Contacts of the helix formed by residues 113 - 145 (chain U) 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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ARG* 4.2 5.2 - - - +
128E GLU* 4.8 1.8 - - - +
4U ASP* 5.8 1.7 + - + +
7U VAL* 3.5 25.2 - - + +
61U ARG* 2.9 14.1 + - - -
65U LEU* 3.8 11.4 - - - +
108U CYS* 2.9 24.2 + - + +
111U VAL* 3.3 5.8 - - + +
112U HIS* 1.3 74.3 - - - +
114U TYR* 1.3 59.4 + - - +
115U VAL 3.7 1.2 + - - -
116U SER* 2.6 41.0 + - - -
117U ARG* 3.1 14.6 + - - +
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Residues in contact with TYR 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ARG* 4.0 14.2 - - + +
105E ILE* 3.5 41.5 - - + -
106E VAL* 3.1 19.6 + - - +
117E ARG* 3.7 18.8 - - - +
121E LYS* 4.4 16.9 - - + +
124E LEU* 4.1 15.0 - - + -
109U GLU* 3.7 33.9 + - - -
112U HIS* 3.0 61.8 + - + -
113U ASP* 1.3 73.2 - - - +
115U VAL* 1.3 57.6 + - - +
117U ARG* 3.2 9.3 + - + +
118U ASP* 2.9 27.2 + - - +
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Residues in contact with VAL 115 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E LYS* 4.9 4.7 - - + +
124E LEU* 3.9 13.0 - - + -
125E GLU* 3.7 43.7 - - + +
128E GLU* 3.6 25.5 + - + +
61U ARG* 3.6 30.9 + - - +
113U ASP* 3.3 1.2 + - - -
114U TYR* 1.3 72.0 - - - +
116U SER* 1.4 65.7 + - - +
118U ASP* 3.2 6.9 + - + +
119U LEU* 3.0 24.5 + - + +
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Residues in contact with SER 116 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7U VAL* 4.0 5.5 - - - +
11U LEU* 4.2 8.9 - - - +
61U ARG* 2.9 26.5 + - - +
65U LEU* 3.8 7.1 - - - +
108U CYS* 3.8 15.0 - - - -
113U ASP* 2.6 38.3 + - - -
115U VAL* 1.4 77.7 - - - +
117U ARG* 1.3 62.9 + - - +
119U LEU* 3.4 6.5 + - - +
120U LEU* 3.1 26.9 + - - +
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Residues in contact with ARG 117 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLU* 2.6 40.0 + - - -
114D TYR* 3.8 19.0 - - - +
117D ARG* 4.2 16.9 - - - +
117E ARG* 4.1 16.0 - - - +
105U ILE* 3.8 24.9 - - + +
106U VAL* 6.1 0.2 - - - +
108U CYS* 4.0 16.3 - - + +
109U GLU* 2.8 41.4 + - - +
113U ASP 3.1 14.2 + - - +
114U TYR* 3.4 12.8 - - - +
115U VAL 3.2 0.2 - - - -
116U SER* 1.3 78.0 - - - +
118U ASP* 1.3 61.6 + - - +
120U LEU* 3.1 7.0 + - - +
121U LYS* 2.9 34.9 + - + +
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Residues in contact with ASP 118 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASP* 5.6 0.5 - - - +
118E ASP* 5.6 1.9 - - - +
121E LYS* 3.9 26.4 - - + +
122E ASP* 5.3 2.1 - - - +
125E GLU* 4.4 11.5 - - - +
114U TYR 2.9 15.6 + - - +
115U VAL* 3.2 7.2 + - + +
117U ARG* 1.3 80.9 - - - +
119U LEU* 1.3 62.9 + - - +
121U LYS* 3.3 17.2 + - - +
122U ASP* 3.1 35.3 + - - +
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Residues in contact with LEU 119 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U LEU* 5.3 2.5 - - + -
57U LYS* 3.9 25.8 - - + +
58U LEU* 4.1 14.1 - - + -
61U ARG* 3.8 37.2 - - + -
115U VAL* 3.0 16.4 + - + +
116U SER* 3.7 5.6 - - - +
118U ASP* 1.3 76.1 - - - +
120U LEU* 1.3 67.2 + - + +
122U ASP* 3.3 10.6 + - - +
123U ILE* 3.1 44.2 + - + +
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Residues in contact with LEU 120 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U LEU* 3.9 24.9 - - + -
14U ILE* 4.0 11.4 - - + -
