.7 - - - +
852C SER* 1.3 57.9 + - - +
854C MET* 4.8 0.2 - - - -
855C ALA* 2.9 26.6 + - - +
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Residues in contact with SER 852 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 2.9 7.4 + - - -
565C SER* 2.8 42.7 + - - -
568C ARG* 2.9 42.7 + - - +
569C GLY 4.0 3.6 - - - -
721C LEU* 4.3 4.9 - - - -
848C ALA 3.2 9.1 + - - -
849C GLY 4.1 0.7 - - - -
851C LEU* 1.3 77.9 - - - +
853C LEU* 1.3 59.6 + - - +
855C ALA 3.4 0.5 + - - -
856C ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 853 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 3.2 28.9 - - - +
565C SER* 3.9 1.2 + - - -
751C ALA* 3.7 14.8 - - + -
752C HIS* 3.6 41.3 - - + +
849C GLY 3.1 7.1 + - - +
850C GLU 4.4 1.1 - - - +
852C SER* 1.3 73.4 - - - +
854C MET* 1.3 62.6 + - - +
856C ALA* 3.2 2.6 + - + +
857C LEU* 2.8 38.5 + - + +
862C LEU* 3.5 29.6 - - + -
202D MAH 3.6 32.3 - - + +
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Residues in contact with MET 854 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728C MET* 3.6 9.7 - - + +
731C VAL* 3.5 22.3 - - + +
732C ASN* 3.4 45.1 - - + +
735C LYS* 3.8 14.6 - - + -
736C ASN* 3.7 10.1 - - - +
751C ALA* 3.7 26.9 - - + -
781C MET* 3.6 21.1 - - + -
850C GLU* 2.9 26.7 + - + +
851C LEU 3.9 2.2 - - - +
853C LEU* 1.3 76.7 - - - +
855C ALA* 1.3 56.1 + - - +
857C LEU* 3.4 5.0 + - - +
858C ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 855 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C ARG* 3.9 4.9 - - - +
721C LEU* 3.4 42.2 - - + +
723C THR* 3.9 4.0 - - + -
728C MET* 3.3 15.0 - - - -
851C LEU 2.9 19.0 + - - +
852C SER 3.6 4.9 - - - +
854C MET* 1.3 75.6 - - - +
856C ALA* 1.3 64.2 + - - +
858C ALA* 3.3 3.0 + - - +
859C ALA* 3.0 26.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 856 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 3.5 30.5 - - - +
568C ARG* 4.0 6.0 - - - +
852C SER 3.0 16.3 + - - +
853C LEU* 3.2 6.0 + - + +
855C ALA* 1.3 78.0 - - - +
857C LEU* 1.3 56.9 + - - +
859C ALA* 3.8 0.6 - - - -
860C GLY 3.0 7.3 + - - -
861C HIS* 2.7 41.2 + - + -
862C LEU* 3.6 14.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 857 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C VAL* 4.4 4.7 - - + -
735C LYS* 3.5 43.1 - - + +
853C LEU* 2.8 33.9 + - + +
854C MET* 3.9 8.7 - - - +
856C ALA* 1.3 73.4 - - - +
858C ALA* 1.3 63.3 + - - +
860C GLY* 3.3 11.3 + - - -
862C LEU* 3.8 22.0 - - + +
202D MAH 4.0 6.7 - - - +
681D LEU 3.7 13.5 - - - +
682D ALA* 4.2 13.5 - - + -
683D VAL* 3.8 31.0 + - + +
684D SER* 4.0 12.1 - - - +
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Residues in contact with ALA 858 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C THR* 3.5 21.3 - - - +
727C ALA* 4.1 20.4 - - + +
728C MET* 4.3 2.9 - - - +
731C VAL* 3.8 25.2 - - + +
854C MET 3.0 17.5 + - - +
855C ALA* 3.6 4.0 - - - +
857C LEU* 1.3 79.8 - - - +
859C ALA* 1.3 60.1 + - - +
860C GLY 3.5 0.2 + - - -
681D LEU 4.7 2.9 - - - +
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Residues in contact with ALA 859 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721C LEU 5.1 0.2 - - - +
722C LYS* 3.4 26.2 - - + +
723C THR* 4.3 3.3 + - - -
855C ALA 3.0 16.6 + - - +
858C ALA* 1.3 74.8 - - - +
860C GLY* 1.3 61.7 + - - +
861C HIS* 3.4 32.0 + - + +
----------------------------------------------------------
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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