Contacts of the helix formed by residues 113 - 144 (chain G) in PDB entry 3E1N
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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 5.9 1.2 - - - +
3G GLY* 5.9 0.2 - - - -
4G ASP* 5.5 4.2 + - + -
7G VAL* 3.4 24.1 - - + +
61G ARG* 2.9 23.0 + - - -
65G LEU* 3.8 11.0 - - - +
108G ALA* 2.9 20.3 + - + +
111G VAL* 3.3 5.8 - - + +
112G HIS* 1.3 73.2 - - - +
114G TYR* 1.3 57.3 + - - +
115G VAL* 3.7 2.1 + - - +
116G SER* 2.5 29.1 + - - -
117G ARG* 3.0 26.4 + - - +
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Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G ASP* 3.3 42.9 + - - -
112G HIS* 2.8 62.6 + + + -
113G ASP* 1.3 74.1 + - - +
115G VAL* 1.3 60.7 + - + +
117G ARG* 3.4 10.0 + - - +
118G ASP* 2.8 29.2 + - - +
302G SO4 5.4 4.0 - - - -
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Residues in contact with VAL 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ARG* 3.1 34.3 - - - +
113G ASP* 3.3 2.1 + - - +
114G TYR* 1.3 76.3 - - + +
116G SER* 1.3 65.7 + - - +
118G ASP* 3.2 6.8 + - + +
119G MET* 2.9 25.9 + - + +
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Residues in contact with SER 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 4.0 11.6 - - - +
11G LEU* 4.3 6.9 - - - +
61G ARG* 2.9 30.3 + - - +
65G LEU* 3.7 5.9 - - - +
108G ALA* 4.7 0.4 - - - -
113G ASP* 2.5 36.3 + - - -
115G VAL* 1.3 75.6 - - - +
117G ARG* 1.3 64.3 + - - +
119G MET* 3.4 6.3 + - - +
120G MET* 2.9 36.3 + - - +
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Residues in contact with ARG 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ILE* 3.3 39.9 + - + +
106G GLY* 4.3 1.2 - - - -
108G ALA* 4.1 6.3 - - + -
109G ASP* 3.1 42.5 + - - +
113G ASP 3.0 15.7 + - - +
114G TYR* 3.4 14.6 - - - +
115G VAL 3.2 0.2 - - - -
116G SER* 1.3 75.5 - - - +
118G ASP* 1.3 64.2 + - - +
120G MET* 2.9 14.4 + - - +
121G ILE* 2.9 27.9 + - + +
302G SO4 2.7 40.8 + - - +
109L ASP* 2.9 25.1 + - - -
114L TYR* 3.7 19.4 + - - -
117L ARG* 4.0 2.8 - - - +
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Residues in contact with ASP 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G TYR 2.8 20.0 + - - +
115G VAL* 3.2 8.7 + - + +
117G ARG* 1.3 72.2 - - - +
119G MET* 1.3 65.2 + - - +
121G ILE* 3.3 11.7 + - - +
122G GLU* 3.1 41.9 + - - +
302G SO4 5.1 7.1 + - - +
118L ASP* 5.5 2.3 - - - +
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Residues in contact with MET 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 5.7 1.8 - - - -
57G ARG* 3.4 67.9 + - + +
58G TYR* 4.6 11.0 - - - -
60G GLU* 6.2 0.4 - - + -
61G ARG* 3.8 32.8 - - + -
115G VAL* 2.9 18.0 + - + +
116G SER* 3.7 6.1 - - - +
118G ASP* 1.3 79.1 + - - +
120G MET* 1.3 61.5 + - - +
122G GLU* 3.4 3.6 + - - +
123G ILE* 3.2 36.1 + - + +
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Residues in contact with MET 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 5.5 2.0 - - + -
10G TYR* 6.2 0.4 - - + -
11G LEU* 3.9 15.0 - - + -
14G LEU* 3.6 25.6 - - - -
58G TYR* 4.4 13.2 - - + -
101G LEU* 3.8 13.4 - - + +
104G ALA* 3.8 25.4 - - + +
105G ILE* 3.6 14.4 - - + -
108G ALA* 3.7 28.9 - - + -
116G SER* 2.9 27.6 + - - +
117G ARG* 2.9 9.6 + - - +
119G MET* 1.3 79.3 - - + +
