Contacts of the helix formed by residues 979 - 1005 (chain E) in PDB entry 5F28
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 979 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975E LEU* 4.1 6.1 - - - +
976E PRO* 2.6 32.7 + - + +
977E ALA 3.0 0.2 - - - -
978E SER* 1.3 89.5 - - - +
980E HIS* 1.3 64.0 + - - +
981E ARG 3.4 1.3 - - - -
982E GLU* 3.6 13.7 + - - +
983E ILE* 3.3 27.9 + - - +
1037E VAL* 6.2 0.7 - - - -
1041E ALA* 3.6 37.2 - - + +
1044E LYS* 5.2 5.8 - - - +
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Residues in contact with HIS 980 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972E ILE* 3.5 36.6 + - + +
973E PRO* 4.8 7.0 - - + -
975E LEU* 3.4 20.7 + - + -
976E PRO 3.2 20.2 - - - -
977E ALA* 3.1 27.6 + - + +
979E THR* 1.3 80.3 - - - +
981E ARG* 1.3 64.5 + - - +
983E ILE* 3.3 5.9 + - + +
984E GLU* 2.9 43.4 + - - +
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Residues in contact with ARG 981 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977E ALA 4.6 1.2 + - - -
978E SER 4.8 4.4 + - - +
979E THR 3.4 0.6 - - - -
980E HIS* 1.3 77.9 - - - +
982E GLU* 1.3 66.5 + - - +
984E GLU* 3.4 11.3 + - - +
985E MET* 3.1 51.3 + - + +
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Residues in contact with GLU 982 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978E SER 5.3 2.1 + - - +
979E THR* 3.6 16.4 + - - +
980E HIS 3.3 1.2 - - - -
981E ARG* 1.3 84.6 - - - +
983E ILE* 1.3 63.8 + - - +
985E MET* 3.6 5.7 + - - +
986E ALA* 3.3 20.8 + - - +
1037E VAL* 3.8 32.9 - - + +
1040E GLN* 4.4 14.3 - - - +
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Residues in contact with ILE 983 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968E VAL* 3.7 19.7 - - + -
972E ILE* 4.0 15.7 - - + -
975E LEU* 3.9 28.9 - - + -
979E THR* 3.3 25.9 + - - +
980E HIS* 3.3 5.7 + - + +
982E GLU* 1.3 75.2 - - - +
984E GLU* 1.3 65.9 + - - +
986E ALA* 3.0 6.7 + - - +
987E GLN* 2.9 36.1 + - - +
1034E LEU* 4.1 8.5 - - + -
1037E VAL* 3.6 22.7 - - + +
1038E ILE* 3.9 12.6 - - + -
1041E ALA* 4.6 5.8 - - + -
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Residues in contact with GLU 984 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972E ILE* 4.3 15.0 - - + +
980E HIS* 2.9 37.6 + - - +
981E ARG* 3.9 8.6 - - - +
983E ILE* 1.3 75.4 - - - +
985E MET* 1.3 59.1 + - + +
987E GLN* 3.2 18.5 + - - +
988E LYS* 2.9 29.3 + - - +
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Residues in contact with MET 985 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981E ARG* 3.1 46.8 + - + +
982E GLU* 3.9 5.8 - - - +
984E GLU* 1.3 76.7 - - + +
986E ALA* 1.3 58.0 + - - +
988E LYS* 3.5 27.3 + - + +
989E LEU* 3.0 27.5 + - - +
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Residues in contact with ALA 986 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982E GLU 3.3 10.5 + - - +
983E ILE* 3.0 9.9 + - - +
985E MET* 1.3 75.6 - - - +
987E GLN* 1.3 65.8 + - - +
989E LEU* 3.3 12.9 + - + +
990E LEU* 3.1 25.7 + - - +
1030E ASP 5.2 2.9 - - - +
1033E ASN* 4.6 13.5 - - - +
1034E LEU* 3.8 30.7 - - + +
1037E VAL* 5.1 4.0 - - + -
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Residues in contact with GLN 987 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965E LEU* 3.8 30.7 + - + +
968E VAL* 3.6 28.5 - - + +
969E ASP* 2.8 29.5 + - - +
972E ILE* 3.3 23.9 - - - +
983E ILE* 2.9 19.6 + - + +
984E GLU* 3.2 16.9 + - - +
986E ALA* 1.3 73.2 - - - +
988E LYS* 1.3 65.9 + - - +
990E LEU* 2.9 15.7 + - - +
991E ASN* 3.0 18.2 + - - +
1034E LEU* 4.6 5.8 - - + -
