Contacts of the helix formed by residues 817 - 839 (chain D) in PDB entry 1S77
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 ILE 817 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446D LEU* 3.4 23.3 - - + -
448D LYS 3.6 21.8 - - - +
450D LYS* 3.2 44.6 - - + +
530D CYS 4.0 3.1 - - - +
531D SER* 3.8 14.1 - - - -
532D LEU 3.7 2.5 - - - -
534D LEU* 4.5 0.2 - - - -
806D SER* 4.3 6.5 - - - +
816D THR* 1.3 81.2 - - + +
818D PRO* 1.3 74.2 - - + +
819D ALA* 4.0 3.6 - - + +
820D ASP* 2.9 42.2 + - - +
821D ALA* 3.0 9.4 + - - -
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Residues in contact with PRO 818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D ILE* 3.5 16.6 - - + -
455D GLU* 4.7 1.0 - - - +
456D GLY* 3.2 35.8 + - - +
459D TRP* 5.0 0.2 - - - -
460D LEU* 4.7 1.8 - - + -
530D CYS* 3.8 33.9 - - - +
532D LEU 3.4 12.8 - - - +
534D LEU* 3.4 32.3 - - + -
816D THR 3.9 0.2 - - - -
817D ILE* 1.3 88.5 - - + +
819D ALA* 1.3 61.3 + - - +
820D ASP 3.1 1.0 + - - -
821D ALA* 3.1 14.8 + - + +
822D ALA 4.5 1.2 + - - -
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Residues in contact with ALA 819 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D LYS* 4.0 30.2 - - + +
451D PRO 3.7 23.6 - - - +
452D ILE* 4.0 10.4 + - - +
455D GLU* 6.2 0.6 - - - +
456D GLY* 4.2 1.8 - - - +
530D CYS 5.5 0.4 + - - +
817D ILE* 3.2 4.5 + - + +
818D PRO* 1.3 79.5 - - - +
820D ASP* 1.3 63.6 + - - +
822D ALA* 5.1 3.4 + - - +
823D ASN* 5.2 3.6 + - - -
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Residues in contact with ASP 820 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D LYS* 2.7 35.1 + - - -
802D TYR 5.7 0.6 - - - +
804D ILE* 4.1 26.5 - - + +
805D GLU* 4.8 2.6 + - - +
806D SER* 5.4 1.0 + - - -
816D THR* 3.6 26.6 - - + +
817D ILE* 2.9 15.7 + - - +
819D ALA* 1.3 82.8 - - - +
821D ALA* 1.3 66.3 + - - +
822D ALA 3.2 2.9 - - - -
823D ASN* 3.0 16.1 + - + +
824D LEU* 3.0 19.4 + - - +
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Residues in contact with ALA 821 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D TRP* 3.7 28.0 - - + -
534D LEU* 4.1 13.0 - - + +
536D PHE* 3.2 24.8 - - + -
816D THR* 4.7 2.7 - - - -
817D ILE 3.0 10.4 + - - +
818D PRO 3.1 14.3 + - - +
820D ASP* 1.3 76.2 - - - +
822D ALA* 1.3 63.3 + - - +
824D LEU* 3.2 4.1 + - - -
825D PHE* 2.8 20.4 + - - +
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Residues in contact with ALA 822 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D GLU* 3.2 42.4 - - + +
459D TRP* 3.8 15.2 - - + +
818D PRO 4.5 1.4 + - - +
819D ALA 5.6 3.4 - - - +
820D ASP 3.1 1.2 + - - -
821D ALA* 1.3 78.4 - - - +
823D ASN* 1.3 61.7 + - - +
825D PHE* 3.0 21.9 - - - +
826D LYS* 3.2 13.6 + - - +
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Residues in contact with ASN 823 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D TYR* 3.3 52.2 + - + +
804D ILE* 4.0 5.7 - - + +
820D ASP* 3.0 19.0 + - - +
822D ALA* 1.3 76.4 - - - +
824D LEU* 1.3 66.8 + - - +
825D PHE 3.0 1.6 - - - -
826D LYS* 3.2 14.7 - - - +
827D ALA* 2.9 26.8 + - - +
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Residues in contact with LEU 824 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536D PHE* 4.3 10.3 - - + -
794D THR* 4.3 14.1 - - + -
798D ALA* 4.0 23.3 - - + -
804D ILE* 3.9 5.8 - - + +
807D PHE* 4.2 13.7 - - + -
814D PHE* 3.5 19.3 - - + +
