Contacts of the helix formed by residues 113 - 144 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 6.4 0.4 - - - -
3I GLY* 5.8 0.3 - - - -
4I ASP* 5.5 4.0 + - + +
7I VAL* 3.4 30.2 - - + +
61I ARG* 2.8 25.3 + - - -
65I LEU* 3.7 11.2 - - - +
108I ALA* 2.8 16.4 + - + +
111I VAL* 3.3 5.8 + - + +
112I HIS* 1.3 72.6 - - - +
114I TYR* 1.3 57.3 + - - +
115I VAL 3.8 1.6 + - - -
116I SER* 2.6 27.7 + - - -
117I ARG* 3.0 26.5 + - - +
102K ARG* 4.7 6.4 + - - +
128K GLU* 4.2 1.6 - - - +
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I ASP* 3.3 39.4 + - - -
112I HIS* 2.9 54.6 + + + -
113I ASP* 1.3 74.6 + - - +
115I VAL* 1.3 58.6 + - - +
117I ARG* 3.5 8.4 - - - +
118I ASP* 3.0 27.7 + - - +
102K ARG* 3.5 26.2 - - - +
105K ILE* 3.6 28.0 - - + -
106K GLY* 3.5 15.2 - - - -
117K ARG* 3.7 20.8 + - - -
121K ILE* 4.2 20.4 - - + +
124K LEU* 4.1 14.9 - - + +
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Residues in contact with VAL 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I ARG* 3.2 30.1 - - - +
113I ASP* 3.3 1.4 + - - -
114I TYR* 1.3 74.2 - - - +
116I SER* 1.3 65.7 + - - +
118I ASP* 3.1 7.8 + - + +
119I MET* 2.9 25.9 + - + +
102K ARG* 4.6 0.7 - - - +
121K ILE* 5.0 3.6 - - + +
124K LEU* 3.8 21.5 - - + -
125K ARG* 4.2 32.8 - - + +
128K GLU* 3.1 31.0 - - + +
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Residues in contact with SER 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 4.1 11.2 - - - +
11I LEU* 4.2 6.9 - - - +
61I ARG* 2.9 31.2 + - - +
65I LEU* 3.8 5.7 - - - +
108I ALA* 4.7 0.7 - - - -
113I ASP* 2.6 36.4 + - - -
115I VAL* 1.3 74.8 - - - +
117I ARG* 1.3 63.5 + - - +
119I MET* 3.3 7.0 + - - +
120I MET* 2.9 36.2 + - - +
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Residues in contact with ARG 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ASP* 2.7 28.5 + - - -
114F TYR* 3.6 17.8 + - - -
117F ARG* 3.9 1.2 - - - +
251F SO4 2.8 40.1 + - - +
105I ILE* 3.4 41.3 + - + +
106I GLY* 4.3 0.6 - - - -
108I ALA* 4.1 5.8 - - + -
109I ASP* 3.2 43.2 + - - +
113I ASP 3.0 15.0 + - - +
114I TYR* 3.5 13.9 - - - +
115I VAL 3.1 0.2 - - - -
116I SER* 1.3 74.8 - - - +
118I ASP* 1.3 52.8 + - - +
120I MET* 3.0 14.6 + - - +
121I ILE* 2.8 40.9 + - + +
117K ARG* 4.1 2.7 - - - +
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Residues in contact with ASP 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP* 5.6 1.2 - - - +
251F SO4 5.0 7.6 + - - -
114I TYR 3.0 16.7 + - - +
115I VAL* 3.1 7.8 + - + +
117I ARG* 1.3 78.2 - - - +
119I MET* 1.3 63.3 + - - +
121I ILE* 3.3 11.2 + - - +
122I GLU* 3.2 32.5 + - - +
118K ASP* 5.6 1.6 - - - +
121K ILE* 4.1 16.2 - - + +
122K GLU* 3.3 25.5 - - - +
125K ARG* 4.1 21.9 + - - -
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Residues in contact with MET 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I LEU* 5.5 1.8 - - - -
57I ARG* 3.6 63.7 + - + +
58I TYR* 4.3 16.4 - - - -
61I ARG* 3.6 35.0 - - + -
115I VAL* 2.9 17.1 + - + +
116I SER* 3.7 5.6 - - - +
118I ASP* 1.3 79.3 + - - +
120I MET* 1.3 63.6 + - - +
122I GLU* 3.4 3.1 + - - +
123I ILE* 3.2 31.2 + - + +
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Residues in contact with MET 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 5.8 1.1 - - + -
11I LEU* 4.0 15.3 - - + -
14I LEU* 3.6 31.2 - - + -
58I TYR* 4.4 11.2 - - + -
101I LEU* 3.7 10.7 - - + +
104I ALA* 3.6 36.6 - - + +
