Contacts of the helix formed by residues 113 - 145 (chain O) in PDB entry 3IS7
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 ASP 113 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N ARG* 4.1 5.6 + - - +
128N GLU* 4.8 2.4 - - - +
4O ASP* 5.8 1.9 + - + +
7O VAL* 3.3 29.7 - - + +
61O ARG* 3.0 24.9 + - - -
65O LEU* 4.0 8.8 - - - +
108O CYS* 3.0 17.9 + - + +
111O VAL* 3.3 6.1 + - + +
112O HIS* 1.3 75.1 - - - +
114O TYR* 1.3 55.5 + - - +
115O VAL 3.7 1.0 + - - -
116O SER* 2.6 31.1 + - - -
117O ARG* 3.0 20.1 + - - +
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Residues in contact with TYR 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N ARG* 3.9 12.9 - - + +
105N ILE* 3.5 40.1 - - + +
106N VAL* 3.0 34.8 + - - +
117N ARG* 3.7 13.0 - - - +
121N LYS* 4.2 18.8 - - + +
124N LEU* 4.0 15.7 - - + -
109O GLU* 3.6 40.5 + - - -
112O HIS* 3.0 44.9 + - + -
113O ASP* 1.3 71.1 - - - +
115O VAL* 1.3 60.0 + - - +
117O ARG* 3.3 7.4 + - - +
118O ASP* 2.9 27.9 + - - +
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Residues in contact with VAL 115 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N LYS* 4.2 9.6 - - - +
124N LEU* 4.0 11.4 - - + -
125N GLU* 3.9 45.3 - - + +
128N GLU* 3.6 34.5 + - + +
61O ARG* 3.6 24.0 - - - +
113O ASP* 3.3 1.0 + - - -
114O TYR* 1.3 74.1 - - - +
116O SER* 1.4 64.5 + - - +
118O ASP* 3.0 5.7 + - + +
119O LEU* 3.0 21.9 + - + +
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Residues in contact with SER 116 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 4.0 4.8 - - - +
11O LEU* 4.1 8.6 - - - +
61O ARG* 2.9 29.9 + - - +
65O LEU* 3.9 4.3 - - - +
108O CYS* 3.7 15.5 - - - -
113O ASP* 2.6 36.1 + - - -
115O VAL* 1.4 71.6 - - - +
117O ARG* 1.3 67.7 + - - +
118O ASP 3.1 0.2 + - - -
119O LEU* 3.1 9.1 + - - +
120O LEU* 3.0 27.2 + - - +
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Residues in contact with ARG 117 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N ARG* 3.8 15.6 - - - +
105O ILE* 4.0 29.2 - - + +
108O CYS* 4.0 16.7 - - + +
109O GLU* 3.0 39.7 + - - +
113O ASP 3.0 14.3 + - - +
114O TYR* 3.4 11.9 - - - +
115O VAL 3.3 0.2 - - - -
116O SER* 1.3 77.3 - - - +
118O ASP* 1.3 54.0 + - - +
120O LEU* 3.2 5.3 + - - +
121O LYS* 2.8 41.5 + - + +
109X GLU* 2.9 41.4 + - - -
114X TYR* 3.4 16.7 + - - +
117X ARG* 3.6 18.3 - - - +
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Residues in contact with ASP 118 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N LYS* 3.5 31.3 - - + +
122N ASP* 5.6 0.7 - - - +
125N GLU* 4.6 7.2 - - - +
114O TYR 2.9 14.0 + - - +
115O VAL* 3.0 9.2 + - + +
117O ARG* 1.3 75.1 - - - +
119O LEU* 1.3 64.2 + - - +
121O LYS* 2.6 34.3 + - - +
122O ASP* 3.1 31.1 + - - +
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Residues in contact with LEU 119 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O LEU* 5.2 1.8 - - + -
57O LYS* 3.9 23.3 - - + +
58O LEU* 3.6 20.2 - - + +
61O ARG* 3.7 38.8 - - + -
115O VAL* 3.0 11.2 + - + +
116O SER* 3.4 9.0 - - - +
118O ASP* 1.3 73.7 - - - +
120O LEU* 1.4 63.4 + - + +
122O ASP* 3.2 11.9 + - - +
123O ILE* 3.0 52.5 + - + +
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Residues in contact with LEU 120 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O HIS* 5.8 0.2 - - + -
11O LEU* 3.8 27.4 - - + -
14O ILE* 4.3 5.4 - - + -
58O LEU* 4.1 7.0 - - + -
101O LEU* 4.0 22.5 - - + +
104O ALA* 3.7 38.1 - - + -
