Contacts of the helix formed by residues 113 - 144 (chain B) in PDB entry 3E1J
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 6.5 0.2 - - - -
3B GLY* 5.8 0.3 - - - -
4B ASP* 5.5 3.6 + - + -
7B VAL* 3.4 29.3 - - + +
61B ARG* 2.8 24.8 + - - -
65B LEU* 3.7 11.0 - - - +
108B ALA* 2.8 20.7 + - + +
111B VAL* 3.3 6.0 + - + +
112B HIS* 1.3 68.4 - - - +
114B TYR* 1.3 56.1 + - - +
115B VAL 3.8 1.4 + - - -
116B SER* 2.6 28.6 + - - -
117B ARG* 3.0 26.9 + - - +
102C ARG* 4.7 6.8 + - - +
128C GLU* 4.3 1.7 - - - +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 3.3 38.9 + - - -
112B HIS* 2.9 53.1 + + + -
113B ASP* 1.3 73.5 + - - +
115B VAL* 1.3 58.3 + - - +
117B ARG* 3.4 8.9 + - - +
118B ASP* 2.9 28.1 + - - +
102C ARG* 3.5 26.0 - - - +
105C ILE* 3.6 27.8 - - + -
106C GLY* 3.5 15.1 - - - -
117C ARG* 3.7 21.6 + - - -
121C ILE* 4.2 20.7 - - + +
124C LEU* 4.1 14.4 - - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 3.2 30.1 - - - +
113B ASP* 3.3 1.2 + - - -
114B TYR* 1.3 73.2 - - + +
116B SER* 1.3 65.8 - - - +
118B ASP* 3.1 7.4 + - + +
119B MET* 2.9 25.7 + - + +
102C ARG* 4.7 0.4 - - - +
121C ILE* 5.0 3.8 - - + +
124C LEU* 3.8 22.2 - - + -
125C ARG* 4.2 33.7 - - + +
128C GLU* 3.2 30.3 - - + +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.1 11.2 - - - +
11B LEU* 4.2 7.3 - - - +
61B ARG* 2.9 30.9 + - - +
65B LEU* 3.8 6.1 - - - +
108B ALA* 4.7 0.7 - - - -
113B ASP* 2.6 35.9 + - - -
115B VAL* 1.3 74.8 - - - +
117B ARG* 1.3 62.8 + - - +
119B MET* 3.3 7.0 + - - +
120B MET* 2.9 35.9 + - - +
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.3 41.3 + - + +
106B GLY* 4.3 1.2 - - - -
108B ALA* 4.1 5.8 - - + -
109B ASP* 3.2 42.1 + - - +
113B ASP 3.0 14.6 + - - +
114B TYR* 3.5 12.3 - - - +
115B VAL 3.2 0.2 - - - -
116B SER* 1.3 75.4 - - - +
118B ASP* 1.3 58.0 + - - +
120B MET* 3.0 15.6 + - - +
121B ILE* 2.8 35.3 + - + +
251B SO4 2.7 39.6 + - - +
117C ARG* 4.1 2.9 - - - +
109H ASP* 2.7 27.5 + - - -
114H TYR* 3.6 17.6 + - - -
117H ARG* 3.9 1.4 - - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR 2.9 17.8 + - - +
115B VAL* 3.5 7.6 - - + +
117B ARG* 1.3 78.0 - - - +
119B MET* 1.3 63.5 + - - +
121B ILE* 3.3 11.3 + - - +
122B GLU* 3.2 32.2 + - - +
251B SO4 4.9 8.1 + - - +
118C ASP* 5.6 2.3 - - - +
121C ILE* 4.0 16.3 - - + +
122C GLU* 3.3 24.0 - - - +
125C ARG* 4.2 21.1 + - - -
118H ASP* 5.6 2.1 - - - +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.5 1.6 - - - -
57B ARG* 3.6 55.3 + - + +
58B TYR* 4.4 16.4 - - - -
61B ARG* 3.6 42.0 - - + -
115B VAL* 2.9 17.6 + - + +
116B SER* 3.7 5.4 - - - +
118B ASP* 1.3 78.8 + - - +
120B MET* 1.3 63.1 + - - +
122B GLU* 3.4 3.3 + - - +
123B ILE* 3.2 31.6 + - + +
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 5.8 1.3 - - + -
10B TYR* 6.2 0.2 - - + -
11B LEU* 4.0 15.5 - - + -
