Contacts of the helix formed by residues 1027 - 1060 (chain B) in PDB entry 5LPN
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 ARG1027 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B ASP* 1.3 81.5 - - + +
1028B GLN* 1.3 62.7 + - - +
1029B ALA 3.5 0.5 + - - -
1030B GLU* 3.8 11.0 + - - +
1031B ASP* 4.2 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1028 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B ASP 3.3 3.8 - - - +
1027B ARG* 1.3 77.1 - - - +
1029B ALA* 1.3 63.8 + - - +
1030B GLU 3.5 0.3 + - - -
1031B ASP* 3.5 14.0 + - - +
1032B GLN* 3.6 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1029 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014B TYR* 4.5 15.4 + - + +
1026B ASP* 3.6 18.9 + - - +
1027B ARG 3.3 1.2 - - - -
1028B GLN* 1.3 79.2 - - - +
1030B GLU* 1.3 62.5 + - - +
1032B GLN* 3.0 19.7 + - - +
1033B VAL* 3.1 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1030 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011B LEU* 4.0 21.5 - - + +
1014B TYR* 3.1 49.5 - - + +
1026B ASP 4.2 2.8 + - - +
1027B ARG 3.8 9.1 + - - +
1028B GLN 3.3 1.0 - - - -
1029B ALA* 1.3 79.8 - - - +
1031B ASP* 1.3 66.5 + - - +
1033B VAL* 2.9 27.3 - - - +
1034B LEU* 2.9 10.2 + - + +
70C ARG* 4.3 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B ARG 4.2 4.3 + - - +
1028B GLN* 3.5 12.5 + - - +
1029B ALA 3.3 0.6 - - - -
1030B GLU* 1.3 80.6 - - - +
1032B GLN* 1.3 63.0 + - - +
1034B LEU* 3.7 16.8 - - - +
1035B ARG* 3.0 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1032 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B GLN 3.6 6.6 + - - +
1029B ALA* 3.0 15.7 + - - +
1031B ASP* 1.3 78.5 + - - +
1033B VAL* 1.3 62.7 + - - +
1035B ARG* 3.2 6.9 + - - +
1036B LYS* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1033 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B LEU* 3.6 34.4 - - + +
1010B GLU* 3.9 21.5 - - + +
1011B LEU* 3.8 14.8 - - + -
1014B TYR* 4.6 14.4 - - + +
1029B ALA 3.1 3.9 + - - +
1030B GLU* 2.9 34.8 - - + +
1032B GLN* 1.3 79.3 - - - +
1034B LEU* 1.3 63.3 + - - +
1036B LYS* 3.1 8.9 + - - +
1037B LEU* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1034 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011B LEU* 3.9 17.7 - - + -
1030B GLU* 2.9 17.5 + - + +
1031B ASP* 3.7 15.3 - - - +
1033B VAL* 1.3 77.6 - - - +
1035B ARG* 1.3 74.5 + - + +
1037B LEU* 3.2 14.5 + - + +
1038B VAL* 3.0 34.6 + - + +
42C ILE* 4.0 26.9 - - + -
43C GLY* 4.9 4.7 - - - -
71C PHE* 4.7 15.3 - - + -
74C ILE* 4.5 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1035 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031B ASP* 3.0 43.3 + - - +
1032B GLN* 3.7 5.6 - - - +
1034B LEU* 1.3 82.8 - - + +
1036B LYS* 1.3 60.5 + - - +
1038B VAL* 3.8 11.9 - - - +
1039B ASP* 2.9 29.1 + - - +
74C ILE* 4.2 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1036 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B LEU* 4.7 14.4 - - + -
1032B GLN 3.0 12.4 + - - +
1033B VAL* 3.1 12.5 + - - +
1035B ARG* 1.3 73.3 - - - +
1037B LEU* 1.3 66.2 + - - +
1039B ASP* 3.3 7.9 + - - +
1040B LEU* 3.0 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1037 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B GLN* 4.7 15.8 - - + +
1007B LEU* 4.1 19.8 - - + +
1008B ASP* 4.0 32.3 - - + +
1011B LEU* 5.0 4.5 - - + -
1033B VAL 3.0 11.1 + - - +
1034B LEU* 3.2 16.8 + - + +
1036B LYS* 1.3 75.2 - - - +
1038B VAL* 1.3 76.6 + - + +
1040B LEU* 3.0 17.3 + - - +
1041B VAL* 3.1 26.5 + - + +
42C ILE* 3.9 37.0 - - + +
44C ILE 4.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1038 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034B LEU* 3.0 25.5 + - + +
1035B ARG* 3.8 14.6 - - + +
1036B LYS 3.3 0.2 - - - -
1037B LEU* 1.3 86.7 - - + +
1039B ASP* 1.3 65.3 + - - +
1041B VAL* 3.0 19.3 + - - +
1042B ASN* 3.0 25.9 + - - +
43C GLY* 5.2 2.2 - - - -
44C ILE* 4.8 9.4 - - + -
74C ILE* 4.1 26.5 - - + -