58U LEU* 4.2 13.0 - - + -
101U LEU* 3.8 25.0 - - + +
104U ALA* 3.6 33.0 - - + -
105U ILE* 3.7 15.3 - - + +
108U CYS* 4.0 19.1 - - - -
116U SER 3.1 18.3 + - - +
117U ARG* 3.6 6.5 - - - +
119U LEU* 1.3 77.1 - - + +
121U LYS* 1.3 58.8 + - - +
123U ILE* 3.2 4.7 + - + +
124U LEU* 2.8 28.4 + - - +
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Residues in contact with LYS 121 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR* 4.3 26.2 - - + +
115D VAL* 4.9 2.7 - - + +
118D ASP* 3.7 38.6 - - + +
105U ILE* 4.0 11.8 - - + +
117U ARG* 2.9 21.1 + - + +
118U ASP* 3.5 20.2 - - - +
120U LEU* 1.3 78.4 - - - +
122U ASP* 1.3 65.1 + - - +
124U LEU* 3.1 5.6 + - + +
125U GLU* 2.9 31.5 + - + +
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Residues in contact with ASP 122 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASP* 5.3 2.4 - - - +
54U HIS* 4.9 1.0 + - - -
118U ASP* 3.1 26.8 + - - +
119U LEU* 3.7 9.6 - - - +
121U LYS* 1.3 86.3 - - - +
123U ILE* 1.3 64.5 + - + +
125U GLU* 3.4 13.9 + - - +
126U SER* 3.4 20.8 + - - -
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Residues in contact with ILE 123 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U ILE* 5.0 0.7 - - + -
18U GLU* 3.5 22.4 - - - +
54U HIS* 3.6 35.2 - - + +
57U LYS* 5.3 1.8 - - + -
58U LEU* 4.0 26.2 - - + -
101U LEU* 4.2 13.7 - - + -
119U LEU* 3.1 38.1 + - + +
120U LEU* 3.6 11.0 - - + +
122U ASP* 1.3 77.7 - - + +
124U LEU* 1.3 56.3 + - - +
126U SER* 3.2 5.7 + - - -
127U GLU* 3.0 38.2 + - + +
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Residues in contact with LEU 124 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR* 3.9 32.3 - - + -
115D VAL* 3.9 13.2 - - + -
98U THR* 3.5 35.9 - - - +
101U LEU* 4.3 15.7 - - + +
102U ARG* 3.7 28.7 - - + +
105U ILE* 4.0 8.7 - - + -
120U LEU 2.8 13.8 + - - +
121U LYS* 3.1 9.8 + - - +
123U ILE* 1.3 76.9 - - - +
125U GLU* 1.3 62.3 + - - +
127U GLU* 3.1 2.7 + - - +
128U GLU* 3.0 37.6 + - - +
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Residues in contact with GLU 125 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D VAL* 3.9 32.4 - - + +
118D ASP* 4.6 12.0 - - - +
121U LYS* 2.9 20.0 + - + +
122U ASP* 3.8 14.3 - - - +
123U ILE 3.3 0.2 - - - -
124U LEU* 1.3 73.5 - - - +
126U SER* 1.3 58.6 + - - +
128U GLU* 3.3 4.3 + - - +
129U GLU* 3.0 47.0 + - + +
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Residues in contact with SER 126 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50U ASP* 5.2 5.7 + - - +
54U HIS* 2.9 32.8 - - - -
122U ASP 3.4 9.8 + - - -
123U ILE 3.2 8.7 + - - -
125U GLU* 1.3 78.1 - - - +
127U GLU* 1.3 63.4 + - - +
129U GLU* 3.4 16.5 + - - +
130U HIS* 3.0 20.6 + - - +
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Residues in contact with GLU 127 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18U GLU* 3.0 17.5 - - - +
51U GLU* 2.6 32.5 - - - +
54U HIS* 3.8 3.4 + - - -
94U GLU* 2.6 42.9 - - - +
97U ALA* 5.1 6.5 - - + -
98U THR* 4.1 12.8 - - - +
101U LEU* 4.2 13.2 - - + -
123U ILE* 3.0 29.5 + - + +
124U LEU* 3.1 5.7 + - - +
126U SER* 1.3 80.0 - - - +
128U GLU* 1.3 55.6 + - - +
130U HIS* 3.1 8.5 + - - +
131U ILE* 2.8 31.6 + - - +
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Residues in contact with GLU 128 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ARG* 2.8 43.3 + - - +
64D PHE* 3.6 18.7 - - + -
