Contacts of the helix formed by residues 984 - 1015 (chain D) in PDB entry 5D4C
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 THR 984 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978D TYR* 3.8 5.1 - - - -
981D GLY 6.0 0.2 - - - +
982D PHE 5.4 1.1 - - - +
983D LEU* 1.3 77.6 - - - +
985D ASP* 1.3 64.6 + - - +
986D ARG* 3.4 7.0 + - - +
987D GLU* 3.2 42.7 + - - +
988D ARG* 3.1 20.6 + - - +
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Residues in contact with ASP 985 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978D TYR* 4.0 24.8 + - + +
984D THR* 1.3 72.4 - - - +
986D ARG* 1.3 61.9 + - - +
988D ARG* 3.2 23.6 + - - +
989D TYR* 2.9 29.7 + - - +
1054D GLU* 5.0 0.3 - - - +
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Residues in contact with ARG 986 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984D THR* 3.4 6.2 + - - +
985D ASP* 1.3 79.5 - - - +
987D GLU* 1.3 60.4 + - + +
989D TYR* 3.4 37.2 + - - +
990D ASP* 2.9 53.5 + - - +
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Residues in contact with GLU 987 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982D PHE 4.1 3.3 - - - +
983D LEU* 3.4 26.5 - - + +
984D THR* 3.2 41.9 + - + +
986D ARG* 1.3 79.1 - - + +
988D ARG* 1.3 57.3 + - - +
990D ASP* 3.5 7.0 + - - +
991D GLN* 2.9 39.3 + - - +
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Residues in contact with ARG 988 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974D ILE* 4.2 20.1 - - + +
975D GLU* 3.3 29.0 + - - +
978D TYR* 3.8 39.2 - - + -
983D LEU* 4.6 7.3 - - + +
984D THR 3.1 19.1 + - - +
985D ASP* 3.2 25.6 + - - +
987D GLU* 1.3 74.3 - - - +
989D TYR* 1.3 62.9 + - - +
991D GLN* 3.3 2.8 + - - +
992D ILE* 2.9 43.1 + - + +
1054D GLU* 2.7 44.8 + - - -
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Residues in contact with TYR 989 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985D ASP* 2.9 21.1 + - - +
986D ARG* 3.6 33.4 - - - +
988D ARG* 1.3 82.2 - - - +
990D ASP* 1.3 69.0 + - - +
992D ILE* 3.1 10.3 + - - +
993D LEU* 2.9 55.7 + - + +
1051D GLU* 3.4 19.9 - - + +
1052D THR* 2.8 52.2 + - - -
1054D GLU* 4.0 26.5 - - + +
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Residues in contact with ASP 990 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986D ARG* 2.9 47.8 + - - +
987D GLU* 3.8 6.8 + - - +
989D TYR* 1.3 91.1 - - - +
991D GLN* 1.3 58.0 + - + +
993D LEU* 3.4 9.0 + - - +
994D GLN* 2.9 29.7 + - - +
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Residues in contact with GLN 991 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970D LYS* 5.7 2.2 + - - +
974D ILE* 3.9 26.8 - - + +
983D LEU* 3.4 42.8 - - - +
987D GLU* 2.9 20.9 + - - +
988D ARG 3.8 3.8 - - - +
990D ASP* 1.3 73.9 - - + +
992D ILE* 1.3 60.0 + - - +
994D GLN* 3.4 6.9 + - - +
995D LEU* 2.9 29.8 + - - +
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Residues in contact with ILE 992 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971D LEU* 3.7 21.5 - - + -
974D ILE* 4.6 10.8 - - + -
975D GLU* 4.2 9.2 - - - +
988D ARG* 2.9 48.8 + - + +
989D TYR* 3.1 8.3 + - - +
991D GLN* 1.3 73.2 - - - +
993D LEU* 1.3 68.8 + - + +
995D LEU* 3.3 5.7 + - - +
996D TRP* 2.9 46.9 + - + +
