Contacts of the helix formed by residues 872 - 899 (chain A) in PDB entry 2PDA
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 ALA 872 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ALA* 3.5 13.3 - - - +
836A ASN 4.2 1.3 - - - -
837A ALA* 3.3 45.5 - - + +
867A SER* 5.4 0.9 - - - +
868A LEU 4.4 2.4 + - - -
869A PHE 4.1 1.6 + - - -
871A ASP* 1.3 76.3 + - - +
873A ALA* 1.3 57.6 + - - +
875A TYR* 3.3 8.6 - - - +
876A GLY 3.0 21.7 + - - -
959A ILE* 3.5 9.0 - - + +
960A PHE 4.4 0.2 - - - +
965A TRP* 3.4 17.9 - - + +
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Residues in contact with ALA 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ASP 3.3 0.4 - - - -
872A ALA* 1.3 74.5 - - - +
874A GLU* 1.3 61.8 + - - +
875A TYR 2.9 4.3 - - - -
876A GLY* 3.0 3.8 + - - -
877A PHE* 2.9 27.7 + - - +
959A ILE* 3.4 25.3 - - + +
965A TRP* 3.7 21.9 - - + -
974A LEU* 3.9 26.9 - - + +
977A VAL* 3.7 11.8 - - + +
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Residues in contact with GLU 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A GLU 3.6 7.5 - - - +
871A ASP* 3.0 43.1 - - + -
872A ALA 4.0 0.2 + - - -
873A ALA* 1.3 84.0 + - - +
875A TYR* 1.3 59.1 + - - +
877A PHE* 3.4 5.1 + - - +
878A GLY 3.2 14.2 + - - -
965A TRP* 5.1 0.3 + - - -
970A GLY 4.5 2.3 - - - +
973A GLY* 3.5 17.1 - - - -
977A VAL* 3.7 10.9 - - + +
61B MET* 3.7 22.2 - - + -
62B GLN* 2.7 32.4 + - - +
66B GLY* 3.6 21.4 - - - +
69B GLY* 4.2 1.8 - - - -
70B ALA* 3.3 14.7 - - - +
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Residues in contact with TYR 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ALA* 3.4 21.1 - - + -
865A GLY* 3.4 26.6 - - - -
866A ASN 4.6 1.0 + - - -
867A SER* 3.4 33.1 + - - +
871A ASP* 3.0 19.3 + - - +
872A ALA* 3.3 4.3 - - - +
873A ALA 2.9 0.2 - - - -
874A GLU* 1.3 74.4 - - - +
876A GLY* 1.3 55.9 + - - +
877A PHE 3.0 3.8 - - - -
878A GLY* 2.8 18.2 + - - -
879A MET* 3.3 26.2 + - + +
69B GLY 3.5 10.5 - - - +
72B HIS* 3.5 27.7 + + - -
73B GLY* 3.2 44.1 - - - -
76B ALA* 4.1 5.6 - - + +
216B ARG* 4.0 22.9 - - - +
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Residues in contact with GLY 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ALA* 3.6 19.5 - - - +
872A ALA 3.0 8.8 + - - -
873A ALA 3.0 7.8 + - - -
875A TYR* 1.3 75.3 - - - +
877A PHE* 1.3 58.1 - - - +
878A GLY 3.2 0.4 - - - -
879A MET* 4.0 8.5 - - - -
880A ASN* 3.5 8.5 + - - +
957A VAL* 3.2 27.5 - - - +
959A ILE* 4.2 11.7 - - - -
984A VAL* 3.8 2.5 - - - +
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Residues in contact with PHE 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A ALA 2.9 14.5 + - - +
874A GLU 3.4 6.5 - - - +
875A TYR 3.0 0.2 - - - -
876A GLY* 1.3 77.2 - - - +
878A GLY* 1.3 65.4 + - - +
879A MET 3.3 0.2 - - - -
880A ASN* 3.4 10.9 - - + +
881A MET* 3.0 44.8 + - - +
976A HIS* 5.9 1.1 - + - -
977A VAL* 3.8 26.7 - - + -
980A SER* 3.0 35.9 - - - -
982A GLU* 3.7 31.0 - - + -
984A VAL* 4.7 4.7 - - + -
59B ARG* 3.9 11.7 - - + -
60B GLU 6.0 0.4 - - - -
61B MET* 3.6 36.1 - - + -
70B ALA* 4.7 1.8 - - + -