78C TYR* 3.7 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1039 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035B ARG 2.9 18.9 + - - +
1036B LYS* 3.3 7.8 + - - +
1038B VAL* 1.3 76.3 - - - +
1040B LEU* 1.3 58.9 + - - +
1042B ASN* 3.0 15.0 + - - +
1043B GLN* 2.6 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1040 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000B LEU* 3.7 31.3 - - + +
1003B LYS* 3.3 40.4 - - + -
1004B GLN* 4.1 13.5 - - + +
1007B LEU* 4.3 11.4 - - + -
1036B LYS* 3.0 16.2 + - + +
1037B LEU* 3.0 10.4 + - - +
1039B ASP* 1.3 75.4 - - - +
1041B VAL* 1.3 66.8 + - - +
1043B GLN* 3.0 35.0 + - - +
1044B ARG* 3.0 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1041 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B GLN* 3.2 26.7 + - - +
1037B LEU* 3.1 18.2 + - + +
1038B VAL* 3.0 11.2 + - - +
1040B LEU* 1.3 75.9 - - - +
1042B ASN* 1.3 61.9 + - - +
1044B ARG* 3.4 9.9 - - - +
1045B ASP* 2.9 24.4 + - - +
44C ILE* 3.7 33.4 - - + +
45C ASP* 4.7 2.5 - - - -
46C PHE* 3.8 9.4 - - + -
63C TRP* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1042 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038B VAL* 3.0 24.2 + - - +
1039B ASP* 3.0 14.0 + - - +
1041B VAL* 1.3 77.0 - - - +
1043B GLN* 1.3 60.6 + - + +
1045B ASP* 3.6 12.5 - - + +
1046B ALA* 2.8 28.2 + - - +
1049B ARG* 5.1 1.7 + - - -
78C TYR* 2.8 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1043 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 5.5 4.5 + - - -
1000B LEU* 3.8 24.5 - - + +
1039B ASP* 2.6 40.4 + - - +
1040B LEU* 3.0 24.6 + - - +
1042B ASN* 1.3 74.8 - - - +
1044B ARG* 1.3 65.4 + - - +
1046B ALA* 3.2 7.1 + - - +
1047B LEU* 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1044 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B GLU* 4.5 14.4 + - + +
1000B LEU* 3.5 32.8 - - + +
1001B GLU* 4.2 24.7 + - - +
1004B GLN* 2.9 41.3 + - - +
1040B LEU 3.0 16.5 + - - +
1041B VAL* 3.4 11.1 - - - +
1043B GLN* 1.3 75.0 - - - +
1045B ASP* 1.3 62.9 + - - +
1047B LEU* 3.1 8.6 + - - +
1048B ILE* 3.1 28.9 + - + +
45C ASP* 3.5 5.7 + - - -
46C PHE* 2.8 60.1 + - + -
47C LYS* 4.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1045 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B VAL 2.9 17.1 + - - +
1042B ASN* 3.6 14.2 - - - +
1044B ARG* 1.3 74.8 - - - +
1046B ALA* 1.3 58.8 + - - +
1048B ILE* 2.9 4.6 + - - +
1049B ARG* 2.8 51.9 + - - +
11C LYS* 5.8 0.2 + - - -
46C PHE* 3.9 8.5 - - + -
61C GLN* 3.0 22.6 + - - +
63C TRP* 3.7 27.3 - - + -
78C TYR* 5.5 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1046 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 4.3 17.4 - - + +
1042B ASN 2.8 22.4 + - - +
1043B GLN* 3.2 8.2 + - - +
1045B ASP* 1.3 72.4 - - - +
1047B LEU* 1.3 60.0 + - + +
1049B ARG* 3.5 24.0 + - - +
1050B PHE* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1047 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.4 19.7 - - + -
56A LYS* 5.9 3.4 - - - -
993B ILE* 4.0 23.1 - - + +
996B GLN* 3.5 49.1 - - + +
997B GLU* 4.1 12.6 - - + +
1000B LEU* 4.2 14.4 - - + -
1043B GLN 3.0 15.6 + - - +
1044B ARG 3.1 8.3 + - - +
1046B ALA* 1.3 78.2 - - + +
1048B ILE* 1.3 67.5 + - + +
1050B PHE* 3.1 7.6 + - + +
1051B GLN* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1048 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B GLU* 3.0 28.9 - - - +
1044B ARG* 3.1 29.0 + - + +
1045B ASP* 2.9 8.7 + - - +
1047B LEU* 1.3 73.7 - - - +
1049B ARG* 1.3 68.1 + - + +
1051B GLN* 3.2 20.6 - - - +
1052B GLU* 3.0 20.6 + - - +
6C TYR* 5.1 0.3 + - - -
9C LEU* 4.6 22.0 - - + -
11C LYS* 5.8 0.7 - - - +
46C PHE* 4.2 13.5 - - + -
48C ILE* 4.0 23.6 - - + -
59C LYS* 5.1 6.5 + - + +
61C GLN* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1049 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 3.4 44.8 + - - +
1042B ASN 5.1 1.4 + - - -
1045B ASP* 2.8 39.1 + - - +
1046B ALA* 3.9 17.9 - - - +
1048B ILE* 1.3 76.4 - - + +
1050B PHE* 1.3 63.1 + - - +