1054D GLU* 3.8 33.0 - - + +
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Residues in contact with LEU 993 (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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989D TYR* 2.9 56.4 + - + +
990D ASP* 3.6 12.1 - - - +
992D ILE* 1.3 80.8 - - + +
994D GLN* 1.3 58.5 + - - +
996D TRP* 3.4 1.6 + - - +
997D THR* 2.9 35.8 + - - +
1044D LEU* 4.0 16.9 - - + +
1052D THR* 3.7 34.5 - - + +
1053D PHE 4.1 8.7 - - - +
1054D GLU* 5.0 0.4 - - - -
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Residues in contact with GLN 994 (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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990D ASP 2.9 18.0 + - - +
991D GLN* 3.6 8.1 - - - +
993D LEU* 1.3 74.5 - - - +
995D LEU* 1.3 66.1 + - - +
997D THR* 3.3 10.5 + - - +
998D GLU* 3.0 61.6 + - - +
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Residues in contact with LEU 995 (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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966D GLU* 5.7 2.0 - - + +
967D ALA* 3.5 33.9 - - + +
970D LYS* 3.8 34.5 - - + +
971D LEU* 3.7 32.8 - - + +
974D ILE* 4.6 6.5 - - + -
991D GLN 2.9 17.9 + - - +
992D ILE 3.6 3.4 - - - +
994D GLN* 1.3 76.0 - - - +
996D TRP* 1.3 57.9 + - + +
998D GLU* 3.5 9.4 + - + +
999D THR* 2.7 45.0 + - - +
1002D LYS* 6.2 1.8 - - - +
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Residues in contact with TRP 996 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964D LEU* 4.2 10.8 - - + -
967D ALA* 3.8 23.6 - - + -
968D ASP* 4.7 0.2 - - - -
971D LEU* 3.7 32.4 - - + +
992D ILE* 2.9 43.4 + - + +
995D LEU* 1.3 79.1 - - + +
997D THR* 1.3 60.0 + - - +
999D THR* 3.3 22.1 + - + -
1000D THR* 2.9 32.4 + - - -
1041D LEU* 4.8 6.3 - - + -
1044D LEU* 3.8 25.1 - - + -
1054D GLU 3.6 12.2 + - - -
1056D PRO* 3.4 37.7 - - + +
1058D ARG* 3.6 35.4 - - + -
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Residues in contact with THR 997 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993D LEU* 2.9 25.0 + - - +
994D GLN* 3.6 11.6 - - - +
996D TRP* 1.3 75.1 - - - +
998D GLU* 1.3 62.3 + - + +
1000D THR* 3.1 10.0 + - - +
1001D GLU* 3.0 31.9 + - + +
1044D LEU* 4.1 11.1 - - - +
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Residues in contact with GLU 998 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994D GLN* 3.0 50.7 + - - +
995D LEU* 3.8 8.4 - - + +
997D THR* 1.3 76.6 - - + +
999D THR* 1.3 56.8 + - - +
1001D GLU* 3.4 8.0 + - - +
1002D LYS* 2.9 46.5 + - - +
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Residues in contact with THR 999 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963D TYR* 4.5 13.0 + - + +
964D LEU* 4.6 3.8 - - + -
967D ALA* 3.8 20.6 - - + +
995D LEU* 2.7 29.5 + - - +
996D TRP* 3.4 29.7 - - + -
998D GLU* 1.3 76.8 - - - +
1000D THR* 1.3 57.7 + - - +
1002D LYS* 3.1 11.8 + - - +
1003D VAL* 2.9 35.3 + - + +
1041D LEU* 4.2 13.2 - - + -
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Residues in contact with THR1000 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996D TRP* 2.9 16.8 + - - -
997D THR* 3.3 12.9 - - + +
999D THR* 1.3 73.6 - - - +
1001D GLU* 1.3 68.1 + - + +