113D ASP* 4.7 0.3 - - - +
115D VAL* 3.6 20.2 - - + +
98U THR* 4.4 4.3 - - - +
102U ARG* 2.8 37.1 + - - +
124U LEU* 3.0 25.6 + - + +
125U GLU* 3.7 6.3 - - - +
127U GLU* 1.3 75.1 - - - +
129U GLU* 1.3 59.5 + - + +
131U ILE* 3.2 14.0 + - + +
132U ASP* 2.8 27.4 + - - +
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Residues in contact with GLU 129 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125U GLU* 3.0 41.2 + - + +
126U SER* 3.5 16.1 - - - +
128U GLU* 1.3 74.6 - - - +
130U HIS* 1.3 64.3 + - - +
132U ASP* 3.1 10.3 + - - +
133U TYR* 2.9 22.0 + - - +
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Residues in contact with HIS 130 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U TYR* 3.5 35.8 + + - -
44U GLU* 4.5 5.3 + - - -
47U GLU* 3.4 43.2 + - + +
51U GLU* 5.8 0.4 - - - -
90U ASP* 4.6 2.0 - - + -
94U GLU* 3.1 24.4 + - - +
126U SER 3.0 14.1 + - - +
127U GLU* 3.1 11.4 + - - +
129U GLU* 1.3 76.6 - - - +
131U ILE* 1.3 62.0 + - - +
133U TYR* 3.2 13.5 + + + -
134U LEU* 2.9 48.7 + - + +
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Residues in contact with ILE 131 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PHE* 4.2 11.4 - - + -
91U LEU* 4.3 12.1 - - + -
94U GLU* 3.8 23.6 - - + +
95U LEU* 4.0 22.7 - - + -
98U THR* 4.0 23.1 - - + +
102U ARG* 6.2 0.2 - - - +
127U GLU 2.8 19.4 + - - +
128U GLU* 3.5 15.9 - - + +
130U HIS* 1.3 71.6 - - - +
132U ASP* 1.3 64.2 + - - +
134U LEU* 3.3 6.8 + - - +
135U GLU* 3.0 48.5 + - + +
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Residues in contact with ASP 132 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASP* 4.5 11.6 - - - +
64D PHE* 3.6 30.6 - - + +
128U GLU 2.8 13.3 + - - +
129U GLU* 3.2 14.0 - - - +
131U ILE* 1.3 78.3 - - - +
133U TYR* 1.3 62.5 + - - +
135U GLU* 4.0 3.7 - - - +
136U THR* 2.8 39.5 + - - -
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Residues in contact with TYR 133 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U LEU* 3.6 26.9 + - - +
43U HIS* 3.4 55.9 - + + +
44U GLU* 5.4 3.4 - - - -
47U GLU* 5.0 0.7 - - - +
87U LEU* 4.5 4.0 - - + -
129U GLU 2.9 14.2 + - - +
130U HIS* 3.5 17.0 - + + +
132U ASP* 1.3 75.0 - - - +
134U LEU* 1.3 80.3 + - + +
136U THR* 3.2 4.9 + - - -
137U GLN* 2.9 71.8 + - + +
153U HIS* 5.0 3.0 + - - -
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Residues in contact with LEU 134 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44U GLU* 5.5 0.9 - - - +
87U LEU* 3.8 38.7 - - + +
90U ASP* 3.8 21.1 - - + +
91U LEU* 3.6 35.7 - - + +
94U GLU* 4.3 4.3 - - + -
130U HIS* 2.9 48.8 + - + +
131U ILE 3.7 3.1 - - - +
133U TYR* 1.3 88.3 - - + +
135U GLU* 1.3 66.8 + - - +
137U GLN* 3.1 5.3 + - - +
138U LEU* 3.0 29.5 + - + +
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Residues in contact with GLU 135 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PHE* 4.4 15.2 - - - +
66D GLU* 4.4 18.2 - - - +
91U LEU* 4.2 23.3 - - + +
95U LEU* 5.9 1.6 - - - +
131U ILE* 3.0 34.2 + - + +
132U ASP* 4.3 1.8 - - - +
134U LEU* 1.3 76.1 - - - +
136U THR* 1.3 62.4 + - - +
138U LEU* 3.6 8.5 + - - +
139U GLY* 3.1 18.5 + - - -
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Residues in contact with THR 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASN 5.0 1.5 + - - +
34C ASP* 3.2 14.8 + - - +
35C TRP* 3.5 32.0 - - - +