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Residues in contact with GLY 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A GLU 3.2 6.7 + - - -
875A TYR 2.8 9.3 + - - -
877A PHE* 1.3 75.8 - - - +
879A MET* 1.3 65.3 + - - +
881A MET* 3.2 9.6 + - - +
882A SER 3.0 18.2 + - - -
70B ALA* 3.3 28.9 - - - -
74B ALA* 3.4 15.8 - - - +
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Residues in contact with MET 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A PHE* 3.4 39.9 - - + -
834A ILE 4.3 4.7 - - - +
835A ALA* 4.0 11.9 - - + -
875A TYR* 3.3 47.1 + - + +
876A GLY* 4.1 9.9 - - - +
877A PHE 3.3 0.2 - - - -
878A GLY* 1.3 75.1 - - - +
880A ASN* 1.3 64.7 + - - +
882A SER* 3.0 4.2 + - - -
883A MET* 2.9 26.5 + - - +
957A VAL* 4.6 6.3 - - + -
73B GLY 3.4 17.2 + - - +
77B ALA* 3.7 13.9 - - + +
208B MET* 3.3 23.8 - - + -
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Residues in contact with ASN 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A GLY 3.5 13.2 + - - +
877A PHE* 3.4 13.4 + - - +
879A MET* 1.3 79.4 - - - +
881A MET* 1.3 61.9 + - - +
883A MET* 3.3 6.6 + - - +
884A PHE* 3.0 21.3 + - - +
957A VAL* 4.4 15.1 - - + +
982A GLU* 3.5 34.4 - - - +
983A ASP* 3.5 24.0 + - - +
984A VAL* 3.7 17.7 - - + +
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Residues in contact with MET 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A PHE* 3.0 36.8 + - + +
878A GLY* 3.4 12.1 - - - +
880A ASN* 1.3 77.9 - - - +
882A SER* 1.3 63.1 + - - +
884A PHE* 3.0 18.2 + - - +
885A ALA* 3.1 14.7 + - - +
982A GLU* 4.3 9.6 - - - +
24B VAL* 3.4 27.9 - - + +
25B ALA 3.4 27.6 - - - +
26B ALA* 4.3 10.5 - - + -
57B THR* 3.8 12.6 - - + +
59B ARG* 3.4 37.2 - - + +
70B ALA* 4.9 1.3 - - - +
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Residues in contact with SER 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A GLY 3.0 11.0 + - - -
879A MET 3.0 7.6 + - - -
881A MET* 1.3 76.0 - - - +
883A MET* 1.3 58.0 + - - +
885A ALA* 3.6 0.5 + - - +
886A ARG* 2.8 34.3 + - - +
24B VAL* 4.3 4.6 - - - +
74B ALA* 3.6 11.9 - - - -
77B ALA* 2.8 37.2 + - - -
79B ALA* 3.2 25.5 + - - +
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Residues in contact with MET 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A PHE* 3.9 28.7 - - + -
879A MET 2.9 15.3 + - - +
880A ASN* 3.6 11.2 - - - +
882A SER* 1.3 77.9 - - - +
884A PHE* 1.3 62.3 + - - +
886A ARG* 4.6 9.4 - - - +
887A ARG* 2.7 44.4 + - + +
951A LEU* 3.5 32.8 - - + -
955A LYS* 3.4 40.8 - - + -
957A VAL* 5.1 5.6 - - + -
77B ALA* 4.7 2.5 - - - +
209B ASN* 4.2 5.6 - - - +
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Residues in contact with PHE 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ASN* 3.0 13.9 + - - +
881A MET* 3.0 12.7 + - - +
883A MET* 1.3 76.7 - - - +
885A ALA* 1.3 53.3 + - - +
887A ARG* 3.4 2.0 - - - +
888A THR* 2.6 56.7 + - + -
982A GLU* 5.3 10.1 - - + +
57B THR* 4.3 19.5 - - + -
59B ARG* 4.5 14.6 - - - -
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Residues in contact with ALA 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A MET 3.1 9.8 + - - +
882A SER 4.0 2.7 - - - +
884A PHE* 1.3 79.8 - - - +
