Contacts of the helix formed by residues 880 - 918 (chain D) in PDB entry 6UZA
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 ASN 880 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875C GLU 3.6 15.6 + - - -
876C SER* 3.7 24.6 + - - +
877C ASP 3.3 14.6 - - - +
878C GLU* 4.2 1.3 - - - +
879C VAL* 4.0 9.6 - - - +
878D GLU 3.6 4.9 + - - +
879D VAL* 1.3 85.1 - - - +
881D GLU* 1.3 63.7 + - - +
882D GLY* 3.4 2.5 + - - -
883D GLU* 3.1 38.7 + - - +
884D LEU* 4.0 3.5 + - - +
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Residues in contact with GLU 881 (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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874C LYS* 3.1 32.0 - - - +
875C GLU* 4.2 10.3 + - + +
877C ASP* 2.8 28.3 + - - +
878C GLU 5.1 1.2 - - - +
879C VAL* 4.6 6.7 - - - +
883C GLU* 3.3 36.6 - - - +
880D ASN* 1.3 74.0 - - - +
882D GLY* 1.3 58.2 + - - +
883D GLU 3.4 1.0 + - - -
884D LEU* 4.0 5.1 + - - +
885D LYS* 3.9 17.0 + - - +
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Residues in contact with GLY 882 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875C GLU* 3.4 36.9 + - - -
171D LYS* 5.6 3.3 + - - -
173D TYR* 5.1 4.5 + - - -
880D ASN* 3.2 3.1 + - - -
881D GLU* 1.3 77.3 - - - +
883D GLU* 1.3 62.9 + - - +
884D LEU 3.6 0.4 - - - -
885D LYS* 4.2 12.9 + - - +
886D GLU* 4.3 11.1 + - - +
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Residues in contact with GLU 883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A GLU* 3.3 41.7 - - - +
884A LEU* 3.3 19.3 - - + +
878D GLU 5.5 0.2 - - - -
879D VAL* 3.4 27.2 - - + +
880D ASN* 3.1 24.5 + - - +
881D GLU 3.4 0.2 - - - -
882D GLY* 1.3 80.3 - - - +
884D LEU* 1.3 58.9 + - - +
885D LYS 3.4 0.7 - - - -
886D GLU* 3.8 20.1 + - - +
887D ILE* 3.4 11.8 - - - +
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Residues in contact with LEU 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A LEU* 3.8 24.0 - - + +
879C VAL* 3.8 28.7 - - + -
883C GLU* 3.3 34.3 - - + +
884C LEU* 3.8 24.9 - - + +
887C ILE* 3.9 16.7 - - + +
879D VAL* 5.5 1.6 - - + -
880D ASN 4.0 9.5 + - - +
881D GLU* 4.0 7.1 + - - +
883D GLU* 1.3 74.8 - - - +
885D LYS* 1.3 60.9 + - - +
886D GLU 3.2 1.8 - - - -
887D ILE* 3.2 10.9 + - + +
888D LYS* 3.0 25.6 + - - +
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Residues in contact with LYS 885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875C GLU* 3.3 28.6 + - - +
142D ALA 3.1 26.7 + - - -
143D ASN* 3.7 21.3 + - - +
171D LYS* 4.3 11.9 - - - +
173D TYR* 4.9 4.0 + - - -
881D GLU 3.9 14.4 + - - +
882D GLY* 4.4 11.5 + - - +
883D GLU 3.4 0.4 - - - -
884D LEU* 1.3 79.2 - - - +
886D GLU* 1.3 58.6 + - - +
888D LYS* 3.3 12.4 + - + +
889D GLN* 2.9 48.2 + - + +
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Residues in contact with GLU 886 (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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888A LYS* 2.8 39.0 + - - +
143D ASN 4.9 4.0 - - - +
144D GLU* 3.6 27.8 - - + +
173D TYR* 3.7 25.6 + - - +
882D GLY 4.3 6.3 + - - +
883D GLU* 3.8 22.3 + - - +
884D LEU 3.2 0.4 - - - -
885D LYS* 1.3 82.9 - - + +
887D ILE* 1.3 58.7 + - + +
889D GLN* 3.4 5.5 + - - +
890D ASP* 3.0 34.2 + - - +
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Residues in contact with ILE 887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A LEU* 3.9 28.3 - - + +