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Residues in contact with LYS 988 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984E GLU 2.9 17.1 + - - +
985E MET* 3.8 27.8 - - + +
987E GLN* 1.3 75.2 - - - +
989E LEU* 1.3 62.7 + - - +
991E ASN* 3.3 14.2 + - + +
992E SER* 3.1 32.1 + - - +
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Residues in contact with LEU 989 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985E MET 3.0 14.7 + - - +
986E ALA* 3.4 14.8 - - + +
987E GLN 3.1 0.2 - - - -
988E LYS* 1.3 78.3 - - - +
990E LEU* 1.3 57.2 + - - +
992E SER* 3.3 9.7 + - - -
993E ASP* 2.9 39.5 + - - +
1030E ASP* 3.4 39.3 - - + +
1033E ASN* 5.7 6.5 - - - +
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Residues in contact with LEU 990 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961E LEU* 3.7 32.6 - - + +
964E LEU* 4.4 4.5 - - + -
965E LEU* 4.2 7.9 - - + -
986E ALA 3.1 14.7 + - - +
987E GLN 2.9 8.7 + - - +
989E LEU* 1.3 73.6 - - - +
991E ASN* 1.3 65.4 + - - +
993E ASP* 3.3 11.9 + - - +
994E LEU* 3.0 24.1 + - - +
1027E LEU* 3.7 34.3 - - + +
1030E ASP* 3.9 8.1 - - + +
1031E ALA* 3.8 23.3 - - + +
1034E LEU* 3.8 29.4 - - + -
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Residues in contact with ASN 991 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ASN* 3.4 40.5 + - + +
961E LEU* 4.7 2.7 - - - +
965E LEU* 3.6 22.2 - - - +
987E GLN* 3.0 16.8 + - - +
988E LYS* 3.5 15.7 - - + +
990E LEU* 1.3 76.3 - - - +
992E SER* 1.3 61.4 + - - +
994E LEU* 3.4 11.0 + - - +
995E GLY* 3.2 17.5 + - - -
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Residues in contact with SER 992 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988E LYS* 3.1 21.6 + - - +
989E LEU* 3.6 13.6 - - - -
991E ASN* 1.3 75.3 - - - +
993E ASP* 1.3 67.5 + - - +
995E GLY* 3.2 3.4 + - - +
996E GLU* 2.9 29.6 + - - +
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Residues in contact with ASP 993 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989E LEU* 2.9 30.6 + - - +
990E LEU* 3.3 8.5 + - - +
992E SER* 1.3 76.2 - - - +
994E LEU* 1.3 58.2 + - - +
996E GLU* 3.2 9.1 + - - +
997E LEU* 2.9 29.5 + - - +
1023E ALA 4.9 5.0 - - - +
1026E ALA* 5.0 4.5 - - - +
1027E LEU* 3.9 30.4 - - + +
1030E ASP* 2.7 39.7 - - - +
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Residues in contact with LEU 994 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 5.9 0.2 - - + -
70D THR* 3.8 28.0 - - - +
71D GLU* 4.1 14.6 - - + +
954E VAL* 5.1 4.0 - - + +
957E VAL* 4.7 11.4 - - + -
958E GLY* 3.8 28.3 - - - +
961E LEU* 3.8 21.3 - - + -
990E LEU 3.0 12.9 + - - +
991E ASN* 3.6 13.2 - - - +
993E ASP* 1.3 76.5 - - - +
995E GLY* 1.3 57.4 + - - +
997E LEU* 3.1 9.7 + - + +
998E ILE* 2.9 47.8 + - + +
1027E LEU* 3.8 7.3 - - + +
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Residues in contact with GLY 995 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLU* 4.6 14.2 - - - +
991E ASN 3.2 8.0 + - - -
992E SER* 3.2 6.3 + - - -
994E LEU* 1.3 78.8 - - - +
996E GLU* 1.3 62.2 + - - +
998E ILE* 3.3 8.5 + - - +
999E SER* 3.0 27.3 + - - -
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Residues in contact with GLU 996 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992E SER* 2.9 19.9 + - - +
993E ASP* 3.5 11.7 - - - +
995E GLY* 1.3 75.7 - - - +
997E LEU* 1.3 56.5 + - - +
999E SER* 3.3 8.4 + - - -
1000E LYS* 2.9 54.5 + - + +
1023E ALA* 4.6 9.0 - - + -
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Residues in contact with LEU 997 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954E VAL* 4.2 22.4 - - + -
957E VAL* 4.1 27.4 - - + -
993E ASP 2.9 13.6 + - - +
994E LEU* 3.5 11.4 - - + +