886A ARG* 1.3 65.1 + - + +
888A THR* 3.2 6.3 + - - -
889A HIS* 2.9 24.6 + - - +
23B GLU* 3.7 24.9 - - + +
24B VAL* 4.1 7.0 - - + -
54B GLN* 5.3 3.2 - - + +
55B THR 5.9 0.9 - - - +
57B THR* 3.4 22.6 + - - +
79B ALA* 5.3 0.2 - - + -
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Residues in contact with ARG 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A SER* 2.8 37.8 + - - +
883A MET* 4.4 7.3 - - - +
885A ALA* 1.3 72.6 - - + +
887A ARG* 1.3 57.5 + - - +
889A HIS* 3.3 8.5 + - - +
890A LEU* 3.2 20.6 + - - +
948A MET* 3.7 8.9 - - + +
950A ASP* 4.2 15.0 + - - -
951A LEU* 3.8 51.1 - - + +
23B GLU* 4.5 12.6 - - - +
77B ALA 3.0 19.0 + - - -
78B GLY* 3.7 25.9 + - - -
79B ALA* 4.4 7.9 - - + -
204B ARG* 3.8 32.4 + - - +
207B SER* 4.9 3.2 - - - -
208B MET 4.9 4.2 + - - -
209B ASN* 4.8 5.9 - - - +
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Residues in contact with ARG 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A MET* 2.7 33.9 + - + +
884A PHE* 3.8 2.5 - - - +
886A ARG* 1.3 71.3 - - - +
888A THR* 1.3 62.2 + - - +
890A LEU* 3.5 6.6 + - + +
891A ALA* 3.2 20.8 + - - +
913A TRP* 4.1 12.8 - - + +
917A LYS* 2.6 38.4 + - + +
918A ASN* 2.9 21.8 - - - +
923A SER* 3.7 0.4 - - - -
951A LEU* 2.8 35.3 + - + +
952A TYR 2.8 20.6 + - - -
953A THR 3.0 1.8 + - - -
954A LYS* 2.6 43.3 - - - +
955A LYS* 5.1 6.6 - - - +
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Residues in contact with THR 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A PHE* 2.6 53.0 + - + -
885A ALA* 3.5 7.2 - - - -
887A ARG* 1.3 72.2 - - - +
889A HIS* 1.3 65.4 + - - +
891A ALA* 3.1 6.9 + - + +
892A ASP* 3.0 34.7 + - - +
54B GLN* 4.5 10.3 - - + +
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Residues in contact with HIS 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ALA 2.9 13.2 + - - +
886A ARG* 3.3 12.7 - - - +
888A THR* 1.3 77.4 - - - +
890A LEU* 1.3 64.0 + - - +
892A ASP* 3.1 1.2 + - - +
893A LEU* 2.9 47.3 + - + +
944A GLN* 4.7 8.4 + - - -
948A MET* 3.8 15.4 - - + +
23B GLU* 4.5 10.7 + - - +
52B PHE* 3.6 43.3 + + + +
54B GLN* 3.5 32.6 - - + +
204B ARG* 6.0 0.6 + - - -
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Residues in contact with LEU 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A ARG 3.2 10.1 + - - +
887A ARG* 3.6 11.0 - - + +
888A THR 3.1 0.2 - - - -
889A HIS* 1.3 80.6 - - - +
891A ALA* 1.3 50.3 + - - +
893A LEU* 3.3 1.7 + - + +
894A ALA* 2.8 32.9 + - + +
913A TRP* 3.6 27.1 - - + -
945A ILE* 3.4 33.7 - - + -
948A MET* 3.6 36.3 - - + +
951A LEU* 4.1 13.5 - - + +
952A TYR* 3.5 27.1 - - + -
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Residues in contact with ALA 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A ARG 3.2 8.3 + - - +
888A THR* 3.1 11.5 + - + +
890A LEU* 1.3 76.9 - - - +
892A ASP* 1.3 64.4 + - - +
893A LEU 3.2 1.3 - - - -
895A ALA* 2.8 29.6 + - - +
913A TRP* 3.6 9.6 - - - -
914A LEU* 3.4 9.9 - - + +
917A LYS* 3.3 34.1 - - - +
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Residues in contact with ASP 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A THR* 3.0 23.3 + - - +