105I ILE* 3.6 16.8 - - + -
108I ALA* 3.6 21.1 - - + -
116I SER* 2.9 25.5 + - - +
117I ARG* 3.0 6.7 + - - +
119I MET* 1.3 77.2 - - + +
121I ILE* 1.3 57.9 + - - +
123I ILE* 3.2 7.0 + - - +
124I LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TYR* 4.1 22.2 - - + +
115F VAL* 5.0 3.2 - - + +
118F ASP* 4.2 25.6 - - + +
251F SO4 4.0 22.2 - - - +
105I ILE* 4.0 22.2 - - + -
117I ARG* 2.8 48.3 + - + +
118I ASP* 3.3 9.8 + - - +
120I MET* 1.3 74.2 - - - +
122I GLU* 1.3 73.4 + - - +
124I LEU* 3.3 3.6 + - - +
125I ARG* 3.0 22.1 + - + +
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Residues in contact with GLU 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP* 3.3 28.4 - - - +
57I ARG* 4.2 19.3 - - - +
118I ASP* 3.2 21.3 + - - +
119I MET 3.4 6.7 + - - +
120I MET 3.3 0.2 - - - -
121I ILE* 1.3 82.3 - - - +
123I ILE* 1.3 62.6 + - - +
125I ARG* 3.2 30.4 + - - +
126I ASP* 3.1 27.6 + - - +
125K ARG* 6.3 1.1 - - - +
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Residues in contact with ILE 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU* 3.7 18.6 - - - +
54I HIS* 3.7 38.4 - - + +
57I ARG* 3.8 13.0 - - + +
58I TYR* 3.6 44.4 - - + +
101I LEU* 4.1 8.7 - - + -
119I MET* 3.2 28.2 + - + +
120I MET 3.2 6.0 + - - +
122I GLU* 1.3 73.9 - - - +
124I LEU* 1.3 58.9 + - - +
126I ASP* 2.9 20.0 + - - +
127I GLU* 2.9 22.6 + - - +
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Residues in contact with LEU 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TYR* 4.1 16.4 - - + -
115F VAL* 3.9 16.8 - - + +
98I ALA* 3.9 35.4 - - + +
101I LEU* 3.9 16.6 - - + -
102I ARG* 4.1 21.1 - - + +
105I ILE* 3.9 21.1 - - + -
120I MET 2.9 16.1 + - - +
121I ILE* 3.6 5.8 - - - +
123I ILE* 1.3 75.8 - - - +
125I ARG* 1.3 57.0 + - - +
127I GLU* 3.1 5.0 + - + +
128I GLU* 2.8 51.3 + - - +
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Residues in contact with ARG 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ARG* 5.2 11.9 - - - +
115F VAL* 4.2 27.3 - - + +
118F ASP* 4.1 19.4 + - - +
122F GLU* 6.4 0.6 - - - +
121I ILE* 3.0 13.7 + - + +
122I GLU* 3.3 32.9 + - - +
123I ILE 3.2 0.2 - - - -
124I LEU* 1.3 78.5 - - - +
126I ASP* 1.3 65.4 + - - +
128I GLU* 3.7 3.7 - - - +
129I GLY* 3.2 17.3 + - - -
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Residues in contact with ASP 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I ASP* 3.8 12.4 - - - +
54I HIS* 2.9 34.2 + - + -
57I ARG* 5.0 4.7 + - - -
122I GLU* 3.1 14.7 + - - +
123I ILE* 2.9 8.5 + - - +
125I ARG* 1.3 80.4 - - - +
127I GLU* 1.3 62.4 + - - +
129I GLY* 3.2 3.6 + - - -
130I HIS* 3.1 26.9 + - - +
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Residues in contact with GLU 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU* 2.7 29.1 - - - +
51I GLU* 2.8 24.5 - - - +
54I HIS* 3.4 7.8 + - - -
94I GLU* 2.6 32.3 - - - +
97I GLY 6.1 0.7 - - - -
98I ALA* 5.4 2.2 - - + +
101I LEU* 3.9 21.7 - - + +
123I ILE* 2.9 20.0 + - - +
124I LEU* 3.1 11.8 + - + +
126I ASP* 1.3 72.3 - - - +
128I GLU* 1.3 57.6 + - - +
130I HIS* 2.9 12.5 + - - +
131I ILE* 2.8 42.5 + - + +
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Residues in contact with GLU 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 3.8 12.3 - - + +
61F ARG* 2.8 34.9 + - - +
64F PHE* 3.4 32.2 - - + -
115F VAL* 3.2 16.6 - - + +
98I ALA* 5.2 1.0 - - - +
102I ARG* 2.7 31.1 + - - -
