Contacts of the helix formed by residues 85 - 114 (chain R) in PDB entry 1JY3
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 85 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N ASN 3.5 13.6 + - - +
46N THR* 3.0 13.8 + - - +
48N CYS* 3.4 35.9 - - + -
21P THR* 3.9 20.9 - - + -
83R CYS 4.2 0.4 - - - -
84R PRO* 1.3 77.0 - - - +
86R GLY* 1.3 66.1 + - - +
87R CYS* 3.2 9.7 + - - +
88R LYS* 3.1 19.8 + - - +
89R LEU* 3.0 24.4 + - - +
19S CYS* 4.4 0.3 - - - -
22S THR* 5.4 0.4 - - - -
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Residues in contact with GLY 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P THR* 5.6 0.2 - - - +
85R THR* 1.3 76.0 - - - +
87R CYS* 1.3 56.1 + - - +
89R LEU* 4.3 2.2 - - - +
90R GLN* 2.9 29.8 + - - +
19S CYS* 4.5 1.8 - - - +
20S PRO* 3.3 32.2 + - - +
21S THR 4.9 3.1 - - - -
22S THR* 5.1 3.9 - - - +
25S ILE* 3.6 18.3 - - - +
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Residues in contact with CYS 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P TYR* 5.6 1.3 - - - -
85R THR* 3.1 6.5 + - - +
86R GLY* 1.3 74.8 - - - +
88R LYS* 1.3 59.7 + - - +
90R GLN* 3.3 11.4 + - - +
91R ASP* 3.0 37.0 + - - +
17S SER* 5.5 1.8 - - - -
18S TYR 3.8 5.8 - - - -
19S CYS* 2.0 52.9 - - - +
20S PRO* 4.2 3.1 - - - -
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Residues in contact with LYS 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N THR* 3.8 37.2 - - + +
47N LYS* 6.1 2.9 - - + +
55Q LYS* 4.7 11.1 - - - +
70R ASP* 5.1 4.0 + - - -
84R PRO* 4.1 15.3 - - + +
85R THR* 3.1 19.8 + - - +
87R CYS* 1.3 78.9 - - - +
89R LEU* 1.3 57.5 + - - +
91R ASP* 3.3 14.1 + - + +
92R THR* 3.0 49.9 + - - +
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Residues in contact with LEU 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q GLY* 3.9 16.4 - - - +
54Q MET* 4.2 6.3 - - + -
55Q LYS* 3.9 18.6 - - + +
58Q ILE* 3.8 20.1 - - + +
84R PRO* 3.6 31.4 - - + +
85R THR 3.0 21.1 + - - +
88R LYS* 1.3 76.6 - - - +
90R GLN* 1.3 56.9 + - - +
92R THR* 3.3 6.8 + - - -
93R LEU* 2.9 32.6 + - - +
22S THR* 3.8 26.7 - - + -
25S ILE* 3.9 24.2 - - + -
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Residues in contact with GLN 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P ASP* 3.8 8.9 + - - -
15P PHE* 3.4 51.3 - - + -
18P TYR* 3.0 24.7 + - - -
86R GLY 2.9 18.1 + - - +
87R CYS* 3.6 10.6 - - - +
89R LEU* 1.3 76.6 - - - +
91R ASP* 1.3 62.7 + - - +
93R LEU* 3.2 2.6 + - - +
94R VAL* 2.9 35.9 + - + +
20S PRO* 3.5 19.3 - - + +
25S ILE* 3.7 3.5 - - + +
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Residues in contact with ASP 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R CYS* 3.0 22.5 + - - +
88R LYS* 3.5 17.0 - - + +
90R GLN* 1.3 82.8 - - - +
92R THR* 1.3 64.0 + - - +
94R VAL* 3.5 5.4 + - - +
95R ARG* 3.0 27.8 + - - +
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Residues in contact with THR 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Q LYS* 4.1 19.5 - - + -
58Q ILE* 4.0 16.6 - - + -
88R LYS* 3.0 33.3 + - - +
89R LEU* 3.5 11.8 - - - -
90R GLN 3.2 0.2 - - - -
91R ASP* 1.3 77.8 - - - +
93R LEU* 1.3 57.3 + - - +
95R ARG* 3.4 22.0 + - - +
96R GLN* 3.0 52.1 + - - +
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Residues in contact with LEU 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P PHE* 4.2 11.0 - - + -
58Q ILE* 3.9 37.2 - - + -
89R LEU 2.9 19.8 + - - +
90R GLN 3.2 3.8 + - - +
92R THR* 1.3 74.5 - - - +
94R VAL* 1.3 60.4 + - - +
96R GLN* 3.8 8.7 - - - +
97R GLU* 2.9 33.0 + - - +
25S ILE* 3.9 20.4 - - + +
28S PHE* 3.8 38.0 - - + -
29S LEU* 4.1 21.1 - - + -
32S TYR* 4.4 10.9 - - + -
