Contacts of the helix formed by residues 113 - 143 (chain R) in PDB entry 2X17
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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K TYR* 5.0 2.4 + - - -
1R MET 5.7 3.1 - - - -
2R LEU* 3.7 17.6 - - - +
3R SER 5.4 0.9 + - - -
6R MET* 4.0 10.0 - - + +
60R TYR* 4.7 0.2 + - - -
64R ARG* 4.7 5.9 + - - -
108R ALA* 2.9 22.7 + - - +
111R GLU* 3.2 13.5 - - + +
112R LYS* 1.3 73.0 - - - +
114R TYR* 1.3 63.1 + - - +
115R SER* 3.6 14.2 + - - -
116R THR* 2.6 31.3 + - - +
117R ARG* 3.3 16.9 + - - +
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Residues in contact with TYR 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K TYR* 3.6 58.6 - + + -
105K ALA* 4.1 10.3 - - + -
106K ALA* 3.4 20.4 - - + +
109K GLU* 2.8 39.5 + - - -
117K ARG* 3.8 18.5 + - - -
124K ILE* 3.6 12.0 - - + +
112R LYS* 3.2 36.1 + - + +
113R ASP* 1.3 73.7 + - - +
115R SER* 1.3 57.6 + - - +
117R ARG* 3.7 8.7 - - + +
118R ALA* 2.9 31.4 + - - +
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Residues in contact with SER 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K TYR* 2.6 28.9 + - - -
124K ILE* 3.9 11.3 + - - +
125K ASN* 5.2 0.7 - - - +
128K VAL* 3.8 17.1 - - - +
60R TYR* 3.1 16.5 + - - -
64R ARG* 3.2 26.6 + - - -
113R ASP* 3.3 4.8 + - - -
114R TYR* 1.3 78.5 - - - +
116R THR* 1.3 57.0 + - - +
118R ALA* 3.5 2.4 + - - +
119R PHE* 3.0 24.9 + - - +
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Residues in contact with THR 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R LEU* 3.6 8.7 - - - +
6R MET* 3.8 23.6 - - + -
10R LEU* 3.9 22.0 - - + -
60R TYR* 2.8 21.4 + - + -
108R ALA* 4.3 4.3 - - + -
113R ASP* 2.6 32.9 + - - -
114R TYR 3.4 0.2 - - - -
115R SER* 1.3 72.8 - - - +
117R ARG* 1.3 61.0 + - - +
119R PHE* 3.2 2.1 + - + +
120R LEU* 2.9 42.1 + - + +
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Residues in contact with ARG 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 4.0 20.0 + - - +
117H ARG* 5.3 9.9 - - - +
118H ALA* 5.8 0.6 - - - +
117K ARG* 5.2 11.4 - - - +
121K GLU* 5.0 1.0 + - - +
105R ALA* 3.7 30.6 - - - +
108R ALA* 3.8 13.1 - - + +
109R GLU* 3.2 29.1 + - + +
113R ASP 3.3 11.9 + - - +
114R TYR* 3.7 13.5 - - + +
116R THR* 1.3 79.6 - - - +
118R ALA* 1.3 59.7 + - - +
120R LEU* 3.5 3.5 + - - +
121R GLU* 2.9 41.5 + - - +
124R ILE* 3.5 18.5 - - - +
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Residues in contact with ALA 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K ARG* 5.7 0.4 - - - +
121K GLU* 3.4 29.5 - - - +
124K ILE* 3.9 17.5 - - + -
125K ASN* 3.6 26.6 + - - +
114R TYR 2.9 18.8 + - - +
115R SER 3.8 4.0 - - - +
117R ARG* 1.3 75.4 - - - +
119R PHE* 1.3 62.8 + - - +
121R GLU* 3.5 15.6 - - - +
122R TRP* 4.5 1.0 + - - +
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Residues in contact with PHE 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125K ASN* 4.3 4.2 + - - -
10R LEU* 4.2 2.0 - - + -
56R ARG* 3.7 15.0 - - + -
57R PHE* 3.4 38.4 - + - -
60R TYR* 3.6 58.1 - + + -
115R SER 3.0 18.2 + - - +
116R THR* 3.4 9.9 - - + +
118R ALA* 1.3 78.3 - - - +
120R LEU* 1.3 69.5 + - + +
121R GLU 3.4 0.5 + - - -
122R TRP* 3.5 18.5 + - + +
123R PHE* 3.5 30.3 - + - -
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Residues in contact with LEU 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R LEU* 5.1 0.2 - - + -