124I LEU* 2.8 26.3 + - - +
125I ARG* 3.7 8.5 - - - +
127I GLU* 1.3 76.2 - - - +
129I GLY* 1.3 55.9 + - - +
131I ILE* 3.3 12.8 + - - +
132I ASP* 2.9 27.9 + - - +
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Residues in contact with GLY 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I ARG 3.2 14.1 + - - -
126I ASP* 3.2 6.3 + - - -
127I GLU 3.1 0.8 - - - -
128I GLU* 1.3 73.4 - - - +
130I HIS* 1.3 65.7 + - - +
132I ASP* 3.2 9.1 + - - +
133I TRP* 3.1 21.3 + - - +
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Residues in contact with HIS 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I TYR* 4.0 4.6 + - - +
47I GLU* 3.2 41.8 - - + +
50I ASP* 3.3 33.6 + - + -
51I GLU* 3.6 21.1 - - - -
54I HIS* 4.7 0.4 - + - -
94I GLU* 3.0 29.9 + - - +
126I ASP* 3.1 14.3 + - - +
127I GLU* 2.9 18.4 + - - +
129I GLY* 1.3 69.2 - - - +
131I ILE* 1.3 66.2 + - - +
133I TRP* 3.1 3.5 + - - +
134I LEU* 2.9 30.4 + - + +
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Residues in contact with ILE 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 4.1 25.1 - - + -
64F PHE* 4.4 1.3 - - + -
91I LEU* 4.0 15.7 - - + -
94I GLU* 3.6 32.1 - - + +
95I LEU* 3.6 26.7 - - + -
98I ALA* 4.3 11.4 - - + -
127I GLU* 2.8 22.8 + - + +
128I GLU* 3.5 15.5 - - - +
130I HIS* 1.3 70.6 - - - +
132I ASP* 1.3 63.5 + - - +
134I LEU* 3.9 1.7 - - - +
135I GLU* 3.0 47.6 + - - +
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Residues in contact with ASP 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ASN* 4.1 15.9 + - - +
64F PHE* 3.7 32.1 - - + +
128I GLU 2.9 14.4 + - - +
129I GLY* 3.2 12.8 + - - +
131I ILE* 1.3 76.7 - - - +
133I TRP* 1.3 58.6 + - - +
135I GLU* 3.8 4.6 - - - +
136I THR* 2.6 42.4 + - - -
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Residues in contact with TRP 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ARG* 4.1 10.9 - - - +
40I LEU* 4.2 16.4 - - + -
43I VAL* 3.5 44.3 - - + +
44I GLU* 3.7 18.6 - - + -
47I GLU* 4.1 16.2 - - - +
87I LEU* 4.7 5.8 - - + -
129I GLY 3.1 12.7 + - - +
130I HIS 3.1 6.3 + - - +
132I ASP* 1.3 77.0 - - - +
134I LEU* 1.3 100.1 + - + +
136I THR* 3.2 7.3 + - - -
137I GLU* 3.0 60.9 + - + +
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Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I TYR* 3.6 23.3 - - - +
44I GLU* 4.0 12.1 - - - +
47I GLU* 4.9 1.6 - - - +
87I LEU* 4.1 19.5 - - + +
90I ASP* 4.3 4.9 - - + -
91I LEU* 4.0 32.8 - - + +
94I GLU* 4.1 12.8 - - + -
130I HIS* 2.9 28.9 + - + +
131I ILE* 3.9 3.6 - - - +
133I TRP* 1.3 103.6 - - + +
135I GLU* 1.3 63.7 + - - +
137I GLU* 3.3 4.4 + - - +
138I LEU* 3.0 29.3 + - + +
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Residues in contact with GLU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 2.8 41.7 + - - +
64F PHE* 4.0 11.4 - - - -
66F GLU* 4.4 3.3 - - - +
91I LEU* 4.1 22.1 - - + +
95I LEU* 5.3 2.9 - - - +
131I ILE* 3.0 33.3 + - - +
132I ASP* 3.8 4.6 - - - +
134I LEU* 1.3 75.5 - - - +
136I THR* 1.3 63.3 + - - +
138I LEU* 3.3 9.1 + - - +
139I ASP* 3.0 32.1 + - - +
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Residues in contact with THR 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ASN 3.5 18.9 + - - +
35E TRP* 3.5 28.2 - - - +
36E GLY* 3.7 9.4 - - - +
132I ASP* 2.6 33.9 + - - -
133I TRP* 3.6 7.6 - - - -
135I GLU* 1.3 77.6 - - - +
137I GLU* 1.3 60.3 + - - +
