Contacts of the helix formed by residues 872 - 899 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B ALA* 3.5 12.8 - - - +
836B ASN 4.2 1.3 - - - -
837B ALA* 3.3 45.8 - - + +
867B SER* 5.4 1.1 - - - +
868B LEU 4.4 2.6 + - - -
869B PHE 4.1 1.6 + - - -
871B ASP* 1.3 76.9 + - - +
873B ALA* 1.3 58.1 + - - +
875B TYR* 3.3 8.6 - - - +
876B GLY 3.0 22.0 + - - -
959B ILE* 3.5 8.5 - - + +
960B PHE 4.4 0.2 - - - +
965B TRP* 3.4 17.5 - - + +
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Residues in contact with ALA 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B ASP 3.3 0.6 - - - -
872B ALA* 1.3 73.9 - - - +
874B GLU* 1.3 62.3 + - - +
875B TYR 2.9 4.7 - - - -
876B GLY* 3.0 3.3 + - - -
877B PHE* 2.9 28.1 + - - +
959B ILE* 3.4 25.7 - - + +
965B TRP* 3.7 21.1 - - + +
974B LEU* 3.9 26.5 - - + +
977B VAL* 3.7 11.3 - - + +
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Residues in contact with GLU 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 3.8 17.3 - - + -
62A GLN* 2.7 32.2 + - - +
66A GLY* 3.6 27.3 + - - +
69A GLY* 4.1 3.6 - - - -
70A ALA* 3.2 19.6 - - - +
870B GLU 3.6 6.7 - - - +
871B ASP* 3.0 43.0 - - + -
872B ALA 4.0 0.2 + - - -
873B ALA* 1.3 82.7 + - - +
875B TYR* 1.3 59.2 + - - +
877B PHE* 3.4 5.1 + - - +
878B GLY 3.2 8.0 + - - -
965B TRP* 5.1 0.3 + - - -
970B GLY 4.5 2.4 - - - +
973B GLY* 3.5 15.8 - - - -
977B VAL* 3.7 10.9 - - + +
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Residues in contact with TYR 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.5 9.2 - - - +
72A HIS* 3.4 35.1 + + - -
73A GLY* 3.2 40.7 - - - -
76A ALA* 4.1 5.0 - - + +
103A GLU* 4.4 0.3 + - - -
216A ARG* 3.9 23.9 + - - +
835B ALA* 3.4 20.6 - - + -
865B GLY* 3.4 26.9 - - - -
866B ASN 4.6 0.7 + - - -
867B SER* 3.4 28.2 + - - +
871B ASP* 3.0 19.5 + - - +
872B ALA* 3.3 4.7 - - - +
873B ALA 2.9 0.6 - - - -
874B GLU* 1.3 74.8 - - - +
876B GLY* 1.3 56.1 + - - +
877B PHE 3.0 3.8 - - - -
878B GLY* 2.8 18.5 + - - -
879B MET* 3.3 26.9 + - + +
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Residues in contact with GLY 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B ALA* 3.6 19.9 - - - +
872B ALA 3.0 8.4 + - - -
873B ALA 3.0 8.3 + - - -
875B TYR* 1.3 76.0 - - - +
877B PHE* 1.3 58.6 + - - +
878B GLY 3.2 0.2 - - - -
879B MET* 4.0 9.0 - - - -
880B ASN* 3.5 8.5 + - - +
957B VAL* 3.2 27.9 - - - +
959B ILE* 4.2 11.9 - - - -
984B VAL* 3.8 2.3 - - - +
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Residues in contact with PHE 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.9 13.0 - - + -
60A GLU 6.0 0.4 - - - -
61A MET* 3.6 35.9 - - + -
70A ALA* 4.5 2.9 - - + -
873B ALA 2.9 14.7 + - - +
874B GLU 3.4 5.4 - - - +
875B TYR 3.0 0.2 - - - -
876B GLY* 1.3 77.3 - - - +
878B GLY* 1.3 65.1 + - - +
879B MET 3.3 0.2 - - - -
880B ASN* 3.4 12.3 + - - +
881B MET* 3.0 43.9 + - - +
976B HIS* 5.9 0.9 - + - -
977B VAL* 3.8 25.4 - - + -
980B SER* 3.0 35.9 - - - -
982B GLU* 3.7 30.1 - - + -
984B VAL* 4.7 4.9 - - + -