1003D VAL* 3.2 11.7 - - - +
1004D THR* 2.9 28.5 + - - +
1036D ARG* 3.3 39.7 - - - +
1041D LEU* 3.3 16.4 - - - +
1043D GLY* 4.2 7.7 - - - -
1044D LEU* 4.8 3.8 + - - +
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Residues in contact with GLU1001 (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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997D THR* 3.0 16.7 + - + +
998D GLU* 3.6 12.3 - - - +
1000D THR* 1.3 76.6 - - + +
1002D LYS* 1.3 57.8 + - + +
1004D THR* 3.3 7.8 + - - -
1005D GLN* 3.0 65.2 + - - +
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Residues in contact with LYS1002 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963D TYR* 3.5 43.1 + - + +
966D GLU* 3.1 28.3 + - - -
995D LEU* 6.2 1.6 - - - +
998D GLU* 2.9 29.9 + - - +
999D THR* 3.1 15.7 + - + +
1001D GLU* 1.3 77.6 - - + +
1003D VAL* 1.3 57.9 + - - +
1005D GLN* 3.4 5.0 + - - +
1006D ALA* 2.9 28.6 + - - +
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Residues in contact with VAL1003 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957D PRO* 4.6 1.2 - - + +
960D LYS* 4.4 20.4 - - + +
963D TYR* 4.1 24.9 - - + -
964D LEU* 5.5 0.4 - - + -
999D THR* 2.9 22.1 + - + +
1000D THR* 3.2 15.5 - - - +
1002D LYS* 1.3 71.2 - - - +
1004D THR* 1.3 59.3 + - - +
1006D ALA* 3.5 7.3 - - - +
1007D VAL* 2.9 34.2 + - + +
1036D ARG* 4.4 7.6 - - + -
1040D GLY* 4.8 3.4 - - - -
1041D LEU* 3.6 46.4 - - + +
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Residues in contact with THR1004 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000D THR* 2.9 20.5 + - - +
1001D GLU* 3.4 12.0 - - - -
1003D VAL* 1.3 75.0 - - - +
1005D GLN* 1.3 75.8 + - - +
1007D VAL* 3.0 7.6 + - - +
1008D PHE* 3.0 37.8 + - + -
1032D PRO* 4.4 22.9 - - + +
1033D GLN* 5.3 5.5 + - - +
1036D ARG* 3.1 28.3 + - + +
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Residues in contact with GLN1005 (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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1001D GLU* 3.0 42.6 + - - +
1002D LYS* 3.8 5.6 - - - +
1004D THR* 1.3 87.8 - - - +
1006D ALA* 1.3 57.9 + - - +
1008D PHE* 3.5 6.6 + - - +
1009D LYS* 2.9 33.2 + - - +
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Residues in contact with ALA1006 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957D PRO* 4.3 9.0 - - + -
959D GLU* 3.9 35.8 - - + +
960D LYS 5.2 0.2 - - - +
963D TYR* 3.9 9.6 - - + +
1002D LYS 2.9 19.2 + - - +
1003D VAL* 3.5 8.1 - - - +
1004D THR 3.1 0.2 - - - -
1005D GLN* 1.3 75.2 - - - +
1007D VAL* 1.3 60.4 + - - +
1009D LYS* 3.9 7.3 - - - +
1010D ASN* 2.9 30.7 + - - +
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Residues in contact with VAL1007 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955D VAL 4.8 2.0 - - - +
957D PRO* 3.6 31.0 - - + -
1003D VAL 2.9 19.8 + - - +
1004D THR* 3.0 9.6 + - - +
1006D ALA* 1.3 75.7 - - - +
1008D PHE* 1.3 68.0 + - + +
1010D ASN* 3.2 4.7 + - - +
1011D PHE* 2.9 54.1 + - + -
1035D ILE* 4.3 8.5 - - + +
1036D ARG* 5.3 3.8 - - - -
1039D CYS* 4.2 25.8 - - + -
1040D GLY* 4.3 7.4 - - - +
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Residues in contact with PHE1008 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004D THR* 3.0 26.4 + - + +