14B LEU* 3.6 31.0 - - + -
58B TYR* 4.4 11.2 - - + -
101B LEU* 3.7 11.0 - - + +
104B ALA* 3.6 37.2 - - + +
105B ILE* 3.6 17.5 - - + -
108B ALA* 3.6 21.1 - - + -
116B SER* 2.9 25.4 + - - +
117B ARG* 3.0 6.3 + - - +
119B MET* 1.3 78.4 - - + +
121B ILE* 1.3 56.5 + - - +
123B ILE* 3.2 6.5 + - - +
124B LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.0 23.8 - - + -
117B ARG* 2.8 41.8 + - + +
118B ASP* 3.3 9.6 + - - +
120B MET* 1.3 74.2 - - - +
122B GLU* 1.3 67.6 + - - +
124B LEU* 3.3 4.0 + - - +
125B ARG* 3.0 22.6 + - + +
251B SO4 3.9 26.5 - - - +
114H TYR* 4.1 21.1 - - + +
115H VAL* 5.0 3.0 - - + +
118H ASP* 4.1 34.8 - - + +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 4.2 19.3 - - - +
118B ASP* 3.2 21.6 + - - +
119B MET* 3.9 7.0 - - - +
120B MET 3.3 0.2 - - - -
121B ILE* 1.3 80.6 - - - +
123B ILE* 1.3 62.4 + - - +
125B ARG* 3.2 30.2 + - - +
126B ASP* 3.1 26.6 + - - +
118H ASP* 3.2 29.0 - - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.7 19.1 - - - +
54B HIS* 3.7 36.1 - - + +
57B ARG* 3.8 13.7 - - + +
58B TYR* 3.6 44.6 - - + +
101B LEU* 4.1 9.0 - - + -
119B MET* 3.2 29.7 + - + +
120B MET* 3.2 6.5 + - - +
122B GLU* 1.3 74.1 - - - +
124B LEU* 1.3 59.8 + - - +
126B ASP* 2.8 20.4 + - - +
127B GLU* 2.9 22.4 + - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 3.9 34.3 - - + +
101B LEU* 3.9 18.4 - - + +
102B ARG* 4.1 20.6 - - + +
105B ILE* 3.9 21.8 - - + -
120B MET 2.9 16.7 + - - +
121B ILE 3.6 5.2 - - - +
123B ILE* 1.3 75.3 - - - +
125B ARG* 1.3 56.9 + - - +
127B GLU* 3.1 4.4 + - + +
128B GLU* 2.8 47.4 + - - +
114H TYR* 4.1 16.2 - - + -
115H VAL* 3.8 21.1 - - + -
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.0 13.2 + - + +
122B GLU* 3.3 32.3 + - - +
123B ILE 3.2 0.2 - - - -
124B LEU* 1.3 76.9 - - - +
126B ASP* 1.3 64.7 + - - +
128B GLU* 3.6 4.0 + - - +
129B GLY* 3.2 17.3 + - - -
57H ARG* 5.1 13.6 - - - +
115H VAL* 4.1 26.8 - - + +
118H ASP* 4.1 21.3 + - - +
122H GLU* 6.3 1.2 - - - +
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 3.8 12.6 - - - +
54B HIS* 2.9 34.0 + - + -
57B ARG* 5.0 5.0 + - - -
122B GLU* 3.1 14.9 + - - +
123B ILE* 2.8 8.9 + - - +
125B ARG* 1.3 80.8 - - - +
127B GLU* 1.3 63.1 + - - +
129B GLY* 3.2 4.7 + - - -
130B HIS* 3.1 26.4 + - - +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 2.7 29.6 - - - +
51B GLU* 2.8 22.9 - - - +
54B HIS* 3.4 8.1 + - - -
94B GLU* 2.6 32.0 - - - +
97B GLY 6.1 0.4 - - - -
98B ALA* 5.4 2.9 - - + +
101B LEU* 3.9 21.5 - - + -
123B ILE* 2.9 19.2 + - - +
124B LEU* 3.1 9.8 + - + +
126B ASP* 1.3 73.6 - - - +
128B GLU* 1.3 56.8 + - - +
130B HIS* 2.9 12.6 + - - +
131B ILE* 2.8 42.5 + - + +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 5.2 1.2 - - - +
102B ARG* 2.7 30.3 + - - -
124B LEU* 2.8 27.0 + - - +
125B ARG* 3.7 8.7 - - - +
127B GLU* 1.3 76.2 - - - +