139I ASP* 3.2 8.1 + - + +
140I LEU* 2.9 34.0 + - + +
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Residues in contact with GLU 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ARG* 3.3 21.0 + - - -
87I LEU* 4.1 11.0 - - + -
133I TRP* 3.0 62.0 + - + +
134I LEU* 3.3 8.0 + - - +
136I THR* 1.3 78.6 - - - +
138I LEU* 1.3 63.9 + - - +
140I LEU* 3.0 28.4 + - - +
141I ILE* 3.0 18.1 + - - +
149I TYR* 2.5 39.5 + - - +
153I GLN* 4.3 0.2 + - - -
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Residues in contact with LEU 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I GLU* 3.9 33.5 - - + +
87I LEU* 3.7 28.0 - - + -
88I ARG* 4.0 37.8 + - - +
91I LEU* 3.7 30.5 - - + -
134I LEU 3.0 19.8 + - - +
135I GLU* 3.7 4.7 - - - +
137I GLU* 1.3 75.9 - - - +
139I ASP* 1.3 65.6 + - - +
141I ILE* 3.4 16.9 + - + +
142I GLN* 3.5 17.0 + - - +
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Residues in contact with ASP 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TRP* 5.6 3.8 - - - -
135I GLU* 3.0 23.4 + - - +
136I THR* 3.7 6.5 - - + +
138I LEU* 1.3 76.0 - - - +
140I LEU* 1.3 67.6 + - - +
142I GLN* 3.2 8.7 + - - +
143I LYS* 2.9 48.9 + - + +
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Residues in contact with LEU 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TRP 3.6 22.4 - - - +
36E GLY* 4.8 5.6 - - - +
37E LEU* 3.8 18.6 - - + -
150E LEU* 5.8 0.9 - - + -
154E ILE* 4.1 22.7 - - + -
39I ARG* 5.5 1.3 - - - +
136I THR* 2.9 21.8 + - + +
137I GLU* 3.0 32.1 + - - +
139I ASP* 1.3 76.3 - - + +
141I ILE* 1.3 62.2 + - - +
143I LYS* 4.4 11.7 - - + +
144I MET* 2.9 53.7 + - + +
149I TYR* 4.2 7.9 - - + -
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Residues in contact with ILE 141 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I VAL* 4.3 8.7 - - + -
84I GLU* 4.2 27.6 - - + +
87I LEU* 4.2 17.0 - - + -
137I GLU 3.0 18.8 + - - +
138I LEU* 3.6 11.2 - - + +
139I ASP 3.2 0.4 - - - -
140I LEU* 1.3 77.4 - - - +
142I GLN* 1.3 71.2 + - - +
145I GLY* 3.0 28.4 + - - -
146I LEU* 4.2 27.6 - - + +
149I TYR* 3.6 41.7 - - + -
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Residues in contact with GLN 142 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E GLN* 4.5 4.9 + - - -
84I GLU* 3.9 25.8 + - - -
88I ARG* 5.0 6.7 - - - +
138I LEU 3.5 10.9 + - - +
139I ASP* 3.2 10.5 + - - +
141I ILE* 1.3 89.5 - - - +
143I LYS* 1.3 64.6 + - + +
144I MET 3.6 0.2 + - - -
145I GLY* 3.8 4.9 + - - -
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Residues in contact with LYS 143 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TRP* 3.8 48.6 + - + +
37E LEU* 6.1 3.8 - - + -
146E LEU* 5.7 1.4 - - - +
147E GLN* 3.5 17.7 + - - +
150E LEU* 4.0 29.4 - - + +
139I ASP* 2.9 42.5 + - - +
140I LEU* 3.1 10.4 + - + +
142I GLN* 1.3 81.7 - - + +
144I MET* 1.3 59.0 + - + +
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Residues in contact with MET 144 (chain I).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E GLN* 3.3 46.1 - - - +
150E LEU* 4.4 6.3 - - + -
151E GLN* 3.7 29.6 - - - +
154E ILE* 3.2 33.4 - - + -
140I LEU* 2.9 42.2 + - + +
143I LYS* 1.3 76.4 - - - +
145I GLY* 1.3 67.0 + - - +
148I ASN* 3.4 19.6 + - + +
149I TYR* 3.8 26.5 - - - +
152I ALA* 4.9 0.2 - - - -
250I SO4 4.7 1.0 + - - -
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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