889A HIS 3.9 2.9 - - - +
891A ALA* 1.3 79.3 - - - +
893A LEU* 1.3 60.0 + - - +
895A ALA* 3.7 6.8 - - - +
896A LYS* 3.0 40.8 + - - +
49B LYS* 3.9 14.6 + - - -
54B GLN* 3.3 30.5 + - - +
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Residues in contact with LEU 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A HIS* 2.9 35.4 + - + +
890A LEU 3.4 4.9 - - - +
892A ASP* 1.3 75.8 - - - +
894A ALA* 1.3 59.3 + - - +
896A LYS* 3.2 20.7 + - - +
897A ALA 2.9 22.3 + - - -
941A LEU* 3.5 34.1 - - + +
944A GLN* 3.6 44.2 - - + +
945A ILE* 3.7 12.6 - - + +
948A MET* 3.9 22.0 - - - -
52B PHE 6.0 0.2 - - - +
54B GLN* 5.4 0.2 - - - +
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Residues in contact with ALA 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A LEU* 2.8 19.9 + - + +
891A ALA 4.0 1.3 - - - +
892A ASP 3.4 0.2 - - - -
893A LEU* 1.3 72.7 - - - +
895A ALA* 1.3 65.6 + - - +
897A ALA* 3.0 13.0 + - - +
898A LEU* 3.2 14.9 + - - +
910A LEU* 3.9 19.2 - - + +
913A TRP* 4.2 9.2 - - + -
914A LEU* 3.0 29.4 - - + -
945A ILE* 3.8 12.3 - - + -
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Residues in contact with ALA 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A ALA 2.8 21.4 + - - +
892A ASP* 3.7 8.5 - - - +
894A ALA* 1.3 78.4 - - - +
896A LYS* 1.3 59.3 + - + +
898A LEU* 3.7 21.7 - - + +
899A GLU* 4.2 10.0 + - - +
914A LEU* 3.8 12.9 - - + +
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Residues in contact with LYS 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A ASP* 3.0 27.8 + - - +
893A LEU* 3.5 27.9 - - + +
894A ALA 3.0 0.4 - - - -
895A ALA* 1.3 75.1 - - + +
897A ALA* 1.3 65.7 + - - +
898A LEU 3.1 2.2 - - - -
899A GLU* 2.9 36.4 + - - +
900A SER* 4.6 0.2 - - - -
941A LEU* 3.6 17.4 - - + +
52B PHE 5.6 1.4 + - - -
53B GLY* 5.5 4.2 + - - -
54B GLN* 4.7 12.1 - - - +
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Residues in contact with ALA 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A LEU 2.9 14.1 + - - +
894A ALA 3.0 2.0 + - - +
896A LYS* 1.3 75.3 - - - +
898A LEU* 1.3 53.1 + - - +
900A SER* 2.6 36.3 + - - +
902A ALA* 4.2 4.7 - - - +
910A LEU* 3.3 29.2 - - + -
941A LEU* 3.3 16.1 - - + +
942A LEU* 4.0 15.0 - - + -
945A ILE* 3.8 11.9 - - + -
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Residues in contact with LEU 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A ALA 3.2 11.9 + - - +
895A ALA* 3.7 17.9 - - - +
896A LYS 3.1 0.6 - - - -
897A ALA* 1.3 75.8 - - - +
899A GLU* 1.3 57.5 + - + +
900A SER 3.1 3.4 + - - -
907A LYS* 3.3 65.3 + - + +
910A LEU* 4.0 9.9 - - + -
911A GLN* 3.5 42.6 - - + +
914A LEU* 4.9 2.5 - - + -
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Residues in contact with GLU 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ALA 4.3 7.2 - - - +
896A LYS* 2.9 29.4 + - - +
897A ALA 3.7 0.2 - - - -
898A LEU* 1.3 75.7 - - + +
900A SER* 1.3 58.7 + - - +
----------------------------------------------------------
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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).
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