129B GLY* 1.3 54.9 + - - +
131B ILE* 3.3 12.3 + - - +
132B ASP* 2.9 25.3 + - - +
1H MET* 3.8 11.0 - - + +
61H ARG* 2.7 35.4 + - - +
64H PHE* 3.4 35.0 - - + -
115H VAL* 3.2 17.3 - - + +
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG 3.2 13.7 + - - -
126B ASP* 3.5 5.6 - - - -
127B GLU 3.1 1.0 - - - -
128B GLU* 1.3 74.1 - - - +
130B HIS* 1.3 65.9 + - - +
132B ASP* 3.2 9.2 + - - +
133B TRP* 3.1 21.1 + - - +
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Residues in contact with HIS 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 4.0 4.5 + - - +
47B GLU* 3.2 41.8 - - + +
50B ASP* 3.3 34.0 + - + -
51B GLU* 3.5 20.6 - - - -
54B HIS* 4.7 0.4 - + - -
94B GLU* 3.0 30.1 + - - +
126B ASP* 3.1 13.9 + - - +
127B GLU* 2.9 19.0 + - - +
129B GLY* 1.3 68.2 - - - +
131B ILE* 1.3 67.8 + - - +
133B TRP* 3.1 4.2 + - - +
134B LEU* 2.9 29.7 + - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.0 15.7 - - + +
94B GLU* 3.6 32.8 - - + +
95B LEU* 3.6 23.8 - - + -
98B ALA* 4.2 11.9 - - + -
127B GLU* 2.8 22.8 + - + +
128B GLU* 3.5 15.3 - - - +
130B HIS* 1.3 70.8 - - - +
132B ASP* 1.3 63.8 + - - +
134B LEU* 3.9 2.5 - - - +
135B GLU* 2.9 48.4 + - - +
1H MET* 4.1 27.1 - - + -
64H PHE* 4.4 1.6 - - + -
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU 2.9 13.9 + - - +
129B GLY* 3.2 12.8 + - - +
131B ILE* 1.3 76.8 - - - +
133B TRP* 1.3 59.0 + - - +
135B GLU* 3.8 4.8 - - - +
136B THR* 2.7 42.3 + - - -
34G ASN* 4.0 19.3 + - - +
64H PHE* 3.6 29.0 - - + +
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Residues in contact with TRP 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 4.2 11.5 - - - +
40B LEU* 4.2 15.9 - - + -
43B VAL* 3.5 44.8 - - + +
44B GLU* 3.7 20.0 - - + -
47B GLU* 4.1 14.4 - - - +
87B LEU* 4.7 5.4 - - + -
129B GLY 3.1 13.7 + - - +
130B HIS 3.1 6.2 + - - +
132B ASP* 1.3 76.8 - - - +
134B LEU* 1.3 98.2 + - + +
136B THR* 3.2 7.2 + - - -
137B GLU* 3.0 61.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.6 24.0 - - + +
44B GLU* 4.0 11.4 - - - +
47B GLU* 5.3 0.4 - - - +
87B LEU* 4.1 19.9 - - + +
90B ASP* 4.3 4.9 - - + -
91B LEU* 4.0 37.2 - - + +
94B GLU* 4.1 8.1 - - + -
130B HIS* 2.9 28.9 + - + +
131B ILE* 3.9 3.6 - - - +
133B TRP* 1.3 105.1 - - + +
135B GLU* 1.3 62.6 + - - +
137B GLU* 3.3 3.9 + - - +
138B LEU* 3.0 30.8 + - + +
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.1 20.7 - - + +
95B LEU* 5.3 2.9 - - - +
131B ILE* 2.9 30.9 + - - +
132B ASP* 3.8 4.3 - - - +
134B LEU* 1.3 75.6 - - - +
136B THR* 1.3 63.6 + - - +
138B LEU* 3.3 9.0 + - - +
139B ASP* 3.0 32.7 + - - +
1H MET* 2.8 40.8 + - - +
64H PHE* 3.9 13.2 - - - -
66H GLU* 4.3 4.1 - - - +
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ASP* 2.7 33.2 + - - -
133B TRP* 3.5 7.9 - - - -
135B GLU* 1.3 78.7 - - - +
137B GLU* 1.3 60.1 + - - +