815D GLY* 3.4 33.4 - - - +
816D THR* 2.7 30.3 - - - +
820D ASP 3.0 8.9 + - - +
821D ALA 3.7 7.9 - - - +
823D ASN* 1.3 76.4 - - - +
825D PHE* 1.3 58.2 + - - +
827D ALA* 4.2 1.1 - - - -
828D VAL* 3.0 32.3 + - + +
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Residues in contact with PHE 825 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D TRP* 3.4 37.7 - + + -
475D PHE* 4.3 2.9 - + - -
536D PHE* 3.8 21.5 - + + -
821D ALA 2.8 12.9 + - - +
822D ALA* 3.0 18.4 - - - +
824D LEU* 1.3 78.1 - - - +
826D LYS* 1.3 62.9 + - + +
828D VAL* 3.4 9.5 - - - +
829D ARG* 2.7 68.9 + - - +
876D LEU 5.6 2.5 - - - -
878D SER 4.7 1.3 - - - -
879D ASP* 3.5 25.1 - - - -
882D PHE* 4.1 8.1 - + - -
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Residues in contact with LYS 826 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D TYR* 2.9 38.4 - - + +
822D ALA 3.2 5.1 + - - +
823D ASN* 3.2 30.5 - - - +
825D PHE* 1.3 81.2 - - + +
827D ALA* 1.3 54.3 + - - +
829D ARG* 2.9 11.8 + - - +
830D GLU* 2.6 48.6 + - + +
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Residues in contact with ALA 827 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794D THR* 4.1 5.6 - - + -
797D TRP* 4.1 8.1 - - + -
798D ALA* 4.0 24.2 - - + +
802D TYR* 3.9 14.6 - - + -
823D ASN 2.9 18.1 + - - +
824D LEU* 3.7 4.0 - - - +
826D LYS* 1.3 75.3 - - - +
828D VAL* 1.3 67.3 + - - +
830D GLU* 4.0 11.2 - - - -
831D THR* 2.9 29.2 + - - +
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Residues in contact with VAL 828 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536D PHE* 5.7 4.5 - - + -
790D HIS* 2.9 34.2 + - - +
794D THR* 3.6 14.9 - - + +
814D PHE* 3.5 33.0 - - + -
824D LEU* 3.0 19.5 + - + +
825D PHE* 3.4 17.0 - - - +
827D ALA* 1.3 73.1 - - - +
829D ARG* 1.3 66.2 + - - +
831D THR* 3.2 0.7 + - - -
832D MET* 3.4 3.6 + - - +
882D PHE* 2.6 26.0 - - - +
883D ALA* 3.3 26.3 - - - +
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Residues in contact with ARG 829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825D PHE* 2.7 66.5 + - - +
826D LYS* 2.9 10.1 + - - +
828D VAL* 1.3 82.7 - - - +
830D GLU* 1.3 64.3 + - + +
832D MET* 3.2 8.7 + - - +
833D VAL* 3.1 25.5 + - - +
875D ILE* 3.3 31.8 + - + +
876D LEU* 3.9 20.2 - - + -
878D SER 2.7 19.2 + - - -
879D ASP 3.1 24.5 + - - -
881D ALA* 4.3 1.6 - - - +
882D PHE* 2.6 47.8 + - - +
883D ALA 4.6 2.2 - - - +
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Residues in contact with GLU 830 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797D TRP* 2.8 42.1 + - + +
802D TYR* 2.6 30.9 + - - -
826D LYS* 2.6 44.3 + - + +
827D ALA* 3.1 3.7 + - - +
829D ARG* 1.3 73.6 - - - +
831D THR* 1.3 58.4 + - - +
833D VAL* 3.3 2.3 + - - +
834D ASP* 2.8 29.6 + - - +
876D LEU* 4.0 19.8 - - + +
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Residues in contact with THR 831 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790D HIS* 2.7 22.5 - - - -
793D LYS* 3.6 20.0 - - + +
794D THR* 2.6 28.4 + - - -
797D TRP* 3.5 43.1 - - + -
827D ALA 2.9 13.5 + - - +
828D VAL 3.2 2.3 + - - -
830D GLU* 1.3 76.2 - - - +
832D MET* 1.3 59.9 + - - +
834D ASP* 4.1 5.8 - - - +
835D THR* 2.8 33.0 + - - -
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Residues in contact with MET 832 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D GLN* 4.2 28.3 - - + +
545D HIS* 4.0 21.8 - - + +