121G ILE* 1.3 58.1 + - - +
123G ILE* 3.2 7.6 + - - +
124G LEU* 2.8 28.2 + - - +
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Residues in contact with ILE 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ILE* 4.0 23.1 - - + -
117G ARG* 2.9 45.8 + - + +
118G ASP* 3.8 11.4 - - - +
120G MET* 1.3 71.8 - - - +
122G GLU* 1.3 68.5 + - + +
124G LEU* 3.3 3.9 + - + +
125G ARG* 3.0 24.3 + - + +
302G SO4 4.0 19.7 - - - +
114L TYR* 4.2 20.4 - - + +
115L VAL* 5.1 2.4 - - - +
118L ASP* 4.0 34.1 - - + +
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Residues in contact with GLU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G ARG* 3.3 29.8 + - - +
118G ASP* 3.1 34.2 + - - +
119G MET 3.8 7.2 - - - +
120G MET 3.3 0.2 - - - -
121G ILE* 1.3 78.0 - - + +
123G ILE* 1.3 63.4 + - - +
125G ARG* 3.3 14.6 + - - +
126G ASP* 3.2 24.2 + - - +
118L ASP* 6.1 1.8 - - - +
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Residues in contact with ILE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G GLU* 4.0 2.2 - - - +
54G HIS* 3.7 38.8 - - + +
57G ARG* 4.0 14.4 - - + +
58G TYR* 3.6 42.0 - - + +
101G LEU* 4.0 7.4 - - + -
119G MET* 3.2 33.6 + - + +
120G MET* 3.5 6.1 - - - +
122G GLU* 1.3 75.1 - - - +
124G LEU* 1.3 58.3 + - - +
126G ASP* 2.8 21.9 + - - +
127G GLU* 2.9 30.6 + - - +
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Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ALA* 4.0 27.1 - - + +
101G LEU* 3.7 21.7 - - + +
102G ARG* 4.1 20.2 - - + +
105G ILE* 3.8 21.8 - - + -
120G MET 2.8 16.7 + - - +
121G ILE* 3.6 6.3 - - - +
122G GLU 3.3 0.4 - - - -
123G ILE* 1.3 74.6 - - - +
125G ARG* 1.3 57.6 + - - +
127G GLU* 2.9 4.8 + - + +
128G GLU* 2.9 44.2 + - - +
114L TYR* 4.0 17.7 - - + -
115L VAL* 3.8 22.0 - - + -
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Residues in contact with ARG 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ILE* 3.0 13.9 + - + +
122G GLU* 3.3 17.7 - - - +
124G LEU* 1.3 75.8 - - - +
126G ASP* 1.3 64.0 + - - +
128G GLU* 3.5 3.8 + - - +
129G GLY* 3.2 17.0 + - - -
57L ARG* 5.0 10.1 - - - +
115L VAL* 4.2 27.0 - - + +
118L ASP* 3.9 16.8 + - - -
122L GLU* 3.6 26.3 + - - -
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Residues in contact with ASP 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ASP* 4.9 8.1 - - - +
54G HIS* 3.0 31.6 + - + +
57G ARG* 5.4 4.0 + - - -
122G GLU 3.2 12.1 + - - +
123G ILE* 2.8 10.7 + - - +
125G ARG* 1.3 78.4 - - - +
127G GLU* 1.3 63.8 - - - +
129G GLY* 3.2 4.8 + - - -
130G HIS* 3.0 30.5 + - + +
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Residues in contact with GLU 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G GLU* 3.2 5.9 - - - +
54G HIS* 3.1 11.3 + - - -
94G GLU* 3.6 8.0 - - - +
97G GLY* 5.7 1.3 - - - -
98G ALA* 5.1 6.7 - - + +
101G LEU* 3.7 22.3 - - + +
123G ILE* 2.9 17.9 + - - +
124G LEU* 2.9 10.9 + - + +
126G ASP* 1.3 76.0 - - - +
128G GLU* 1.3 58.7 + - - +
130G HIS* 2.8 12.4 + - - +
131G ILE* 2.8 37.5 + - + +
300G FE2 1.9 30.8 - - - -
301G FE2 2.0 29.4 - - - -
400G UNK 3.2 5.9 + - - -
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ALA* 5.3 0.9 - - - +
102G ARG* 2.5 34.2 + - - -
124G LEU* 2.9 19.1 + - - +
125G ARG* 3.7 8.3 - - - +
127G GLU* 1.3 77.8 - - - +