105O ILE* 3.7 15.6 - - + +
108O CYS* 4.0 18.4 - - - -
116O SER 3.0 12.8 + - - +
117O ARG 3.6 5.6 - - - +
119O LEU* 1.4 86.2 - - + +
121O LYS* 1.3 61.5 + - - +
123O ILE* 3.3 5.8 + - + +
124O LEU* 2.8 29.3 + - - +
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Residues in contact with LYS 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105O ILE* 4.1 8.2 - - + +
117O ARG* 2.8 26.5 + - + +
118O ASP* 2.6 33.1 + - - +
120O LEU* 1.3 78.4 - - - +
122O ASP* 1.3 77.7 + - - +
124O LEU* 3.2 8.6 + - - +
125O GLU* 2.9 30.8 + - + +
114X TYR* 4.3 26.9 - - + +
115X VAL* 4.7 3.9 - - + +
118X ASP* 3.5 41.4 + - + +
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Residues in contact with ASP 122 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O HIS* 5.4 1.1 - - - -
118O ASP* 3.1 20.6 + - - +
119O LEU* 3.4 10.9 - - - +
121O LYS* 1.3 91.8 + - - +
123O ILE* 1.3 66.1 + - + +
125O GLU* 3.2 11.4 + - - +
126O SER* 3.1 22.7 + - - -
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Residues in contact with ILE 123 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O ILE* 4.8 1.1 - - + -
18O GLU* 3.4 21.3 - - - +
54O HIS* 3.7 33.9 - - + +
57O LYS* 5.7 2.5 - - + -
58O LEU* 3.9 26.5 - - + -
101O LEU* 3.9 20.2 - - + -
119O LEU* 3.0 41.8 + - + +
120O LEU* 3.6 10.8 - - + +
122O ASP* 1.3 77.2 - - + +
124O LEU* 1.3 59.1 + - - +
126O SER* 3.2 3.5 + - - -
127O GLU* 2.8 41.3 + - - +
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Residues in contact with LEU 124 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O THR* 3.4 26.2 - - - +
101O LEU* 4.3 23.3 - - + -
102O ARG* 3.8 29.6 - - + +
105O ILE* 4.1 19.5 - - + -
120O LEU 2.8 16.2 + - - +
121O LYS* 3.5 7.0 - - - +
122O ASP 3.2 0.2 - - - -
123O ILE* 1.3 78.3 - - - +
125O GLU* 1.3 64.3 + - - +
127O GLU* 3.2 1.2 + - + +
128O GLU* 2.9 33.8 + - + +
114X TYR* 4.2 14.6 - - + -
115X VAL* 3.9 15.0 - - + -
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Residues in contact with GLU 125 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121O LYS* 2.9 15.8 + - + +
122O ASP* 3.2 17.4 + - - +
124O LEU* 1.3 75.9 - - - +
126O SER* 1.3 64.5 + - - +
128O GLU* 3.3 3.5 + - + +
129O GLU* 3.0 43.7 + - + +
115X VAL* 3.8 28.6 - - + +
118X ASP* 4.5 12.9 - - - +
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Residues in contact with SER 126 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O GLU* 5.6 0.3 - - - +
50O ASP* 5.2 5.7 + - - +
54O HIS* 3.0 32.7 - - - -
122O ASP 3.1 12.7 + - - -
123O ILE 3.5 7.0 - - - -
125O GLU* 1.3 79.0 - - - +
127O GLU* 1.3 62.3 + - - +
129O GLU* 3.3 17.0 + - - +
130O HIS* 3.1 19.4 + - - +
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Residues in contact with GLU 127 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O GLU* 3.0 18.2 - - - +
51O GLU* 2.8 30.5 - - - +
54O HIS* 3.8 1.6 + - - -
94O GLU* 2.7 38.2 - - + +
97O ALA* 5.2 6.2 - - + +
98O THR* 4.0 13.5 - - - +
101O LEU* 4.0 19.7 - - + -
123O ILE* 2.8 27.9 + - - +
124O LEU 3.2 3.3 + - - +
126O SER* 1.3 74.5 + - - +
128O GLU* 1.3 61.9 + - - +
130O HIS* 3.1 7.0 + - - +
131O ILE* 2.9 31.7 + - - +
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Residues in contact with GLU 128 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O THR* 4.5 4.0 - - - +
102O ARG* 2.7 40.2 + - - +
124O LEU* 2.9 21.3 + - + +
125O GLU* 3.8 4.9 - - - +
127O GLU* 1.3 76.3 - - - +
129O GLU* 1.3 58.3 + - + +