548D ALA* 5.0 2.9 - - + -
561D LEU* 5.1 5.4 - - + -
790D HIS* 3.7 21.8 - - - +
828D VAL 3.5 10.5 - - - +
829D ARG* 3.2 13.2 + - - +
831D THR* 1.3 84.4 + - - +
833D VAL* 1.3 60.5 + - - +
835D THR* 3.8 1.5 - - - -
836D TYR* 3.3 50.8 + - + +
875D ILE* 4.0 27.2 - - + +
883D ALA* 3.3 19.5 - - - +
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Residues in contact with VAL 833 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829D ARG 3.1 8.8 + - - +
830D GLU* 3.7 3.6 - - - +
832D MET* 1.3 79.1 - - - +
834D ASP* 1.3 66.6 + - - +
835D THR 3.2 0.2 - - - -
836D TYR 4.0 0.2 - - - -
837D GLU* 2.9 53.8 + - + +
872D LEU* 3.0 31.6 - - - +
873D ARG* 4.1 16.8 - - - +
875D ILE* 3.7 12.6 - - + -
876D LEU* 3.3 31.6 - - + -
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Residues in contact with ASP 834 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793D LYS* 5.7 3.6 + - + -
797D TRP* 3.4 32.7 - - + -
830D GLU 2.8 20.1 + - - +
831D THR* 4.1 2.7 - - - +
833D VAL* 1.3 74.5 - - - +
835D THR* 1.3 58.5 + - - +
837D GLU* 3.6 3.1 - - - +
838D SER* 2.8 42.2 + - - -
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Residues in contact with THR 835 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730D PRO* 4.0 30.3 - - + -
786D GLN* 5.2 0.7 - - - +
790D HIS* 5.2 7.8 + - + -
793D LYS* 3.2 28.7 - - + +
831D THR 2.8 20.8 + - - -
832D MET* 3.8 4.3 - - - -
834D ASP* 1.3 77.3 - - - +
836D TYR* 1.3 75.5 + - + +
838D SER* 3.1 3.7 + - - -
839D CYS* 2.7 39.0 + - + +
841D VAL* 5.4 0.2 - - + -
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Residues in contact with TYR 836 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545D HIS* 2.6 45.5 + + - +
548D ALA* 3.4 26.4 - - + +
549D MET* 3.6 36.9 - - + +
551D ARG* 3.4 12.1 + - - -
786D GLN* 3.7 19.2 + - - +
790D HIS* 5.8 1.6 - - + -
832D MET* 3.3 35.7 + - - +
835D THR* 1.3 91.2 - - + +
837D GLU* 1.3 57.8 + - - +
839D CYS 3.6 14.7 - - - +
841D VAL* 4.2 21.5 - - + -
872D LEU* 3.1 26.9 - - + +
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Residues in contact with GLU 837 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D ARG* 4.1 11.6 + - - +
833D VAL* 2.9 33.4 + - - +
834D ASP* 3.9 3.4 - - - +
836D TYR* 1.3 78.5 - - - +
838D SER* 1.3 60.0 + - - +
839D CYS 5.4 0.4 - - - -
871D ASN* 5.0 3.8 + - - -
872D LEU* 3.9 15.9 + - + +
873D ARG* 2.7 49.5 + - - -
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Residues in contact with SER 838 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834D ASP* 2.8 33.3 + - - -
835D THR* 3.7 2.2 - - - -
837D GLU* 1.3 82.0 - - - +
839D CYS* 1.3 66.5 + - - +
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Residues in contact with CYS 839 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D MET* 6.0 0.5 - - - -
730D PRO* 4.1 27.4 - - + -
793D LYS* 6.2 0.9 - - - -
835D THR* 2.7 20.0 + - - +
836D TYR* 3.6 23.4 - - - +
837D GLU 3.7 0.2 - - - -
838D SER* 1.3 86.4 - - - +
840D ASP* 1.3 60.9 + - - +
841D VAL* 3.5 17.4 + - + +
844D ASP* 3.9 11.9 - - - +
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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
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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) + - + + + + + -
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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