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Residues in contact with VAL 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ARG* 4.7 11.0 - - - +
15P PHE* 4.0 24.5 - - + -
90R GLN* 2.9 23.6 + - + +
91R ASP* 4.0 5.4 - - - +
93R LEU* 1.3 77.5 - - - +
95R ARG* 1.3 62.5 + - - +
96R GLN 3.5 0.2 + - - -
97R GLU* 4.0 9.2 - - - +
98R ARG* 3.7 25.6 + - + +
28S PHE* 5.5 0.2 - - + -
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Residues in contact with ARG 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Q LYS* 5.9 1.2 - - - +
91R ASP 3.0 17.5 + - - +
92R THR* 3.6 32.6 + - - +
94R VAL* 1.3 79.6 - - - +
96R GLN* 1.3 79.1 + - - +
98R ARG* 4.2 6.8 + - - +
99R PRO* 3.0 25.3 - - - +
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Residues in contact with GLN 96 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Q ILE* 3.3 28.7 + - - +
59Q ASP* 4.2 8.5 - - - +
62Q ASP* 3.6 41.6 + - - +
92R THR* 3.0 34.1 + - - +
93R LEU* 3.3 10.8 + - - +
95R ARG* 1.3 96.9 + - - +
97R GLU* 1.3 64.2 + - - +
99R PRO* 3.3 17.7 - - - +
100R ILE* 3.4 15.9 - - - +
32S TYR* 4.1 9.6 - - + +
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Residues in contact with GLU 97 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ARG* 3.0 42.9 + - - -
93R LEU 2.9 17.8 + - - +
94R VAL* 4.0 8.3 - - - +
95R ARG 3.5 0.2 - - - -
96R GLN* 1.3 76.8 - - - +
98R ARG* 1.3 65.0 + - + +
100R ILE* 3.4 1.2 + - - +
101R ARG* 2.9 52.7 + - + +
28S PHE* 3.9 12.4 - - + -
32S TYR* 3.6 32.4 + - + +
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Residues in contact with ARG 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R VAL* 3.7 16.7 + - + +
95R ARG* 4.2 5.5 + - - +
96R GLN 3.3 0.4 - - - -
97R GLU* 1.3 80.9 - - + +
99R PRO* 1.3 72.5 - - + +
101R ARG* 3.9 3.7 - - - +
102R LYS* 3.0 36.3 + - - +
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Residues in contact with PRO 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R ARG 3.0 24.7 - - - +
96R GLN* 3.3 16.2 - - - +
98R ARG* 1.3 96.2 - - + +
100R ILE* 1.3 59.2 + - + +
102R LYS* 4.0 12.3 - - + +
103R SER* 2.7 39.5 + - - +
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Residues in contact with ILE 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q ASP* 4.2 11.7 - - - +
65Q PHE* 4.0 19.5 - - + -
66Q THR* 4.2 16.4 - - - +
69Q ILE* 3.7 24.0 - - + -
96R GLN 3.4 15.0 - - - +
97R GLU 3.4 2.0 + - - +
98R ARG 3.3 0.8 - - - -
99R PRO* 1.3 80.8 - - + +
101R ARG* 1.3 63.2 + - - +
103R SER* 3.7 1.6 - - - -
104R ILE* 3.1 33.2 + - + +
32S TYR* 3.6 21.8 - - - +
36S VAL* 3.7 32.5 - - + -
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Residues in contact with ARG 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ARG* 6.0 0.2 - - - +
97R GLU* 2.9 47.7 + - + +
98R ARG* 3.9 3.6 - - - +
100R ILE* 1.3 76.2 - - - +
102R LYS* 1.3 62.8 + - - +
104R ILE* 3.3 10.1 + - - +
105R GLU* 3.1 32.5 + - + +
32S TYR* 4.5 7.3 + - - +
35S SER* 3.1 36.4 + - - -
36S VAL* 3.7 31.6 - - + +
39S ASP* 4.0 17.0 + - - -
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Residues in contact with LYS 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R ARG* 3.0 23.5 + - - +
99R PRO* 4.0 11.7 - - + +
101R ARG* 1.3 76.0 - - - +
103R SER* 1.3 69.3 + - - +
105R GLU* 3.1 16.0 + - - +
106R ASP* 2.9 41.0 + - - +
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Residues in contact with SER 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ILE* 3.9 20.5 - - - +
73Q ARG* 3.6 26.9 + - - +
99R PRO* 2.7 26.8 + - - +
100R ILE 3.7 3.6 - - - -
102R LYS* 1.3 81.6 - - - +
104R ILE* 1.3 57.8 + - - +
106R ASP* 3.9 7.0 - - - +
107R LEU* 2.9 33.4 + - - +
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Residues in contact with ILE 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ILE* 4.4 7.6 - - + -