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Residues in contact with GLY 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.2 31.2 - - - -
74A ALA* 3.3 16.2 - - - +
874B GLU 3.2 5.1 + - - -
875B TYR 2.8 10.3 + - - -
877B PHE* 1.3 75.8 - - - +
879B MET* 1.3 64.9 + - - +
881B MET* 3.2 8.0 + - - +
882B SER 3.0 18.2 + - - -
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Residues in contact with MET 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY 3.4 18.3 + - - +
77A ALA* 3.6 13.3 - - + +
208A MET* 3.3 39.5 - - + -
833B PHE* 3.5 26.0 - - + -
834B ILE 4.3 4.3 - - - +
835B ALA* 4.0 12.3 - - + -
875B TYR* 3.3 45.0 + - + +
876B GLY* 4.1 9.9 - - - +
877B PHE 3.3 0.2 - - - -
878B GLY* 1.3 75.1 - - - +
880B ASN* 1.3 64.0 + - - +
882B SER* 3.0 4.3 + - - -
883B MET* 2.9 26.2 + - - +
957B VAL* 4.6 6.3 - - + -
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Residues in contact with ASN 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876B GLY 3.5 14.1 + - - +
877B PHE* 3.4 14.2 - - - +
879B MET* 1.3 79.4 - - - +
881B MET* 1.3 62.1 + - - +
883B MET* 3.3 6.8 + - - +
884B PHE* 3.0 21.0 + - - +
957B VAL* 4.4 15.4 - - + +
982B GLU* 3.5 33.9 - - - +
983B ASP* 3.5 24.6 + - - +
984B VAL* 3.7 17.0 - - + +
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Residues in contact with MET 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.3 35.2 - - + +
25A ALA 3.4 22.7 - - - +
26A ALA* 4.3 10.5 - - + +
57A THR* 3.8 13.3 - - + +
59A ARG* 3.5 34.5 - - + -
70A ALA* 4.8 1.1 - - - +
877B PHE* 3.0 36.5 + - + +
878B GLY* 3.2 12.5 + - - +
880B ASN* 1.3 77.6 - - - +
882B SER* 1.3 61.2 + - - +
884B PHE* 3.0 18.4 + - - +
885B ALA* 3.1 14.7 + - - +
982B GLU* 4.3 9.9 - - - +
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Residues in contact with SER 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 4.3 3.3 - - - +
74A ALA* 3.5 21.3 - - - -
77A ALA* 2.7 29.2 + - - -
79A ALA* 3.1 25.4 + - - +
878B GLY 3.0 10.5 + - - -
879B MET 3.0 7.8 + - - -
881B MET* 1.3 76.9 - - - +
883B MET* 1.3 57.7 + - - +
885B ALA* 3.6 0.5 + - - +
886B ARG* 2.8 34.3 + - - +
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Residues in contact with MET 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 4.5 11.4 - - - +
209A ASN* 4.1 5.4 - - - +
833B PHE* 3.9 28.9 - - + -
879B MET 2.9 14.8 + - - +
880B ASN* 3.6 11.9 - - - +
881B MET 3.2 0.2 - - - -
882B SER* 1.3 75.5 - - - +
884B PHE* 1.3 61.8 + - - +
886B ARG* 4.6 2.5 - - - +
887B ARG* 2.7 46.0 + - + +
951B LEU* 3.5 32.8 - - + -
955B LYS* 3.4 40.4 - - + -
957B VAL* 5.1 6.1 - - + -
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Residues in contact with PHE 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 4.3 21.5 - - + -
59A ARG* 4.5 13.9 - - - -
880B ASN* 3.0 13.9 + - - +
881B MET* 3.0 12.3 + - - +
883B MET* 1.3 75.8 - - - +
885B ALA* 1.3 54.2 + - - +
887B ARG* 3.4 2.4 - - - +
888B THR* 2.6 59.1 + - + -
982B GLU* 5.3 10.5 - - + +
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Residues in contact with ALA 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 3.7 26.6 - - + +
24A VAL* 4.1 6.7 - - + -