36C GLY* 3.5 12.1 - - - +
132U ASP* 2.8 30.9 + - - -
133U TYR* 3.4 6.3 - - - -
134U LEU 3.1 0.2 - - - -
135U GLU* 1.3 79.7 - - - +
137U GLN* 1.3 72.0 + - - +
139U GLY* 3.2 3.6 + - - -
140U LEU* 3.1 22.4 + - + +
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Residues in contact with GLN 137 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87U LEU* 3.9 15.9 - - + -
133U TYR* 2.9 67.3 + - + +
134U LEU 3.1 5.1 + - - +
136U THR* 1.3 87.2 - - - +
138U LEU* 1.3 64.2 + - - +
140U LEU* 3.0 14.8 + - - +
141U ILE* 2.9 27.5 + - - +
149U TYR* 2.8 44.0 + - - +
153U HIS* 4.0 10.7 + - - -
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Residues in contact with LEU 138 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84U GLN* 4.1 13.9 - - + +
87U LEU* 3.6 34.3 - - + -
88U GLN* 3.8 30.7 - - + +
91U LEU* 4.0 21.3 - - + -
134U LEU 3.0 21.1 + - - +
135U GLU* 3.8 6.5 - - - +
137U GLN* 1.3 76.6 - - - +
139U GLY* 1.3 60.3 + - - +
141U ILE* 3.5 20.3 + - + +
142U GLN* 3.5 19.3 + - - +
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Residues in contact with GLY 139 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP 5.5 0.9 - - - -
135U GLU 3.1 14.3 + - - -
136U THR* 3.2 4.2 + - - -
137U GLN 3.1 0.6 - - - -
138U LEU* 1.3 75.8 - - - +
140U LEU* 1.3 58.8 + - - +
142U GLN* 3.3 8.5 + - - +
143U LYS* 2.9 45.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP 3.3 23.8 - - - +
36C GLY* 4.0 18.4 - - - +
37C LEU* 4.1 14.1 - - + -
154C MET* 3.9 39.9 - - + -
136U THR 3.1 11.1 + - - +
137U GLN* 3.0 31.5 + - - +
139U GLY* 1.3 72.2 - - - +
141U ILE* 1.3 69.1 + - - +
143U LYS* 4.1 7.6 - - + +
144U VAL* 2.8 35.0 + - + +
149U TYR* 3.8 9.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83U THR* 4.9 1.8 - - + -
84U GLN* 4.6 17.9 - - + +
87U LEU* 3.9 28.5 - - + -
137U GLN 2.9 13.7 + - - +
138U LEU* 3.6 18.2 - - + +
139U GLY 3.2 0.2 - - - -
140U LEU* 1.3 76.7 - - - +
142U GLN* 1.3 69.5 + - - +
145U GLY* 2.9 28.8 + - - -
146U LEU* 4.3 27.8 - - + +
149U TYR* 3.6 34.7 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLU* 4.6 5.4 - - - +
138U LEU 3.5 14.0 + - - +
139U GLY* 3.3 9.3 + - - +
140U LEU 3.2 0.4 - - - -
141U ILE* 1.3 88.8 - - - +
143U LYS* 1.3 65.5 + - + +
145U GLY* 4.2 2.3 + - - -
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Residues in contact with LYS 143 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 3.7 58.3 + - + +
37C LEU* 4.6 13.2 - - + -
146C LEU* 5.7 1.0 - - - +
147C GLU* 3.7 15.0 - - - +
150C LEU* 3.7 26.4 - - + +
139U GLY* 2.9 32.1 + - - +
140U LEU* 3.0 7.2 + - + +
142U GLN* 1.3 81.1 - - + +
144U VAL* 1.3 62.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.9 0.2 - - + -
147C GLU* 3.5 26.5 - - - +
150C LEU* 3.6 26.2 - - + +
151C GLN* 3.7 14.8 - - + +
154C MET* 4.4 15.3 - - - -
140U LEU* 2.8 30.6 + - + +
143U LYS* 1.3 80.0 - - + +
145U GLY* 1.3 69.1 + - - +
148U ASN* 3.1 30.0 + - + +
149U TYR* 3.6 22.2 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLU* 3.9 14.2 + - - -
141U ILE 2.9 17.7 + - - -
142U GLN 4.2 1.3 + - - -
143U LYS 3.6 1.6 - - - -
144U VAL* 1.3 79.7 - - - +
146U LEU* 1.3 61.4 + - - -
147U GLU 3.4 2.2 - - - -
148U ASN 3.4 1.0 + - - -
149U TYR* 2.8 30.3 + - - +
----------------------------------------------------------
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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