887A ILE* 4.8 10.3 - - + -
888A LYS* 3.7 39.9 - - + +
891A ILE* 3.7 24.2 - - + -
887C ILE* 4.8 9.0 - - + -
883D GLU 3.4 18.8 - - - +
884D LEU* 3.2 13.0 + - + +
886D GLU* 1.3 76.3 - - + +
888D LYS* 1.3 64.8 + - - +
890D ASP* 3.2 5.8 + - + +
891D ILE* 3.0 36.1 + - + +
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Residues in contact with LYS 888 (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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144C GLU* 3.3 19.0 + - - -
886C GLU* 2.8 37.4 + - - +
887C ILE* 3.7 16.5 - - + +
890C ASP* 2.9 33.1 + - - +
884D LEU 3.0 14.0 + - - +
885D LYS* 3.3 15.7 + - + +
887D ILE* 1.3 77.0 - - - +
889D GLN* 1.3 69.4 + - - +
891D ILE* 3.3 8.7 + - - +
892D SER* 3.0 27.0 + - - -
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Residues in contact with GLN 889 (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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107D GLU* 3.4 20.3 - - - +
108D TYR* 3.7 29.8 - - - +
143D ASN* 3.8 35.0 + - + +
145D HIS* 3.6 14.9 + - + -
885D LYS* 2.9 39.4 + - + +
886D GLU 3.9 2.2 - - - +
888D LYS* 1.3 86.5 - - - +
890D ASP* 1.3 61.8 + - - +
892D SER* 3.7 7.1 - - - -
893D SER* 3.0 30.8 + - - -
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Residues in contact with ASP 890 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LYS* 2.9 36.2 + - - +
891A ILE* 4.5 18.6 - - + +
144D GLU* 3.2 24.0 - - - +
145D HIS* 5.7 0.6 + - - -
886D GLU 3.0 19.2 + - - +
887D ILE* 3.2 13.5 + - - +
889D GLN* 1.3 78.6 - - - +
891D ILE* 1.3 58.0 + - - +
893D SER* 3.9 4.0 - - - -
894D LEU* 3.0 29.3 + - - +
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Residues in contact with ILE 891 (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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891A ILE* 3.8 26.7 - - + -
887C ILE* 3.7 31.0 - - + +
890C ASP* 4.5 22.0 - - + +
891C ILE* 3.8 25.4 - - + -
894C LEU* 4.1 22.3 - - + +
887D ILE* 3.0 17.4 + - + +
888D LYS* 3.3 5.8 + - - +
890D ASP* 1.3 75.5 - - - +
892D SER* 1.3 56.8 + - - +
894D LEU* 3.4 7.3 + - + +
895D ARG* 2.9 28.2 + - + +
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Residues in contact with SER 892 (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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175C ARG* 4.9 6.1 + - - -
108D TYR* 3.0 24.0 + - - +
888D LYS* 3.0 18.1 + - - -
889D GLN* 3.7 13.5 - - - -
890D ASP 3.3 0.4 - - - -
891D ILE* 1.3 77.0 - - - +
893D SER* 1.3 61.2 + - - +
895D ARG* 3.3 9.9 + - - +
896D TYR* 3.1 36.0 + - - -
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Residues in contact with SER 893 (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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895A ARG* 5.3 2.4 + - - -
108D TYR 4.5 0.6 + - - -
109D GLY* 3.7 19.9 - - - +
111D ILE* 3.6 21.9 - - - +
145D HIS* 4.2 16.2 - - - -
147D GLU* 3.8 8.1 + - - -
889D GLN 3.0 17.2 + - - -
890D ASP* 3.9 4.7 - - - -
892D SER* 1.3 76.5 - - - +
894D LEU* 1.3 63.2 + - - +
896D TYR* 3.4 1.7 + - - +
897D GLU* 3.0 28.6 + - - +
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Residues in contact with LEU 894 (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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891A ILE* 4.1 26.5 - - + +
894A LEU* 4.6 20.0 - - + -
895A ARG* 3.7 38.8 - - + +