1005D GLN* 4.2 7.6 - - - +
1007D VAL* 1.3 85.1 - - + +
1009D LYS* 1.3 57.2 + - - +
1011D PHE* 3.6 5.6 - + - +
1012D GLU* 2.9 29.6 + - - +
1021D TYR* 3.9 26.9 - + - -
1024D ALA* 4.2 18.4 - - + -
1025D GLN* 4.0 17.0 - - - -
1032D PRO* 3.5 48.9 - - + -
1035D ILE* 3.9 26.7 - - + -
1036D ARG* 5.1 0.7 - - - -
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Residues in contact with LYS1009 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959D GLU* 4.7 14.6 + - - +
1005D GLN 2.9 19.7 + - - +
1006D ALA* 3.9 6.1 - - - +
1008D PHE* 1.3 73.6 - - - +
1010D ASN* 1.3 61.2 + - - +
1012D GLU* 4.4 11.0 - - - +
1013D GLU* 2.9 67.5 + - + +
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Residues in contact with ASN1010 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955D VAL* 3.7 30.7 + - - +
956D ILE 4.6 0.4 + - - -
957D PRO* 3.9 24.8 - - + +
958D GLU 5.3 0.4 - - - +
959D GLU* 4.5 9.8 + - - +
1006D ALA 2.9 19.4 + - - +
1007D VAL* 3.5 5.1 - - - +
1009D LYS* 1.3 78.0 - - - +
1011D PHE* 1.3 58.1 + - - +
1013D GLU* 5.2 0.7 - - - -
1014D ASN* 2.9 53.6 + - - +
1015D TYR* 3.5 9.2 + - - -
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Residues in contact with PHE1011 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953D ASP 4.2 2.2 - - - -
955D VAL* 3.6 28.7 - - + -
1007D VAL* 2.9 42.2 + - + +
1008D PHE* 3.6 5.8 - + - +
1009D LYS 3.2 0.2 - - - -
1010D ASN* 1.3 75.2 - - - +
1012D GLU* 1.3 62.1 + - - +
1015D TYR* 2.8 43.5 + + + +
1018D ASN* 3.2 40.8 - - + -
1020D LEU* 4.5 5.2 - - + -
1021D TYR* 3.4 32.8 - + + -
1035D ILE* 4.0 17.7 - - + -
1039D CYS* 3.9 18.8 - - - -
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Residues in contact with GLU1012 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008D PHE 2.9 20.5 + - - +
1009D LYS* 3.4 12.4 + - - +
1011D PHE* 1.3 74.5 - - - +
1013D GLU* 1.3 74.5 + - + +
1016D PRO* 3.7 16.8 - - - +
1021D TYR* 3.3 30.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU1013 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799D LYS* 3.4 19.1 + - - +
1009D LYS* 2.9 58.4 + - + +
1010D ASN* 5.8 0.3 - - - -
1012D GLU* 1.3 87.3 - - + +
1014D ASN* 1.3 72.8 + - - +
1016D PRO* 4.4 4.9 - - - +
----------------------------------------------------------
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Residues in contact with ASN1014 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951C GLY* 6.0 0.5 - - - -
799D LYS* 3.1 23.6 + - - +
1010D ASN* 2.9 31.4 + - - +
1013D GLU* 1.3 84.7 - - - +
1015D TYR* 1.3 88.5 + - + +
1016D PRO* 3.8 4.9 - - - +
----------------------------------------------------------
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Residues in contact with TYR1015 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950C LEU 4.1 18.2 - - - +
951C GLY* 4.3 20.6 + - - -
952C LEU* 5.8 2.7 - - + -
955D VAL* 4.4 24.1 - - + +
1010D ASN* 3.9 20.9 - - - -
1011D PHE* 2.8 28.1 + + + +
1014D ASN* 1.3 100.1 - - + +
1016D PRO* 1.3 66.8 - - - +
1017D PHE 3.2 2.7 - - - -
1018D ASN* 3.1 34.3 + - + +
1021D TYR* 4.2 1.9 - - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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