54A GLN* 5.4 2.6 - - - +
57A THR* 3.5 22.2 + - - +
79A ALA* 5.2 0.2 - - + -
881B MET 3.1 9.1 + - - +
882B SER 4.0 2.2 - - - +
884B PHE* 1.3 79.8 - - - +
886B ARG* 1.3 64.0 + - + +
888B THR* 3.2 6.7 + - - -
889B HIS* 2.9 24.6 + - - +
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Residues in contact with ARG 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.5 4.9 - - - +
77A ALA 3.0 18.6 + - - -
78A GLY* 3.5 27.3 + - - -
79A ALA* 4.4 8.7 - - + -
204A ARG* 3.8 39.9 + - - +
207A SER* 4.7 5.1 - - - -
208A MET 4.8 6.1 + - - -
209A ASN* 4.8 3.4 - - - +
882B SER* 2.8 37.2 + - - +
883B MET* 4.4 5.1 - - - +
885B ALA* 1.3 73.0 - - - +
887B ARG* 1.3 56.8 + - - +
889B HIS* 3.3 8.7 + - - +
890B LEU* 3.2 20.8 + - - +
948B MET* 3.7 9.3 - - + +
950B ASP* 4.2 14.8 + - - -
951B LEU* 3.8 52.5 - - + +
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Residues in contact with ARG 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883B MET* 2.7 35.2 + - + +
884B PHE* 3.8 2.2 - - - +
886B ARG* 1.3 70.5 - - - +
888B THR* 1.3 63.1 + - - +
890B LEU* 3.5 7.1 + - - +
891B ALA* 3.2 20.6 + - - +
913B TRP* 4.1 11.7 - - + +
917B LYS* 2.6 38.4 + - + +
918B ASN* 2.9 22.2 - - - +
923B SER* 3.7 0.2 - - - -
951B LEU* 2.8 34.7 + - + +
952B TYR 2.8 20.0 + - - -
953B THR 3.0 2.2 + - - -
954B LYS* 2.6 43.2 - - - +
955B LYS* 5.1 6.6 - - - +
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Residues in contact with THR 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 4.4 11.2 - - + +
884B PHE* 2.6 53.3 + - + -
885B ALA* 3.5 7.4 - - - -
887B ARG* 1.3 72.2 - - - +
889B HIS* 1.3 66.6 + - - +
891B ALA* 3.1 7.4 + - + +
892B ASP* 3.0 34.7 + - - +
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Residues in contact with HIS 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.5 11.2 + - - +
52A PHE* 3.6 41.6 + + + +
54A GLN* 3.6 32.6 + - + +
204A ARG* 5.8 1.6 + - - -
885B ALA 2.9 12.6 + - - +
886B ARG* 3.3 12.7 - - - +
888B THR* 1.3 77.0 - - - +
890B LEU* 1.3 64.7 + - - +
892B ASP* 3.1 1.0 + - - -
893B LEU* 2.9 47.8 + - + +
944B GLN* 4.7 9.1 + - - -
948B MET* 3.8 16.0 - - + +
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Residues in contact with LEU 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886B ARG 3.2 8.7 + - - +
887B ARG* 3.6 10.5 - - - +
888B THR 3.1 0.6 - - - -
889B HIS* 1.3 80.7 - - - +
891B ALA* 1.3 51.2 + - - +
893B LEU* 3.3 1.5 + - - +
894B ALA* 2.8 32.6 + - + +
913B TRP* 3.6 26.9 - - + -
945B ILE* 3.4 33.4 - - + -
948B MET* 3.6 37.4 - - + +
951B LEU* 4.1 13.2 - - + +
952B TYR* 3.5 27.6 - - + -
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Residues in contact with ALA 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B ARG 3.2 9.0 + - - +
888B THR* 3.1 11.9 + - + +
890B LEU* 1.3 76.0 - - - +
892B ASP* 1.3 64.4 + - - +
893B LEU 3.2 1.3 - - - -
895B ALA* 2.8 28.8 + - - +
913B TRP* 3.6 9.2 - - - -
914B LEU* 3.4 9.7 - - + +
917B LYS* 3.3 33.2 - - - +
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Residues in contact with ASP 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 3.9 13.9 + - - -
