Contacts of the helix formed by residues 979 - 1007 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975F LEU* 4.1 4.5 - - - +
976F PRO* 2.8 27.1 + - + +
977F ALA 3.0 0.2 - - - -
978F SER* 1.3 89.1 - - - +
980F HIS* 1.3 65.3 + - - +
981F ARG 3.4 2.2 - - - -
982F GLU* 3.6 14.9 + - - +
983F ILE* 3.1 27.5 + - - +
1037F VAL* 5.5 2.2 - - - +
1040F GLN* 5.3 6.1 - - + +
1041F ALA* 3.4 40.6 - - + +
1044F LYS* 5.1 5.6 - - - +
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Residues in contact with HIS 980 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972F ILE* 3.5 35.9 + - + +
973F PRO* 4.5 9.1 - - + +
975F LEU* 3.0 23.0 + - + -
976F PRO 3.1 19.4 + - - -
977F ALA* 3.0 27.5 + - + +
978F SER 3.6 0.2 - - - -
979F THR* 1.3 78.8 - - - +
981F ARG* 1.3 64.9 + - + +
983F ILE* 3.3 7.3 + - + +
984F GLU* 3.0 36.7 + - - +
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Residues in contact with ARG 981 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977F ALA 4.7 0.4 + - - -
978F SER 5.5 0.6 - - - -
979F THR 3.4 0.2 - - - -
980F HIS* 1.3 79.8 - - + +
982F GLU* 1.3 65.7 + - - +
983F ILE 3.2 1.3 - - - -
984F GLU* 3.4 21.9 + - - +
985F MET* 3.3 34.3 + - + +
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Residues in contact with GLU 982 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978F SER 5.2 5.9 + - - +
979F THR* 3.6 16.7 + - - +
980F HIS 3.4 0.4 - - - -
981F ARG* 1.3 78.6 - - - +
983F ILE* 1.3 61.0 + - - +
985F MET* 3.9 6.5 + - - +
986F ALA* 3.7 15.9 + - - +
1037F VAL* 3.8 33.9 - - + +
1040F GLN* 6.1 1.5 - - - +
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Residues in contact with ILE 983 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968F VAL* 3.9 27.8 - - + -
972F ILE* 3.9 15.3 - - + -
975F LEU* 3.8 29.4 - - + -
979F THR* 3.1 22.7 - - - +
980F HIS* 3.3 9.3 + - + +
981F ARG 3.2 0.4 - - - -
982F GLU* 1.3 77.2 - - - +
984F GLU* 1.3 63.8 + - - +
985F MET 3.2 0.6 + - - -
986F ALA* 3.3 6.6 + - - +
987F GLN* 3.2 19.8 + - + +
1034F LEU* 4.0 12.2 - - + +
1037F VAL* 3.6 21.1 - - + -
1038F ILE* 4.0 14.6 - - + -
1041F ALA* 4.3 6.3 - - + -
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Residues in contact with GLU 984 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972F ILE* 4.3 15.1 - - + +
980F HIS* 3.0 28.2 + - - +
981F ARG* 3.4 29.1 + - - +
982F GLU 3.5 0.2 - - - -
983F ILE* 1.3 76.0 - - - +
985F MET* 1.3 62.5 + - + +
987F GLN* 3.4 22.2 - - - +
988F LYS* 3.3 33.2 + - - +
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Residues in contact with MET 985 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981F ARG* 3.3 22.2 + - + +
982F GLU* 4.2 5.6 - - - +
983F ILE 3.2 0.4 - - - -
984F GLU* 1.3 78.0 - - + +
986F ALA* 1.3 60.6 + - - +
987F GLN 3.2 0.2 - - - -
988F LYS* 3.3 11.0 + - + +
989F LEU* 2.9 29.0 + - - +
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Residues in contact with ALA 986 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982F GLU 3.7 10.4 + - - +
983F ILE* 3.3 4.8 + - - +
985F MET* 1.3 74.9 - - - +
987F GLN* 1.3 65.2 + - - +
989F LEU* 3.5 11.4 + - + +
990F LEU* 3.2 27.9 + - - +
1030F ASP 4.7 4.0 - - - +
1033F ASN* 4.3 15.7 - - - +
1034F LEU* 3.7 35.9 - - + +
1037F VAL* 5.3 2.5 - - + -
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Residues in contact with GLN 987 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965F LEU* 3.7 33.5 + - + +
968F VAL* 3.4 33.8 - - + +
969F ASP* 3.1 27.1 + - - +
972F ILE* 4.0 7.9 - - - +
983F ILE 3.2 12.3 + - - +
984F GLU* 3.4 24.8 - - - +
985F MET 3.2 0.4 - - - -
986F ALA* 1.3 76.3 - - - +
988F LYS* 1.3 65.2 + - + +
990F LEU* 3.0 16.0 + - - +
991F ASN* 3.0 17.8 + - - +
1034F LEU* 4.4 6.7 - - + +
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Residues in contact with LYS 988 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984F GLU* 3.3 21.9 + - - +
985F MET* 3.3 11.6 + - + +
987F GLN* 1.3 76.5 - - + +
989F LEU* 1.3 62.2 + - - +