129G GLY* 1.3 55.9 + - - +
131G ILE* 3.3 10.5 + - - +
132G ASP* 2.9 27.6 + - - +
1L MET* 3.8 12.3 - - + +
61L ARG* 2.7 37.3 + - - +
64L PHE* 3.4 29.4 - - + -
115L VAL* 3.2 19.4 - - + +
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Residues in contact with GLY 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLU* 5.3 0.2 - - - -
125G ARG 3.2 9.9 + - - -
126G ASP* 3.2 8.1 + - - -
128G GLU* 1.3 71.2 - - - +
130G HIS* 1.4 66.0 + - - +
132G ASP* 3.2 9.7 + - - +
133G TRP* 3.0 22.5 + - - +
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Residues in contact with HIS 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR* 4.0 4.5 - - - +
47G GLU* 3.1 37.1 - - + +
50G ASP* 2.9 34.3 + - + +
51G GLU* 3.1 25.6 - - - -
54G HIS* 4.2 6.3 - + - -
94G GLU* 3.0 17.9 + - - +
126G ASP* 3.0 17.1 + - - +
127G GLU* 2.8 17.7 + - - +
129G GLY* 1.4 74.1 - - - +
131G ILE* 1.3 63.1 + - - +
133G TRP* 3.2 3.5 + - - +
134G LEU* 3.0 29.9 + - - +
301G FE2 2.4 23.1 - - - -
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Residues in contact with ILE 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 3.9 15.3 - - + -
94G GLU* 3.6 31.2 - - + +
95G LEU* 3.8 25.1 - - + -
98G ALA* 4.2 12.1 - - + -
127G GLU 2.8 23.9 + - - +
128G GLU* 3.4 12.8 - - + +
130G HIS* 1.3 76.9 - - - +
132G ASP* 1.3 63.9 + - - +
134G LEU* 3.8 2.8 - - - +
135G GLU* 2.9 46.8 + - - +
1L MET* 4.2 20.6 - - + -
64L PHE* 4.6 1.1 - - + -
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Residues in contact with ASP 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G GLU 2.9 13.5 + - - +
129G GLY* 3.4 12.8 - - - +
131G ILE* 1.3 75.8 - - - +
133G TRP* 1.3 62.5 + - - +
135G GLU* 3.3 4.7 + - - +
136G THR* 2.8 40.6 + - - -
34K ASN* 4.4 15.0 + - - +
64L PHE* 3.7 32.5 - - + +
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Residues in contact with TRP 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ARG* 4.1 8.4 - - - +
40G LEU* 4.0 22.2 - - + -
43G VAL* 3.4 40.8 - - + +
44G GLU* 3.7 20.4 - - + -
47G GLU* 4.0 19.5 - - - +
87G LEU* 4.9 4.7 - - + -
129G GLY 3.0 12.5 + - - +
130G HIS 3.2 6.0 + - - +
132G ASP* 1.3 78.8 - - - +
134G LEU* 1.3 89.6 + - + +
136G THR* 3.4 7.1 + - + -
137G GLU* 3.0 59.8 + - + +
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR* 3.6 23.3 - - - +
44G GLU* 4.2 4.9 - - - +
47G GLU* 4.6 2.7 - - - +
87G LEU* 3.9 26.2 - - + +
90G ASP* 4.1 8.5 - - + -
91G LEU* 3.9 34.1 - - + +
94G GLU* 4.0 12.3 - - + -
130G HIS 3.0 28.6 + - - +
131G ILE* 3.9 3.6 - - - +
133G TRP* 1.3 102.3 - - + +
135G GLU* 1.3 63.8 + - - +
137G GLU* 3.2 3.8 + - - +
138G LEU* 2.9 29.3 + - + +
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Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 4.2 23.4 - - + +
95G LEU* 5.2 2.9 - - - +
131G ILE* 2.9 29.9 + - - +
132G ASP* 3.8 5.3 - - - +
134G LEU* 1.3 76.1 - - - +
136G THR* 1.3 63.7 + - - +
138G LEU* 3.4 5.3 + - - +
139G ASP* 3.0 31.5 + - - +
1L MET* 2.8 40.9 + - - +
64L PHE* 3.9 13.2 - - - -
66L GLU* 4.3 4.2 - - - +
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Residues in contact with THR 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G ASP* 2.8 27.5 + - - -
133G TRP* 3.7 7.1 - - + -
135G GLU* 1.3 74.2 - - - +
137G GLU* 1.3 63.7 + - - +