54A GLN* 3.1 32.2 + - - +
888B THR* 3.0 24.3 + - - +
889B HIS 3.9 2.9 - - - +
891B ALA* 1.3 78.8 - - - +
893B LEU* 1.3 59.1 + - - +
895B ALA* 3.6 7.0 + - - +
896B LYS* 3.0 41.5 + - - +
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Residues in contact with LEU 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE 6.0 0.2 - - - +
54A GLN* 5.5 0.4 - - - +
889B HIS* 2.9 34.7 + - + +
890B LEU 3.4 5.2 - - - +
892B ASP* 1.3 76.2 - - - +
894B ALA* 1.3 59.1 + - - +
896B LYS* 3.2 20.4 + - - +
897B ALA 2.9 22.3 + - - -
941B LEU* 3.5 35.1 - - + +
944B GLN* 3.6 43.7 - - + +
945B ILE* 3.7 12.9 - - + +
948B MET* 3.9 22.4 - - - -
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Residues in contact with ALA 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B LEU* 2.8 20.3 + - + +
891B ALA 4.0 1.1 - - - +
893B LEU* 1.3 73.1 - - - +
895B ALA* 1.3 65.9 + - - +
897B ALA* 3.0 12.5 + - - +
898B LEU* 3.2 15.2 + - - +
910B LEU* 3.9 19.3 - - + +
913B TRP* 4.2 9.0 - - + -
914B LEU* 3.0 28.9 - - + -
945B ILE* 3.8 12.5 - - + +
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Residues in contact with ALA 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891B ALA 2.8 19.8 + - - +
892B ASP* 3.7 9.0 - - - +
894B ALA* 1.3 77.7 - - - +
896B LYS* 1.3 60.5 + - + +
898B LEU* 3.7 21.6 - - + +
899B GLU* 4.2 9.9 + - - +
914B LEU* 3.8 12.5 - - + +
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Residues in contact with LYS 896 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE 5.5 1.8 + - - -
53A GLY* 5.5 4.2 + - - -
54A GLN* 4.7 12.3 - - - +
892B ASP* 3.0 27.6 + - - +
893B LEU* 3.5 27.6 - - + +
894B ALA 3.0 0.2 - - - -
895B ALA* 1.3 75.8 - - + +
897B ALA* 1.3 67.7 + - - +
898B LEU 3.1 1.6 - - - -
899B GLU* 2.9 35.7 + - - +
900B SER* 4.6 0.3 - - - -
941B LEU* 3.6 17.1 - - + +
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Residues in contact with ALA 897 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B LEU 2.9 13.7 + - - +
894B ALA 3.0 3.1 + - - +
896B LYS* 1.3 76.2 - - - +
898B LEU* 1.3 53.3 + - - +
900B SER* 2.6 37.0 + - - -
902B ALA* 4.2 5.2 - - + +
907B LYS* 4.5 0.4 - - - -
910B LEU* 3.3 28.0 - - + -
941B LEU* 3.3 16.1 - - + +
942B LEU* 4.0 13.9 - - + -
945B ILE* 3.8 12.1 - - + -
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Residues in contact with LEU 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B ALA 3.2 13.1 + - - +
895B ALA* 3.7 18.4 - - - +
896B LYS 3.1 0.8 + - - -
897B ALA* 1.3 75.2 - - - +
899B GLU* 1.3 57.4 + - + +
900B SER 3.1 3.7 + - - -
907B LYS* 3.3 64.5 + - + +
910B LEU* 4.0 10.3 - - + +
911B GLN* 3.5 43.3 - - + +
914B LEU* 4.9 2.5 - - + -
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Residues in contact with GLU 899 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B ALA 4.3 7.0 - - - +
896B LYS* 2.9 29.4 + - - +
898B LEU* 1.3 76.6 - - + +
900B SER* 1.3 58.8 + - - +
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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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