898A LEU* 5.3 0.9 - - + -
899A LEU* 5.7 0.9 - - + -
894C LEU* 4.6 14.8 - - + -
890D ASP 3.0 18.7 + - - +
891D ILE* 3.7 6.7 - - + +
892D SER 3.3 0.2 - - - -
893D SER* 1.3 77.0 + - - +
895D ARG* 1.3 57.1 + - - +
897D GLU* 3.9 6.5 - - + +
898D LEU* 3.0 62.0 + - + +
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Residues in contact with ARG 895 (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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147C GLU* 3.7 34.7 + - - +
893C SER* 5.3 2.1 + - - -
894C LEU* 3.7 32.8 - - + +
897C GLU* 3.0 37.8 + - - +
891D ILE* 2.9 19.0 + - + +
892D SER* 3.3 8.7 + - - +
894D LEU* 1.3 77.0 - - - +
896D TYR* 1.3 95.5 + - - +
898D LEU* 4.1 0.6 - - - +
899D LEU* 3.0 42.0 + - + +
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Residues in contact with TYR 896 (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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175C ARG* 3.4 28.7 + - - -
108D TYR* 3.6 28.2 - - + +
109D GLY 4.0 3.1 - - - +
110D ASN* 3.8 53.3 - - + +
111D ILE 5.0 0.2 - - - +
112D PRO* 4.6 4.5 - - + +
892D SER* 3.1 30.2 + - - +
893D SER 3.9 4.3 - - - +
895D ARG* 1.3 101.1 + - - +
897D GLU* 1.3 62.5 + - - +
899D LEU* 4.0 3.8 - - + +
900D GLU* 3.1 26.0 + - - +
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Residues in contact with GLU 897 (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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895A ARG* 3.0 41.4 + - - +
899A LEU* 3.6 25.0 - - + +
111D ILE* 3.6 28.2 - - + +
112D PRO* 4.8 6.0 - - + +
115D ARG* 4.7 16.9 + - - +
147D GLU* 5.2 0.2 - - - +
893D SER* 3.0 19.0 + - - +
894D LEU* 3.9 5.0 - - + +
896D TYR* 1.3 76.8 - - - +
898D LEU* 1.3 58.8 + - + +
900D GLU* 3.5 6.5 + - - +
901D GLU* 3.0 29.9 + - + +
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Residues in contact with LEU 898 (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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898A LEU* 3.7 40.2 - - + +
899A LEU* 3.9 22.9 - - + -
902A LYS* 5.8 2.7 - - + -
894C LEU* 5.3 2.2 - - + -
898C LEU* 3.7 37.4 - - + +
894D LEU* 3.0 42.6 + - + +
895D ARG* 4.1 2.0 - - - +
897D GLU* 1.3 73.0 - - - +
899D LEU* 1.3 62.4 + - - +
901D GLU* 3.3 5.9 + - + +
902D LYS* 3.0 29.3 + - - +
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Residues in contact with LEU 899 (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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894C LEU* 5.7 0.7 - - + -
897C GLU* 3.6 43.1 - - + +
898C LEU* 3.9 23.8 - - + -
901C GLU* 4.8 9.9 - - + -
895D ARG* 3.0 48.4 + - + +
896D TYR* 4.1 4.7 - - + +
898D LEU* 1.3 75.3 - - - +
900D GLU* 1.3 58.6 + - - +
902D LYS* 3.4 4.1 + - + +
903D SER* 3.0 28.6 + - - -
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Residues in contact with GLU 900 (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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112D PRO* 3.4 37.5 - - + +
115D ARG* 4.4 9.8 + - - -
896D TYR 3.1 18.7 + - - +
897D GLU* 4.0 4.9 - - - +
899D LEU* 1.3 77.9 - - - +
901D GLU* 1.3 61.6 + - - +
903D SER* 2.9 23.1 + - - +
904D GLN* 2.9 37.5 + - - +
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Residues in contact with GLU 901 (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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899A LEU* 4.8 9.9 - - + -