100R ILE* 3.1 23.0 + - + +
101R ARG* 3.7 9.9 - - - +
103R SER* 1.3 73.9 - - - +
105R GLU* 1.3 65.9 + - + +
107R LEU* 3.6 7.7 + - + +
108R ARG* 3.1 34.9 + - - +
36S VAL* 3.6 36.6 - - + +
39S ASP* 3.9 27.1 - - + +
40S LEU* 3.8 25.4 - - + -
43S LEU* 4.5 11.7 - - + +
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Residues in contact with GLU 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R ARG* 3.1 18.6 + - + +
102R LYS* 3.5 18.0 - - - +
104R ILE* 1.3 79.4 - - + +
106R ASP* 1.3 64.6 + - - +
108R ARG* 3.2 26.7 + - - +
109R ASN* 3.3 20.8 + - - +
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Residues in contact with ASP 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Q ARG* 6.2 0.4 - - - +
102R LYS* 2.9 38.9 + - - +
103R SER* 3.9 6.0 - - - +
105R GLU* 1.3 77.3 - - - +
107R LEU* 1.3 62.1 + - - +
109R ASN* 3.1 14.9 + - - +
110R THR* 2.8 32.9 + - - +
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Residues in contact with LEU 107 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ILE* 4.3 23.6 - - + +
72Q LEU* 3.8 35.9 - - + -
73Q ARG* 4.2 17.0 - - + +
76Q LEU* 3.9 33.9 - - + -
103R SER 2.9 20.4 + - - +
104R ILE* 3.8 8.7 - - + +
106R ASP* 1.3 75.5 - - - +
108R ARG* 1.3 64.7 + - - +
110R THR* 3.2 6.5 + - - -
111R VAL* 3.0 28.9 + - + +
40S LEU* 5.8 0.2 - - + -
43S LEU* 4.6 12.8 - - + -
47S LEU* 6.0 1.6 - - + -
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Residues in contact with ARG 108 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R ILE* 3.1 31.8 + - - +
105R GLU* 3.3 16.7 - - - +
106R ASP 3.2 0.4 - - - -
107R LEU* 1.3 76.6 - - - +
109R ASN* 1.3 65.0 + - - +
111R VAL* 3.3 17.1 - - - +
112R ASP* 3.5 13.8 + - - +
39S ASP* 3.2 37.0 + - - +
42S THR* 6.1 3.9 - - - +
43S LEU* 4.2 28.2 - - + +
----------------------------------------------------------
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Residues in contact with ASN 109 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R GLU* 3.5 19.6 + - - +
106R ASP* 3.1 15.1 + - - +
108R ARG* 1.3 78.1 - - - +
110R THR* 1.3 61.6 + - - +
112R ASP* 3.0 13.5 + - - +
113R SER* 2.8 28.8 + - - -
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Residues in contact with THR 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q LEU* 3.8 30.7 - - + -
77Q PHE* 6.4 0.9 - - + -
106R ASP* 2.8 21.5 + - - +
107R LEU* 3.7 9.0 - - - -
109R ASN* 1.3 73.8 - - - +
111R VAL* 1.3 66.8 + - - +
113R SER* 3.3 11.7 + - - +
114R VAL* 3.0 35.0 + - + +
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Residues in contact with VAL 111 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q LEU* 4.3 11.9 - - + -
107R LEU* 3.0 19.8 + - + +
108R ARG* 3.3 9.9 - - - +
109R ASN 3.2 0.2 - - - -
110R THR* 1.3 76.4 - - - +
112R ASP* 1.3 67.5 + - - +
114R VAL* 3.6 18.3 - - - +
43S LEU* 4.1 10.8 - - + -
46S ILE* 3.9 27.4 - - + -
47S LEU* 3.9 28.7 - - + -
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Residues in contact with ASP 112 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R ARG 3.5 14.7 + - - +
109R ASN* 3.0 12.9 + - - +
111R VAL* 1.3 85.0 - - - +
113R SER* 1.3 61.6 + - - +
114R VAL 3.3 2.5 + - - -
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Residues in contact with SER 113 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109R ASN* 2.8 14.3 + - - -
110R THR* 3.3 23.6 + - - +
112R ASP* 1.3 72.1 - - - +
114R VAL* 1.3 65.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 114 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q LEU* 4.5 16.8 - - + +
77Q PHE* 3.7 42.8 - - + -
110R THR* 3.0 35.7 + - + +
111R VAL* 3.6 15.3 - - - +
112R ASP 3.3 2.7 - - - -
113R SER* 1.3 82.8 + - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il