57R PHE* 4.0 31.4 - - + -
101R ILE* 4.3 15.7 - - + +
104R LEU* 3.6 51.1 - - + +
105R ALA* 3.7 13.0 - - + +
108R ALA* 4.6 0.4 - - + -
116R THR* 2.9 34.1 + - + +
117R ARG* 3.5 9.4 + - - +
118R ALA 3.4 0.2 - - - -
119R PHE* 1.3 76.7 - - + +
121R GLU* 1.3 58.8 + - - +
122R TRP 3.1 2.9 - - - -
123R PHE* 3.0 24.4 + - + +
124R ILE* 3.1 18.0 + - + +
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Residues in contact with GLU 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ARG* 4.9 0.9 + - - +
118H ALA* 3.7 27.2 - - - +
121H GLU* 4.1 22.3 - - + +
121K GLU* 4.3 13.9 - - + +
117R ARG* 2.9 41.8 + - - +
118R ALA 3.5 15.0 - - - +
119R PHE 3.2 0.2 - - - -
120R LEU* 1.3 77.7 - - - +
122R TRP* 1.3 59.7 + - - +
124R ILE* 3.6 9.2 + - - +
125R ASN* 2.9 39.3 + - - +
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Residues in contact with TRP 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709 MET* 3.8 36.3 - - + -
53R HIS* 3.6 30.1 - + - -
56R ARG* 3.4 49.7 - - - +
118R ALA 4.5 1.0 + - - -
119R PHE* 3.5 13.2 + - + +
120R LEU 3.1 0.6 - - - -
121R GLU* 1.3 79.8 - - - +
123R PHE* 1.3 83.8 - + + +
125R ASN* 3.7 5.7 + - - +
126R GLU* 3.0 34.4 + - + +
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Residues in contact with PHE 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R GLU* 4.3 8.7 - - - -
53R HIS* 3.7 20.2 - + + -
56R ARG* 3.8 20.9 - - + -
57R PHE* 3.4 37.0 - + - -
101R ILE* 4.1 21.8 - - + -
119R PHE* 3.5 42.6 - + - -
120R LEU* 3.0 12.1 + - - +
122R TRP* 1.3 104.2 - + + +
124R ILE* 1.3 60.4 + - - +
126R GLU* 3.6 13.8 - - - +
127R GLN* 2.9 35.7 + - - +
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Residues in contact with ILE 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 3.7 41.7 - - + +
115H SER* 3.8 14.2 + - - +
118H ALA* 3.8 9.4 - - + -
101R ILE* 3.9 17.9 - - + -
102R TYR* 4.5 7.9 - - + -
105R ALA* 4.6 10.5 - - + -
117R ARG* 3.5 35.2 - - - +
120R LEU* 3.1 15.2 + - + +
121R GLU* 3.7 13.5 - - - +
123R PHE* 1.3 78.4 - - - +
125R ASN* 1.3 60.6 + - - +
127R GLN* 3.6 3.6 + - - +
128R VAL* 3.3 22.6 + - - +
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Residues in contact with ASN 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H SER 5.0 0.9 - - - +
118H ALA* 3.4 37.4 + - - +
119H PHE* 4.1 3.8 + - - -
121R GLU* 2.9 31.5 + - - +
122R TRP* 4.0 5.7 - - - +
124R ILE* 1.3 74.5 - - - +
126R GLU* 1.3 64.0 + - - +
128R VAL* 3.7 15.0 + - - +
129R GLU* 3.8 16.3 + - - +
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Residues in contact with GLU 126 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709 MET* 3.5 34.1 - - + +
53R HIS* 3.3 18.8 + - - +
122R TRP* 3.0 30.4 + - + +
123R PHE* 3.6 16.8 - - - +
124R ILE 3.3 0.4 - - - -
125R ASN* 1.3 76.3 - - - +
127R GLN* 1.3 84.3 + - - +
129R GLU* 3.2 9.6 + - - +
130R GLU* 2.9 56.5 + - - +
1172R AG 3.9 1.0 - - - -
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Residues in contact with GLN 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ARG* 5.3 0.9 - - - -
17R GLU* 4.5 8.3 + - - -
50R GLU* 5.1 2.8 + - - -
53R HIS* 5.1 0.4 - - - -
94R GLU* 2.8 30.5 + - - +
97R ILE* 3.5 24.8 - - + +
98R SER* 3.2 33.5 + - - +
101R ILE* 4.7 7.6 - - + +
102R TYR* 6.1 0.2 - - - +
123R PHE* 2.9 22.6 + - + +
124R ILE* 3.6 5.6 + - - +
125R ASN 3.5 0.2 - - - -
126R GLU* 1.3 96.0 + - - +
128R VAL* 1.3 60.6 + - + +