139B ASP* 3.2 7.6 + - + +
140B LEU* 2.8 34.0 + - + +
34G ASN* 3.4 24.0 + - - +
35G TRP* 3.4 23.1 - - - +
36G GLY* 3.6 9.6 - - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.3 20.7 + - - -
87B LEU* 4.1 11.0 - - + -
133B TRP* 3.0 63.2 + - + +
134B LEU* 3.7 7.9 - - - +
136B THR* 1.3 78.4 - - - +
138B LEU* 1.3 62.4 + - - +
140B LEU* 3.0 28.6 + - - +
141B ILE* 3.0 19.3 + - - +
149B TYR* 2.5 39.8 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.9 32.4 - - + +
87B LEU* 3.7 28.3 - - + -
88B ARG* 4.0 39.2 + - + +
91B LEU* 3.8 29.4 - - + -
134B LEU 3.0 19.5 + - - +
135B GLU* 3.7 4.9 - - - +
137B GLU* 1.3 76.7 - - - +
139B ASP* 1.3 64.3 + - - +
141B ILE* 3.4 16.3 + - + +
142B GLN* 3.5 16.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 3.0 23.4 + - - +
136B THR* 3.7 7.1 - - + +
138B LEU* 1.3 75.9 - - - +
140B LEU* 1.3 66.1 + - - +
142B GLN* 3.2 8.5 + - - +
143B LYS* 2.9 48.9 + - - +
35G TRP* 5.6 4.0 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 5.5 1.1 - - - +
136B THR* 2.8 21.6 + - + +
137B GLU* 3.0 32.0 + - - +
139B ASP* 1.3 77.6 - - + +
141B ILE* 1.3 63.0 + - - +
143B LYS* 4.4 11.4 - - + +
144B MET* 2.9 53.8 + - + +
149B TYR* 4.2 8.1 - - + -
35G TRP 3.5 23.3 - - - +
36G GLY* 4.7 6.1 - - - +
37G LEU* 3.8 19.1 - - + -
150G LEU* 5.8 1.1 - - + -
154G ILE* 4.2 22.4 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 4.3 8.7 - - + -
84B GLU* 4.2 27.8 - - + +
87B LEU* 4.2 17.5 - - + -
137B GLU 3.0 18.1 + - - +
138B LEU* 3.6 11.4 - - + +
139B ASP 3.2 0.2 - - - -
140B LEU* 1.3 76.8 - - - +
142B GLN* 1.3 70.9 + - - +
145B GLY* 3.0 28.6 + - - -
146B LEU* 4.2 28.3 - - + +
149B TYR* 3.6 40.6 - - + -
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Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.9 25.6 + - - -
88B ARG* 5.1 6.5 - - - +
138B LEU 3.5 11.3 + - - +
139B ASP* 3.2 10.3 + - - +
141B ILE* 1.3 90.4 + - - +
143B LYS* 1.3 67.1 + - + +
145B GLY* 3.8 4.7 + - - -
147G GLN* 4.5 4.2 + - - -
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP* 2.9 41.7 + - + +
140B LEU* 3.1 11.2 + - + +
142B GLN* 1.3 82.4 - - + +
144B MET* 1.3 57.9 + - + +
35G TRP* 3.7 49.9 + - + +
37G LEU* 5.9 3.8 - - + +
146G LEU* 5.6 1.4 - - - +
147G GLN* 3.6 17.5 + - - +
150G LEU* 4.0 29.2 - - + +
----------------------------------------------------------
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Residues in contact with MET 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 2.9 41.5 + - + +
143B LYS* 1.3 76.6 - - - +
145B GLY* 1.3 66.7 + - - +
148B ASN* 3.4 18.6 + - + +
149B TYR* 3.8 26.2 - - + +
250B SO4 4.7 0.7 + - - -
147G GLN* 3.3 43.9 - - - +
150G LEU* 4.3 6.5 - - + -
151G GLN* 3.6 28.7 - - - +
154G ILE* 3.2 36.3 - - + -
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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