902A LYS* 4.7 20.2 - - + +
897D GLU 3.0 18.3 + - - +
898D LEU* 3.7 8.3 - - + +
900D GLU* 1.3 82.2 + - - +
902D LYS* 1.3 58.2 + - - +
904D GLN* 3.9 5.1 - - - +
905D ASN* 3.0 31.1 + - - +
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Residues in contact with LYS 902 (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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898C LEU* 5.8 2.9 - - + -
901C GLU* 4.7 22.0 - - + +
905C ASN* 5.6 2.8 - - - +
898D LEU 3.0 17.4 + - - +
899D LEU* 3.8 8.3 - - + +
901D GLU* 1.3 76.8 - - - +
903D SER* 1.3 57.0 + - - +
905D ASN* 3.4 5.5 + - - +
906D THR* 3.0 29.5 + - - -
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Residues in contact with SER 903 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899D LEU 3.0 14.3 + - - -
900D GLU* 2.9 23.9 + - - +
902D LYS* 1.3 76.7 - - - +
904D GLN* 1.3 58.8 + - - +
906D THR* 3.4 5.8 + - - -
907D GLU* 2.9 30.5 + - - +
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Residues in contact with GLN 904 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900D GLU* 2.9 36.0 + - - +
901D GLU* 3.9 6.3 - - - +
903D SER* 1.3 78.9 + - - +
905D ASN* 1.3 56.6 + - - +
907D GLU* 3.4 10.1 + - - +
908D ASP* 2.9 34.9 + - + +
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Residues in contact with ASN 905 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902A LYS* 5.6 4.0 - - + +
906A THR* 4.8 20.4 - - - -
901D GLU 3.0 18.1 + - - +
902D LYS* 3.8 5.2 - - - +
904D GLN* 1.3 78.1 - - - +
906D THR* 1.3 57.9 + - - +
908D ASP* 3.4 5.2 + - - +
909D LEU* 3.0 30.7 + - - +
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Residues in contact with THR 906 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905C ASN* 4.8 19.7 - - - +
908C ASP* 6.5 0.7 - - - -
902D LYS 3.0 18.0 + - - -
903D SER* 3.8 6.3 - - - -
905D ASN* 1.3 76.5 - - - +
907D GLU* 1.3 57.9 + - - +
909D LEU* 3.5 5.4 + - - +
910D ALA* 2.9 31.0 + - - +
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Residues in contact with GLU 907 (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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903D SER 2.9 18.5 + - - +
904D GLN* 3.8 12.8 - - - +
905D ASN 3.3 0.2 - - - -
906D THR* 1.3 77.6 - - - +
908D ASP* 1.3 56.4 + - - +
910D ALA* 3.4 4.9 + - - +
911D GLU* 2.9 30.7 + - - +
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Residues in contact with ASP 908 (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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906A THR* 6.5 0.9 - - - -
904D GLN* 2.9 23.4 + - + +
905D ASN* 3.9 4.9 - - - +
907D GLU* 1.3 75.5 - - - +
909D LEU* 1.3 59.4 + - - +
911D GLU* 3.4 4.8 + - - +
912D LEU* 3.0 39.5 + - + +
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Residues in contact with LEU 909 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A LEU* 5.8 8.5 - - + -
909C LEU* 5.8 7.4 - - + -
905D ASN 3.0 18.9 + - - +
906D THR* 3.9 4.9 - - - +
908D ASP* 1.3 77.2 - - - +
910D ALA* 1.3 57.4 + - - +
912D LEU* 3.5 4.0 + - - +
913D ILE* 2.9 38.7 + - + +
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Residues in contact with ALA 910 (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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912C LEU* 4.4 21.0 - - + +
906D THR 2.9 19.4 + - - +
907D GLU* 3.9 5.6 - - - +
909D LEU* 1.3 76.1 - - - +