129R GLU 3.4 0.2 - - - -
130R GLU* 3.8 6.2 + - - +
131R GLU* 2.8 36.0 + - - +
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Residues in contact with VAL 128 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H TYR* 4.2 14.1 - - + -
63H ASP* 4.1 21.8 - - + +
64H ARG* 3.8 30.3 - - - +
115H SER* 3.6 32.3 - - - +
124R ILE 3.3 17.5 + - - +
125R ASN* 3.8 11.9 - - - +
126R GLU 3.2 0.6 - - - -
127R GLN* 1.3 77.5 - - - +
129R GLU* 1.3 62.3 + - + +
131R GLU* 4.2 0.9 - - - +
132R ALA* 3.2 24.8 + - - +
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Residues in contact with GLU 129 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709 MET* 3.4 27.4 - - + +
63H ASP* 5.9 4.7 - - - +
125R ASN 3.8 10.2 + - - +
126R GLU* 3.2 9.2 + - - +
128R VAL* 1.3 78.9 - - + +
130R GLU* 1.3 58.4 + - - +
132R ALA* 3.5 4.7 + - - +
133R SER* 2.9 32.1 + - - -
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Residues in contact with GLU 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709 MET* 6.4 0.2 - - - -
46R GLN* 2.9 33.7 + - - +
50R GLU* 3.0 21.0 - - - +
53R HIS* 3.5 8.0 - - - -
94R GLU* 3.3 30.3 - - - +
126R GLU* 2.9 36.0 + - - +
127R GLN* 3.6 11.8 + - - +
128R VAL 3.3 0.2 - - - -
129R GLU* 1.3 77.1 - - - +
131R GLU* 1.3 60.6 + - - +
133R SER* 3.5 7.6 + - - -
134R VAL* 3.3 29.9 + - + +
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Residues in contact with GLU 131 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET 5.4 4.9 + - - -
63H ASP 5.3 2.5 - - - +
64H ARG* 4.0 21.4 + - - +
91R TYR* 3.9 20.9 + - + -
94R GLU* 3.7 25.6 - - + +
95R LYS* 3.9 23.0 - - - +
98R SER* 2.7 31.0 + - - +
102R TYR* 5.0 1.2 + - - -
127R GLN* 2.8 22.1 + - - +
128R VAL* 4.2 4.0 - - - +
130R GLU* 1.3 71.2 - - - +
132R ALA* 1.3 60.1 + - - +
134R VAL* 3.2 4.5 + - - +
135R LYS* 2.8 31.5 + - - +
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Residues in contact with ALA 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H TYR 5.1 1.3 - - - +
63H ASP* 3.4 41.2 + - + +
128R VAL 3.2 18.2 + - - +
129R GLU* 3.9 4.0 - - - +
131R GLU* 1.3 78.8 - - - +
133R SER* 1.3 58.2 + - - +
135R LYS* 4.1 6.0 - - - +
136R LYS* 3.1 30.5 + - - +
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Residues in contact with SER 133 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R TRP* 3.7 20.4 - - - -
46R GLN* 5.0 1.6 + - - -
129R GLU 2.9 19.6 + - - -
130R GLU* 3.5 12.3 - - - -
132R ALA* 1.3 78.9 - - - +
134R VAL* 1.3 59.8 + - - +
136R LYS* 3.9 6.5 + - - +
137R ILE* 3.5 25.9 + - - +
161R ARG* 5.2 1.0 + - - -
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Residues in contact with VAL 134 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R TYR* 4.9 5.8 - - + +
42R TRP* 4.4 17.5 - - + -
46R GLN* 5.6 3.4 - - - +
87R PHE* 3.9 27.3 - - + +
90R ALA* 4.0 6.1 - - + -
91R TYR* 3.8 33.0 - - + +
94R GLU* 4.1 19.5 - - + +
130R GLU* 3.3 15.0 + - + +
131R GLU 3.2 6.6 + - - +
133R SER* 1.3 78.3 - - - +
135R LYS* 1.3 59.6 + - - +
136R LYS 3.3 0.2 - - - -
137R ILE* 3.3 5.1 + - - +
138R LEU* 3.0 25.3 + - - +
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Residues in contact with LYS 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 5.3 1.6 - - - -
65H ASN* 3.3 41.7 + - + +
91R TYR* 3.6 41.9 - - + +
131R GLU 2.8 16.9 + - - +
132R ALA* 4.1 7.4 - - - +
134R VAL* 1.3 74.1 - - - +
136R LYS* 1.3 59.4 + - - +