991F ASN* 3.2 15.1 + - - +
992F SER* 3.0 27.2 + - - -
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Residues in contact with LEU 989 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985F MET 2.9 16.8 + - - +
986F ALA* 3.7 11.4 - - + +
987F GLN 3.2 0.2 - - - -
988F LYS* 1.3 78.3 - - - +
990F LEU* 1.3 57.2 + - - +
992F SER* 3.6 7.3 + - - -
993F ASP* 3.0 38.9 + - - +
1030F ASP* 3.3 39.9 - - + +
1033F ASN* 6.0 3.6 - - - +
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Residues in contact with LEU 990 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931E LEU* 4.9 0.9 - - + -
961F LEU* 3.8 35.0 - - + +
964F LEU* 4.4 2.9 - - + -
965F LEU* 4.6 4.7 - - + -
986F ALA 3.2 14.5 + - - +
987F GLN* 3.0 9.2 + - - +
989F LEU* 1.3 75.3 - - - +
991F ASN* 1.3 64.1 + - - +
993F ASP* 3.2 8.2 + - - +
994F LEU 3.0 18.0 + - - -
1027F LEU* 3.7 25.0 - - + +
1030F ASP* 3.8 14.6 - - + +
1031F ALA* 3.6 36.3 - - + +
1034F LEU* 3.7 30.3 - - + -
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Residues in contact with ASN 991 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 3.1 48.0 + - - +
961F LEU* 4.4 4.9 - - - +
965F LEU* 3.2 25.8 - - - +
987F GLN* 3.0 17.5 + - - +
988F LYS* 3.2 17.9 + - - +
990F LEU* 1.3 74.0 - - - +
992F SER* 1.3 65.2 + - - +
994F LEU* 3.0 16.6 + - - +
995F GLY* 3.1 12.0 + - - -
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Residues in contact with SER 992 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988F LYS 3.0 15.9 + - - -
989F LEU* 3.9 10.7 - - - -
991F ASN* 1.3 75.2 - - - +
993F ASP* 1.3 54.0 + - - +
995F GLY* 3.4 1.9 + - - +
996F GLU* 2.7 37.6 + - - +
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Residues in contact with ASP 993 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989F LEU* 3.0 28.5 + - - +
990F LEU* 3.3 12.4 - - - +
991F ASN 3.2 0.4 - - - -
992F SER* 1.3 77.4 - - - +
994F LEU* 1.3 57.6 + - - +
996F GLU* 3.5 10.0 + - - +
997F LEU* 2.9 27.0 + - - +
1023F ALA* 4.7 4.0 - - - +
1026F ALA* 3.4 20.0 - - - +
1027F LEU* 3.6 21.7 - - + +
1030F ASP* 2.7 38.9 - - - +
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Residues in contact with LEU 994 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 5.4 0.2 - - + -
70B THR* 3.9 25.8 - - - +
71B GLU* 4.7 2.2 - - - +
73B ASN* 5.9 2.7 - - - +
954F VAL* 4.7 4.5 - - + +
957F VAL* 4.4 14.4 - - + -
958F GLY* 3.8 36.3 - - - +
961F LEU* 3.8 26.7 - - + -
990F LEU 3.0 5.3 + - - -
991F ASN* 3.0 9.1 + - - +
993F ASP* 1.3 75.2 - - - +
995F GLY* 1.3 60.4 + - - +
997F LEU* 2.9 14.3 + - + +
998F ILE* 2.8 49.5 + - + +
1027F LEU* 4.2 5.3 - - + +
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Residues in contact with GLY 995 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLU* 4.5 14.9 - - - +
991F ASN 3.1 13.3 + - - -
992F SER* 3.9 2.5 - - - -
994F LEU* 1.3 75.7 - - - +
996F GLU* 1.3 61.1 + - - +
998F ILE* 3.4 12.6 + - - +
999F SER* 3.0 26.7 + - - -
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Residues in contact with GLU 996 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992F SER 2.7 23.4 + - - +
993F ASP* 3.6 9.0 - - - +
995F GLY* 1.3 71.2 - - - +
997F LEU* 1.3 66.9 + - - +
999F SER* 3.2 16.8 + - - -
1000F LYS* 3.2 42.6 + - - +
1019F GLN 4.9 1.4 - - - +
1022F THR* 6.1 0.5 - - - +
1023F ALA* 3.8 20.5 + - + +
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Residues in contact with LEU 997 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938E MET* 4.1 30.1 - - + -
954F VAL* 4.0 25.4 - - + -
957F VAL* 4.2 11.7 - - + -
993F ASP 2.9 13.9 + - - +
994F LEU* 2.9 12.8 + - + +
996F GLU* 1.3 75.2 - - - +
998F ILE* 1.3 62.3 + - - +
1000F LYS* 3.3 3.3 + - - -
1001F MET* 3.1 20.4 + - - +
1020F MET* 3.8 35.9 - - + +
1023F ALA* 4.0 14.8 - - + -
1024F ALA 4.4 2.0 - - - +
1027F LEU* 3.8 22.4 - - + -
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Residues in contact with ILE 998 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.9 23.1 - - + +