139G ASP* 3.2 7.9 + - + +
140G LEU* 2.8 35.3 + - + +
34K ASN 3.3 14.4 + - - +
35K TRP* 3.6 34.1 - - - +
36K GLY* 3.6 10.5 - - - -
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Residues in contact with GLU 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ARG* 3.0 32.6 + - - -
40G LEU* 4.2 0.2 - - - +
87G LEU* 4.2 11.2 - - + -
133G TRP* 3.0 55.1 + - + +
134G LEU* 3.6 4.9 - - - +
136G THR* 1.3 76.1 - - - +
138G LEU* 1.3 64.2 + - - +
140G LEU* 3.0 19.7 + - - +
141G ILE* 3.0 27.6 + - - +
149G TYR* 2.5 39.7 + - - +
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLU* 3.9 31.3 - - + +
87G LEU* 3.6 31.4 - - + +
88G ARG* 3.8 40.0 + - + +
91G LEU* 3.8 30.3 - - + -
134G LEU 2.9 18.7 + - - +
135G GLU* 3.8 4.5 - - - +
137G GLU* 1.3 74.9 - - - +
139G ASP* 1.3 65.8 + - - +
141G ILE* 3.4 18.9 + - + +
142G GLN* 3.5 13.9 + - - +
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Residues in contact with ASP 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G GLU* 3.0 22.9 + - - +
136G THR* 3.6 6.3 - - - +
138G LEU* 1.3 76.5 - - - +
140G LEU* 1.3 67.0 + - - +
142G GLN* 3.0 8.9 + - - +
143G LYS* 2.9 49.3 + - + +
35K TRP* 5.4 5.4 - - - -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ARG* 5.0 2.7 - - - +
136G THR* 2.8 24.1 + - + +
137G GLU* 3.0 31.8 + - - +
139G ASP* 1.3 76.3 - - - +
141G ILE* 1.3 63.5 + - - +
143G LYS* 4.4 10.8 - - + +
144G MET* 2.9 50.8 + - + +
149G TYR* 4.3 7.9 - - + -
35K TRP 3.5 21.5 - - - +
36K GLY* 4.8 4.7 - - - +
37K LEU* 3.8 18.4 - - + -
150K LEU* 5.9 0.9 - - + -
154K ILE* 4.2 22.2 - - + -
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Residues in contact with ILE 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G VAL* 4.6 3.8 - - + -
84G GLU* 4.2 30.1 - - + +
87G LEU* 4.3 16.8 - - + -
137G GLU 3.0 14.1 + - - +
138G LEU* 3.5 11.4 - - + +
139G ASP 3.1 0.2 - - - -
140G LEU* 1.3 76.1 - - - +
142G GLN* 1.3 71.3 + - - +
145G GLY* 2.9 30.5 + - - -
146G LEU* 4.4 28.9 - - + +
149G TYR* 3.6 40.6 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLU* 3.7 26.6 + - - -
88G ARG* 4.9 7.8 - - - +
138G LEU 3.5 11.7 + - - +
139G ASP* 3.0 9.8 + - - +
141G ILE* 1.3 88.9 - - - +
143G LYS* 1.3 69.7 + - + +
144G MET 3.5 0.3 + - - -
145G GLY* 3.7 5.2 + - - -
147K GLN* 4.5 4.3 + - - -
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Residues in contact with LYS 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G ASP* 2.9 43.2 + - + +
140G LEU* 4.0 11.7 - - + +
142G GLN* 1.3 81.2 - - + +
144G MET* 1.3 58.5 + - + +
35K TRP* 4.0 47.3 + - + +
37K LEU* 5.8 4.2 - - + +
146K LEU* 5.7 1.4 - - - +
147K GLN* 3.7 15.6 + - - +
150K LEU* 4.1 31.7 - - + +
----------------------------------------------------------
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Residues in contact with MET 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G LEU* 2.9 41.3 + - + +
143G LYS* 1.3 76.4 - - - +
145G GLY* 1.3 69.1 + - - +
148G ASN* 3.4 16.4 + - + +
149G TYR* 3.7 26.7 - - + +
152G ALA* 4.8 0.2 - - - -
250G SO4 4.6 0.9 + - - -
147K GLN* 3.5 42.9 - - - +
150K LEU* 4.4 7.0 - - + -
151K GLN* 3.7 31.9 - - - +
154K ILE* 3.3 33.0 - - + -
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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