138R LEU* 3.5 11.9 - - + +
139R ASP* 2.7 68.0 + - - +
142R LYS* 5.7 3.2 - - - +
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Residues in contact with LYS 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R ALA 3.1 18.8 + - - +
133R SER* 4.0 8.3 - - - +
135R LYS* 1.3 77.2 - - - +
137R ILE* 1.3 64.0 + - + +
139R ASP* 3.7 5.2 + - - +
140R LYS* 3.4 53.7 + - - +
35Z GLY* 5.8 3.6 - - - +
37Z GLU* 2.9 43.6 + - + +
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Residues in contact with ILE 137 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R PHE* 4.5 2.9 - - + -
42R TRP* 3.5 33.7 - - + +
87R PHE* 3.7 37.7 - - + -
133R SER 3.5 19.3 + - - +
134R VAL 3.3 2.1 + - - +
136R LYS* 1.3 79.1 - - + +
138R LEU* 1.3 65.2 + - - +
140R LYS* 3.2 11.4 + - + +
141R LEU* 3.1 27.8 + - + +
154R LEU* 4.8 8.7 - - + -
158R LEU* 3.8 31.6 - - + -
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Residues in contact with LEU 138 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R LEU* 4.0 2.9 - - + +
87R PHE* 3.4 37.8 - - + +
88R GLU* 3.8 23.8 - - + -
91R TYR* 3.6 29.8 - - + -
134R VAL 3.0 16.1 + - - +
135R LYS* 3.3 13.2 + - + +
137R ILE* 1.3 76.5 - - - +
139R ASP* 1.3 69.4 + - - +
141R LEU* 3.1 16.0 + - - +
142R LYS* 3.1 39.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ASN* 4.4 3.6 - - - +
135R LYS* 2.7 55.0 + - - +
136R LYS* 4.0 6.1 - - - +
138R LEU* 1.3 80.8 - - - +
140R LYS* 1.3 58.4 + - + +
142R LYS* 3.4 15.2 + - - +
143R PHE* 2.9 27.1 + - - +
33Z ASP 5.6 1.6 - - - +
34Z LEU 5.9 2.9 - - - +
35Z GLY* 6.2 3.8 - - - -
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Residues in contact with LYS 140 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R LYS* 3.4 45.7 + - + +
137R ILE* 3.2 14.4 + - + +
139R ASP* 1.3 78.2 - - + +
141R LEU* 1.3 57.9 + - - +
143R PHE* 3.4 15.7 - - + +
144R ALA* 3.3 24.3 + - - +
150R ILE* 5.1 0.7 - - - +
154R LEU* 3.8 35.8 - - + +
157R GLU* 3.6 21.0 + - - -
35Z GLY* 4.4 18.4 - - - +
37Z GLU* 6.3 0.4 - - - +
152Z PHE* 4.8 12.8 - - + -
155Z ASP* 5.5 5.6 + - - -
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Residues in contact with LEU 141 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R PHE* 4.2 13.2 - - + -
83R PRO* 3.5 31.0 - - + +
84R LEU* 3.8 27.9 - - + +
87R PHE* 3.6 28.5 - - + -
137R ILE* 3.1 23.9 + - + +
138R LEU* 3.1 7.1 + - - +
140R LYS* 1.3 76.4 - - - +
142R LYS* 1.3 61.8 + - - +
143R PHE 3.2 0.4 - - - -
144R ALA* 3.3 25.0 - - + +
145R LYS* 3.7 3.3 + - - -
151R LEU* 3.9 28.5 - - + -
154R LEU* 4.5 7.9 - - + -
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Residues in contact with LYS 142 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R LEU* 3.7 17.7 - - + -
88R GLU* 4.1 14.4 - - - -
135R LYS* 5.7 2.8 - - - +
138R LEU* 3.1 32.7 + - + +
139R ASP* 3.5 18.4 + - - +
141R LEU* 1.3 75.1 - - - +
143R PHE* 1.3 62.2 + - - +
144R ALA 3.2 0.7 - - - -
145R LYS* 3.3 35.7 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R ASP 2.9 18.0 + - - +
140R LYS* 3.4 16.8 - - + +
141R LEU 3.2 0.2 - - - -
142R LYS* 1.3 77.8 - - - +
144R ALA* 1.3 55.3 + - - +
145R LYS 3.8 1.2 + - - -
150R ILE* 4.4 17.2 - - + +
34Z LEU 5.4 7.9 - - - -
36Z LEU* 5.1 11.0 - - + -
148Z PRO* 3.9 38.9 - - + +
151Z LEU* 3.7 30.3 - - + -
152Z PHE* 4.9 14.4 - + + -
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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