131O ILE* 3.3 10.4 + - + -
132O ASP* 3.0 24.4 + - - +
61X ARG* 2.8 37.3 + - - +
64X PHE* 3.5 24.6 - - + -
65X LEU* 6.1 0.4 - - - -
113X ASP* 4.7 0.5 - - - +
115X VAL* 3.7 22.5 - - + +
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Residues in contact with GLU 129 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125O GLU* 3.0 42.0 + - + +
126O SER* 3.4 15.9 - - - +
128O GLU* 1.3 77.0 - - - +
130O HIS* 1.3 61.2 + - - +
132O ASP* 3.1 10.9 + - + +
133O TYR* 3.0 22.7 + - - +
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Residues in contact with HIS 130 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O TYR* 3.5 35.6 - + - -
44O GLU* 4.6 3.6 + - - -
47O GLU* 3.4 47.9 + - + +
51O GLU* 5.4 0.8 + - - -
90O ASP* 4.6 2.7 - - + -
94O GLU* 3.0 22.8 + - - +
126O SER 3.1 14.3 + - - +
127O GLU* 3.1 10.7 + - - +
129O GLU* 1.3 74.6 - - - +
131O ILE* 1.3 63.3 + - - +
133O TYR* 3.2 11.7 + + - -
134O LEU* 3.0 53.2 + - + +
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Residues in contact with ILE 131 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O LEU* 4.1 14.4 - - + -
94O GLU* 3.6 26.7 - - + +
95O LEU* 4.2 20.4 - - + -
98O THR* 4.1 22.7 - - + +
127O GLU 2.9 18.6 + - - +
128O GLU* 3.6 15.3 - - + +
129O GLU 3.3 0.2 - - - -
130O HIS* 1.3 74.2 - - - +
132O ASP* 1.3 63.7 + - - +
134O LEU* 3.7 6.5 - - - +
135O GLU* 3.0 46.6 + - - +
64X PHE* 4.2 11.0 - - + -
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Residues in contact with ASP 132 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128O GLU 3.0 13.8 + - - +
129O GLU* 3.2 14.5 - - - +
131O ILE* 1.3 77.3 - - - +
133O TYR* 1.3 61.6 + - - +
135O GLU* 3.9 4.3 - - - +
136O THR* 2.8 38.5 + - - -
34W ASP* 4.5 13.3 - - - +
64X PHE* 3.7 30.0 - - + +
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Residues in contact with TYR 133 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O LEU* 3.7 25.1 - - - +
43O HIS* 3.2 54.5 - + + +
44O GLU* 5.4 3.5 + - - -
47O GLU* 4.9 1.3 - - - +
87O LEU* 4.6 3.6 - - + -
129O GLU 3.0 11.3 + - - +
130O HIS* 3.2 17.7 + + + +
132O ASP* 1.3 77.8 - - - +
134O LEU* 1.3 71.5 + - + +
136O THR* 3.1 6.8 + - - -
137O GLN* 2.8 76.9 + - + +
153O HIS* 5.1 2.8 + - - -
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Residues in contact with LEU 134 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O GLU* 5.7 0.4 - - - +
87O LEU* 3.9 33.7 - - + +
90O ASP* 3.9 16.8 - - + +
91O LEU* 3.8 35.7 - - + +
94O GLU* 4.1 4.9 - - + -
130O HIS* 3.0 56.3 + - + +
131O ILE* 3.7 5.4 - - - +
133O TYR* 1.3 87.5 - - + +
135O GLU* 1.3 62.9 + - - +
137O GLN* 3.1 5.8 + - - +
138O LEU* 3.0 29.1 + - + +
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Residues in contact with GLU 135 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O LEU* 4.3 19.4 - - + +
95O LEU* 6.1 1.2 - - - +
131O ILE* 3.0 35.2 + - + +
132O ASP* 4.0 3.0 - - - +
134O LEU* 1.3 74.5 - - - +
136O THR* 1.3 63.1 + - - +
138O LEU* 3.5 8.2 + - - +
139O GLY* 3.0 20.6 + - - -
64X PHE* 4.4 14.9 - - - +
66X GLU* 4.1 18.6 - - - +
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Residues in contact with THR 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132O ASP* 2.8 29.1 + - - -
133O TYR* 3.1 9.4 + - - -
135O GLU* 1.3 78.2 - - - +
137O GLN* 1.3 65.4 + - - +
139O GLY* 3.4 1.7 + - - -
140O LEU* 3.0 28.5 + - + +
33W ASN 5.1 1.1 + - - +
34W ASP 3.0 17.9 + - - -
35W TRP* 3.7 5.7 - - - +