71B GLU* 3.6 44.6 - - + +
954F VAL* 4.1 19.3 - - + -
994F LEU* 2.8 34.5 + - + +
995F GLY* 3.7 5.8 - - - +
997F LEU* 1.3 76.1 - - - +
999F SER* 1.3 63.2 + - - +
1001F MET* 3.4 14.1 + - + +
1002F LYS* 3.2 48.5 + - - +
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Residues in contact with SER 999 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995F GLY 3.0 16.4 + - - -
996F GLU* 3.2 15.1 + - - -
998F ILE* 1.3 77.5 - - - +
1000F LYS* 1.3 65.7 + - - +
1002F LYS* 3.5 7.3 + - - +
1003F LEU* 3.2 28.3 + - - +
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Residues in contact with LYS1000 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996F GLU* 3.2 43.1 + - - +
997F LEU* 3.3 5.6 + - - +
999F SER* 1.3 77.1 - - - +
1001F MET* 1.3 65.3 + - - +
1003F LEU* 3.2 20.2 + - + +
1004F ALA* 2.9 24.1 + - - +
1016F TYR* 4.1 6.0 - - + +
1019F GLN* 3.0 45.8 + - + +
1020F MET* 3.6 26.6 - - + +
1023F ALA* 4.9 0.4 - - + -
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Residues in contact with MET1001 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.7 23.1 - - + -
950F TYR* 3.7 22.6 - - + -
951F VAL* 4.0 25.1 - - + -
954F VAL* 3.7 26.7 - - + -
997F LEU 3.1 16.7 + - - +
998F ILE* 3.8 9.4 - - + +
999F SER 3.3 0.2 - - - -
1000F LYS* 1.3 76.6 - - - +
1002F LYS* 1.3 79.9 + - + +
1004F ALA* 3.2 3.8 + - - +
1005F GLN* 3.0 45.7 + - - +
1020F MET* 3.6 21.0 - - + +
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Residues in contact with LYS1002 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 5.6 2.0 - - - -
71B GLU* 4.6 8.7 + - - -
998F ILE* 3.2 37.1 + - + +
999F SER* 3.9 7.0 - - - +
1001F MET* 1.3 91.6 - - + +
1003F LEU* 1.3 63.0 + - + +
1005F GLN* 3.4 12.5 + - - +
1006F GLN* 3.1 21.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU1003 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999F SER* 3.2 17.7 + - - +
1000F LYS* 3.2 21.5 + - + +
1002F LYS* 1.3 77.1 - - + +
1004F ALA* 1.3 64.6 + - - +
1006F GLN* 3.2 23.6 + - - +
1007F TYR* 3.0 28.2 - - + +
1016F TYR* 3.5 48.0 - - + +
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Residues in contact with ALA1004 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947F PRO* 3.7 13.2 - - + +
950F TYR* 4.0 23.6 - - + -
1000F LYS 2.9 12.7 + - - +
1001F MET 3.2 8.5 + - - +
1003F LEU* 1.3 75.2 - - - +
1005F GLN* 1.3 61.2 + - - +
1007F TYR* 3.4 20.6 + - - +
1008F VAL 3.7 0.9 + - - -
1013F GLN* 4.6 8.2 - - + +
1016F TYR* 3.8 23.6 - - + +
1017F LYS* 4.5 3.8 - - + +
1020F MET* 4.1 6.3 - - - -
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Residues in contact with GLN1005 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS* 4.1 8.9 - - - +
947F PRO* 3.7 11.4 - - + -
948F GLU* 3.4 61.8 + - - +
950F TYR* 5.0 0.4 - - + -
951F VAL* 3.6 17.1 - - - +
1001F MET* 3.0 48.5 + - + +
1002F LYS* 3.5 13.6 - - - +
1003F LEU 3.2 0.2 - - - -
1004F ALA* 1.3 74.5 - - - +
1006F GLN* 1.3 66.3 + - - +
1008F VAL* 3.1 21.6 - - - +
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Residues in contact with GLN1006 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002F LYS 3.1 13.8 + - - +
1003F LEU* 3.2 23.7 + - - +
1005F GLN* 1.3 76.7 - - - +
1007F TYR* 1.3 87.7 + - + +
1008F VAL 3.5 1.6 + - - -
1010F THR* 5.0 1.7 - - - +
----------------------------------------------------------
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Residues in contact with TYR1007 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003F LEU* 3.0 28.7 + - + +
1004F ALA 3.5 4.0 - - - +
1005F GLN 3.1 0.6 - - - -
1006F GLN* 1.3 106.3 + - + +
1008F VAL* 1.3 64.2 + - - +
1009F MET 3.2 3.6 + - - -
1010F THR* 3.1 36.0 + - + +
1012F LEU* 4.2 16.9 - - + +
1013F GLN* 3.0 31.8 - - - +
1016F TYR* 3.5 30.5 + + + -
----------------------------------------------------------
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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