911D GLU* 1.3 57.8 + - - +
913D ILE* 3.4 0.9 + - - +
914D ARG* 2.9 30.5 + - - +
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Residues in contact with GLU 911 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907D GLU 2.9 18.3 + - - +
908D ASP* 3.9 5.6 - - - +
910D ALA* 1.3 77.9 - - - +
912D LEU* 1.3 62.8 + - + +
914D ARG* 3.3 17.2 + - - +
915D GLU* 3.0 31.2 + - - +
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Residues in contact with LEU 912 (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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910A ALA* 4.4 24.0 - - + +
913A ILE* 3.7 40.9 - - + +
914A ARG* 5.3 2.7 - - + +
908D ASP* 3.0 24.5 + - + +
909D LEU* 4.2 4.5 - - - +
911D GLU* 1.3 81.3 - - + +
913D ILE* 1.3 61.7 + - - +
915D GLU* 4.1 8.1 - - + +
916D LEU* 3.8 16.3 + - - +
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Residues in contact with ILE 913 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A ILE* 3.7 28.5 - - + -
912C LEU* 3.7 47.6 - - + +
913C ILE* 3.7 26.7 - - + -
916C LEU* 4.6 8.8 - - + +
909D LEU* 2.9 24.4 + - + +
910D ALA 4.0 2.7 - - - +
912D LEU* 1.3 79.3 - - - +
914D ARG* 1.3 59.8 + - - +
915D GLU 3.3 0.4 - - - -
916D LEU* 3.3 12.1 + - + +
917D GLY* 2.9 25.5 + - - -
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Residues in contact with ARG 914 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912C LEU* 5.3 2.7 - - + +
910D ALA 2.9 18.8 + - - +
911D GLU* 3.3 18.1 + - - +
913D ILE* 1.3 78.3 - - - +
915D GLU* 1.3 84.9 + - - +
916D LEU 3.1 0.2 - - - -
917D GLY* 3.7 2.5 - - - +
918D GLU* 3.0 48.5 + - + +
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Residues in contact with GLU 915 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911D GLU 3.0 17.0 + - - +
912D LEU* 4.4 9.2 - - + +
913D ILE 3.3 0.2 - - - -
914D ARG* 1.3 96.8 - - - +
916D LEU* 1.3 56.8 + - - +
918D GLU* 4.3 5.6 + - - +
919D LYS* 3.7 24.6 + - - +
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Residues in contact with LEU 916 (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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913A ILE* 4.6 12.1 - - + +
916A LEU* 3.1 35.7 - - + +
917A GLY* 4.0 23.3 - - - +
920A LEU* 4.9 13.0 - - + -
916C LEU* 3.1 43.1 - - + -
912D LEU 3.8 14.8 + - - +
913D ILE* 3.3 10.8 + - + +
914D ARG 3.1 0.4 - - - -
915D GLU* 1.3 76.0 - - - +
917D GLY* 1.3 61.4 + - - +
918D GLU 3.3 1.6 - - - -
919D LYS* 3.4 21.2 + - + +
920D LEU* 3.6 17.6 - - + +
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Residues in contact with GLY 917 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916C LEU* 4.0 14.5 - - - +
919C LYS* 5.5 5.7 - - - -
913D ILE 2.9 16.9 + - - -
914D ARG* 3.2 4.0 + - - -
916D LEU* 1.3 72.1 - - - +
918D GLU* 1.3 58.3 + - - +
919D LYS 3.2 7.1 + - - -
920D LEU* 4.0 15.3 + - - +
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Residues in contact with GLU 918 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914D ARG* 3.0 42.0 + - + +
915D GLU* 4.7 5.6 - - - +
916D LEU 3.3 0.8 - - - -
917D GLY* 1.3 78.1 - - - +
919D LYS* 1.3 60.7 + - + +
920D LEU 3.7 3.1 - - - -
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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
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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