996E GLU* 1.3 76.1 - - - +
998E ILE* 1.3 58.7 + - - +
1000E LYS* 3.4 1.3 + - - +
1001E MET* 3.0 27.7 + - - +
1020E MET* 3.3 39.3 - - + +
1023E ALA* 4.0 12.7 - - + +
1024E ALA* 3.8 26.2 - - + +
1027E LEU* 5.0 6.3 - - + -
938F MET* 4.3 7.2 - - + -
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Residues in contact with ILE 998 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 4.2 20.6 - - + +
70D THR* 5.0 0.4 - - - +
71D GLU* 3.7 46.7 - - + +
954E VAL* 4.1 19.3 - - + -
994E LEU* 2.9 34.7 + - + +
995E GLY* 3.7 5.2 - - - +
997E LEU* 1.3 77.3 - - - +
999E SER* 1.3 64.2 + - - +
1001E MET* 3.2 12.7 + - + +
1002E LYS* 3.0 49.7 + - + +
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Residues in contact with SER 999 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995E GLY 3.0 17.4 + - - -
996E GLU* 3.7 9.8 + - - -
998E ILE* 1.3 78.3 - - - +
1000E LYS* 1.3 66.5 + - - +
1002E LYS* 3.2 10.4 + - - +
1003E LEU* 3.1 31.3 + - - +
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Residues in contact with LYS1000 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996E GLU* 2.9 37.8 + - - +
997E LEU* 3.8 3.6 - - - +
999E SER* 1.3 77.9 - - - +
1001E MET* 1.3 56.6 + - - +
1003E LEU* 3.4 20.0 + - + +
1004E ALA* 2.9 27.9 + - - +
1016E TYR* 4.0 7.1 - - + +
1019E GLN* 2.9 47.9 + - + +
1020E MET* 3.7 23.3 - - - +
1023E ALA* 4.2 7.9 - - + -
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Residues in contact with MET1001 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 3.8 22.0 - - + -
950E TYR* 3.3 49.6 - - + +
951E VAL* 3.8 14.1 - - + -
954E VAL* 3.8 13.7 - - + -
997E LEU 3.0 18.9 + - - +
998E ILE* 3.5 9.6 - - + +
1000E LYS* 1.3 77.0 - - - +
1002E LYS* 1.3 89.2 + - + +
1004E ALA* 3.1 3.0 + - - +
1005E GLN* 2.9 32.2 + - - +
1020E MET* 3.6 21.0 - - + +
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Residues in contact with LYS1002 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 5.7 3.1 - - - -
68D LYS* 6.3 1.2 - - - +
71D GLU* 5.0 6.3 + - - -
998E ILE* 3.0 40.4 + - + +
999E SER* 3.2 8.5 + - - +
1001E MET* 1.3 89.9 - - + +
1003E LEU* 1.3 60.1 + - + +
1005E GLN* 3.6 11.4 + - - +
1006E GLN* 3.2 24.9 + - - +
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Residues in contact with LEU1003 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999E SER* 3.1 19.2 + - - +
1000E LYS* 3.7 19.1 - - - +
1002E LYS* 1.3 77.5 - - + +
1004E ALA* 1.3 64.3 + - - +
1005E GLN 3.1 1.8 - - - -
1006E GLN* 2.9 32.0 + - - +
1007E TYR* 3.1 26.2 + - + +
1016E TYR* 3.7 38.9 - - + +
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Residues in contact with ALA1004 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947E PRO* 4.6 4.9 - - - +
950E TYR* 3.9 23.5 - - + -
1000E LYS 2.9 17.3 + - - +
1001E MET* 3.1 7.6 + - - +
1003E LEU* 1.3 76.4 - - - +
1005E GLN* 1.3 59.7 + - - +
1006E GLN 3.6 0.2 + - - -
1007E TYR* 4.0 14.9 + - - +
1008E VAL* 4.1 5.7 - - - +
1013E GLN* 5.1 6.7 - - - +
1016E TYR* 3.8 29.7 - - - +
1017E LYS* 3.9 7.4 - - + +
1020E MET* 4.5 2.2 - - - -
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Residues in contact with GLN1005 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D LYS* 5.9 1.8 - - - +
947E PRO* 2.6 33.6 + - + +
948E GLU* 3.7 9.5 + - - +
950E TYR* 3.7 21.7 - - + +
951E VAL* 3.7 27.0 - - - +
1001E MET* 2.9 26.0 + - - +
1002E LYS* 3.8 9.5 - - - +
1003E LEU 3.1 0.2 - - - -
1004E ALA* 1.3 75.2 - - - +
1006E GLN* 1.3 59.1 + - - +
1007E TYR 3.6 0.2 - - - -
1008E VAL* 3.1 23.2 - - + +
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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