1052B GLU* 3.2 10.1 + - + +
1053B GLU* 3.0 36.6 + - + +
11C LYS* 4.2 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1050 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.6 37.7 - - + -
9A LEU 4.2 18.8 - - - -
10A PHE* 4.4 3.8 - + - -
83A MET* 4.1 15.5 - - + -
174A THR* 3.9 32.5 - - + +
175A PRO* 4.3 5.1 + - + -
993B ILE* 4.4 17.3 - - + -
1046B ALA 2.9 19.8 + - - +
1047B LEU* 3.4 7.2 - - + +
1049B ARG* 1.3 76.5 - - - +
1051B GLN* 1.3 66.2 + - - +
1053B GLU* 3.1 10.0 + - - +
1054B ARG* 3.0 56.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1051 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990B GLU* 3.3 29.1 - - - +
993B ILE* 3.5 28.1 - - + +
997B GLU* 4.5 9.3 + - - -
1047B LEU 3.0 11.7 + - - +
1048B ILE* 3.2 29.5 - - - +
1050B PHE* 1.3 77.6 - - - +
1052B GLU* 1.3 62.5 + - - +
1054B ARG* 3.3 11.7 + - + +
1055B ARG* 3.0 24.1 + - - +
6C TYR* 4.2 8.8 + - + +
59C LYS* 3.0 31.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1052 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048B ILE* 3.0 14.2 + - + +
1049B ARG* 3.3 14.8 - - + +
1050B PHE 3.2 0.2 - - - -
1051B GLN* 1.3 78.1 - - - +
1053B GLU* 1.3 61.2 + - + +
1055B ARG* 2.6 39.2 + - - +
1056B LEU* 3.0 41.0 + - + +
6C TYR* 2.6 27.7 + - - +
8C LEU* 4.8 4.5 - - - +
9C LEU* 3.3 29.4 - - + +
11C LYS* 5.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1053 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 5.6 1.6 - - - +
173A LYS 4.8 6.2 - - - +
174A THR 4.1 11.8 - - - +
175A PRO 3.8 17.6 - - - +
1049B ARG* 3.0 25.9 + - + +
1050B PHE* 3.8 7.3 - - + +
1052B GLU* 1.3 75.2 - - + +
1054B ARG* 1.3 66.4 + - - +
1056B LEU* 3.5 16.2 + - + +
1057B SER* 2.9 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1054 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 4.9 2.8 + - - -
11A LYS* 4.7 8.3 - - - +
81A GLY* 2.9 28.7 + - - -
82A ALA 5.2 0.2 + - - -
83A MET* 3.4 34.6 - - - +
1050B PHE* 3.0 55.0 + - + +
1051B GLN* 3.6 9.6 - - + +
1052B GLU 3.3 0.2 - - - -
1053B GLU* 1.3 80.7 + - - +
1055B ARG* 1.3 66.7 + - - +
1057B SER* 2.2 56.0 + - - -
1058B GLU* 3.0 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1055 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051B GLN 3.0 12.6 + - - +
1052B GLU* 2.6 50.8 + - - +
1054B ARG* 1.3 75.2 - - - +
1056B LEU* 1.3 83.8 + - - +
1058B GLU* 3.2 5.6 + - - +
1059B LEU* 3.1 53.9 + - + +
6C TYR* 3.2 52.1 + - + +
7C ASP 3.4 20.2 + - - -
8C LEU* 4.2 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1056 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052B GLU* 3.0 32.5 + - + +
1053B GLU* 3.5 19.1 - - + +
1055B ARG* 1.3 91.6 - - - +
1057B SER* 1.3 65.7 + - - +
1059B LEU* 3.2 23.4 + - + +
1060B ALA* 3.5 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1057 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.3 10.1 - - - +
81A GLY* 4.5 1.8 + - - -
112A ASN* 3.2 41.8 + - - +
1053B GLU 2.9 12.1 + - - -
1054B ARG* 2.2 56.5 + - - -
1056B LEU* 1.3 77.7 - - - +
1058B GLU* 1.3 63.3 + - - +
1059B LEU 3.3 0.2 + - - -
1060B ALA* 3.7 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1058 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 4.6 17.4 - - - +
81A GLY* 5.0 5.8 - - - -
1054B ARG 3.0 7.3 + - - +
1055B ARG* 4.0 6.5 - - - +
1057B SER* 1.3 79.9 + - - +
1059B LEU* 1.3 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1059 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055B ARG* 3.1 47.0 + - + +
1056B LEU* 3.2 14.5 + - + +
1058B GLU* 1.3 81.5 - - - +
1060B ALA* 1.3 70.7 + - - +
7C ASP 5.5 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1060 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 5.6 7.0 - - + -
111A ALA 6.1 0.9 - - - +
112A ASN* 4.0 13.9 - - - +
1056B LEU 3.5 6.0 + - - +
1057B SER 3.7 14.6 - - - +
1059B LEU* 1.3 86.1 - - - +
----------------------------------------------------------
Back to top of page
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