36W GLY* 3.4 37.0 - - - +
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Residues in contact with GLN 137 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O LEU* 4.1 16.2 - - + -
133O TYR* 2.8 71.9 + - + +
134O LEU 3.1 4.9 + - - +
136O THR* 1.3 80.9 - - - +
138O LEU* 1.3 66.3 + - - +
140O LEU* 3.0 22.7 + - - +
141O ILE* 3.0 18.8 + - - +
149O TYR* 2.6 47.2 + - + +
153O HIS* 3.9 12.1 + - - -
154W MET* 5.4 0.2 - - - +
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Residues in contact with LEU 138 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O GLN* 4.2 31.1 + - + +
87O LEU* 3.9 28.5 - - + +
88O GLN* 3.9 31.2 - - + +
91O LEU* 4.0 20.4 - - + -
134O LEU 3.0 21.7 + - - +
135O GLU* 3.7 5.8 - - - +
137O GLN* 1.3 77.9 - - - +
139O GLY* 1.3 61.8 + - - +
141O ILE* 3.4 8.6 + - + +
142O GLN* 3.4 24.6 + - - +
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Residues in contact with GLY 139 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135O GLU 3.0 14.5 + - - -
136O THR* 3.8 3.6 - - - -
138O LEU* 1.3 76.9 - - - +
140O LEU* 1.3 57.0 + - - +
142O GLN* 3.2 11.1 + - - +
143O LYS* 2.8 45.3 + - - +
35W TRP 5.7 0.9 - - - -
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Residues in contact with LEU 140 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O THR* 3.0 18.8 + - + +
137O GLN* 3.0 30.4 + - - +
139O GLY* 1.3 72.4 - - - +
141O ILE* 1.3 59.0 + - - +
143O LYS* 4.1 8.1 - - + +
144O VAL* 2.7 45.0 + - + +
149O TYR* 3.9 10.5 - - + -
35W TRP 3.4 19.5 - - - +
36W GLY* 4.1 17.9 - - - +
37W LEU* 4.0 24.5 - - + -
154W MET* 4.0 31.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O THR* 4.8 1.1 - - + -
84O GLN* 3.8 35.7 - - + +
87O LEU* 4.0 21.5 - - + -
137O GLN 3.0 16.5 + - - +
138O LEU* 3.5 18.6 - - + +
139O GLY 3.4 0.2 - - - -
140O LEU* 1.3 73.4 - - - +
142O GLN* 1.3 62.2 + - - +
145O GLY* 2.9 30.8 + - - -
146O LEU* 4.1 27.4 - - + +
149O TYR* 3.5 40.1 - - + -
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Residues in contact with GLN 142 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O GLN* 3.5 26.1 - - - +
138O LEU 3.4 12.0 + - - +
139O GLY* 3.2 12.0 + - - +
140O LEU 3.1 0.4 - - - -
141O ILE* 1.3 83.5 - - - +
143O LYS* 1.3 64.3 + - + +
144O VAL 3.6 0.2 + - - -
145O GLY* 4.1 2.9 + - - -
147W GLU* 5.0 3.3 - - - +
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Residues in contact with LYS 143 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O GLY* 2.8 34.1 + - - +
140O LEU* 3.0 12.1 + - + +
142O GLN* 1.3 76.6 - - + +
144O VAL* 1.3 63.5 + - + +
35W TRP* 3.9 49.4 + - + +
37W LEU* 4.5 18.2 - - + -
146W LEU* 5.6 0.5 - - - +
147W GLU* 3.9 11.2 - - - +
150W LEU* 3.6 28.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O LEU* 2.7 29.4 + - + +
143O LYS* 1.3 79.9 - - + +
145O GLY* 1.3 70.7 + - - +
148O ASN* 3.3 22.9 + - + +
149O TYR* 3.7 22.7 - - + +
147W GLU* 3.2 30.4 - - - +
150W LEU* 3.7 13.7 - - + +
151W GLN* 3.7 27.1 - - + +
154W MET* 4.3 17.3 - - - -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141O ILE 2.9 16.2 + - - -
142O GLN 4.1 1.7 + - - -
143O LYS 3.6 1.4 - - - -
144O VAL* 1.3 84.0 - - - +
146O LEU* 1.3 66.6 + - - -
147O GLU 3.4 2.6 + - - -
148O ASN 3.5 0.4 + - - -
149O TYR* 3.0 19.6 + - - +
147W GLU* 3.9 16.2 + - - -
----------------------------------------------------------
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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