Contacts of the helix formed by residues 114 - 142 (chain B) in PDB entry 5PNZ
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 THR 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.7 11.5 - - + +
111B ALA* 2.7 41.3 + - + +
112B ARG 3.1 2.4 + - - -
113B ASP* 1.3 80.7 - - - +
115B VAL* 1.3 64.6 + - - +
117B TYR* 3.2 15.6 + - - +
118B ARG* 3.1 35.3 + - - +
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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
----------------------------------------------------------
54B ILE* 5.4 11.7 - - + -
114B THR* 1.3 79.3 - - - +
117B TYR 3.4 13.0 - - - -
118B ARG* 3.4 19.2 + - - +
119B ALA* 2.9 36.9 + - + +
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS* 2.7 41.3 + + - +
71A ILE* 5.4 0.3 - - - +
108A LYS* 3.5 24.9 + - - +
109A TYR* 4.4 4.9 - - - -
106B CYS* 4.5 15.6 - - - -
107B MET* 3.3 41.3 - - + +
110B ASN* 3.5 32.5 - - + +
111B ALA 3.2 17.0 - - - +
112B ARG* 3.2 31.2 - - + +
114B THR* 3.2 18.1 + - - +
115B VAL 3.4 16.4 + - - -
118B ARG* 1.3 71.3 + - + +
119B ALA* 3.2 2.5 - - - +
120B ALA* 3.1 9.3 + - - +
121B VAL* 3.1 32.6 + - + +
201B NA 3.6 0.4 - - - -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS* 6.5 0.2 - - + -
112B ARG 3.9 7.2 + - - +
113B ASP* 3.0 39.2 + - - +
114B THR* 3.1 32.5 + - - +
115B VAL* 3.8 18.5 - - - +
117B TYR* 1.3 81.6 - - + +
119B ALA* 1.3 57.5 + - - +
121B VAL* 3.4 9.4 + - + +
122B ARG* 2.9 28.8 + - - +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.9 27.6 - - + -
55B PHE* 4.1 14.5 - - + -
115B VAL* 2.9 19.4 + - + +
117B TYR 3.2 1.5 - - - +
118B ARG* 1.3 77.2 - - - +
120B ALA* 1.3 58.7 + - - +
122B ARG* 3.3 21.2 + - - +
123B LEU* 2.9 30.0 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.8 11.9 - - + -
103B ILE* 3.6 17.4 - - + +
106B CYS* 3.8 30.4 - - + -
107B MET* 3.8 19.5 - - + -
117B TYR* 3.1 10.6 + - - +
119B ALA* 1.3 76.5 - - - +
121B VAL* 1.3 61.1 + - - +
123B LEU 3.4 0.3 + - - -
124B ARG* 2.8 32.3 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASP 4.4 9.2 - - - +
70A HIS* 5.2 2.7 - - + +
107B MET* 3.9 19.3 - - + -
117B TYR* 3.1 37.1 + - + +
118B ARG* 3.7 11.4 - - + +
119B ALA 3.3 0.2 - - - -
120B ALA* 1.3 75.0 - - - +
122B ARG* 1.3 63.6 + - - +
124B ARG* 3.4 26.4 + - - +
125B ASP* 3.1 24.0 + - + +
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 2.9 30.9 + - - +
50B ASP* 4.5 10.3 + - - +
51B PRO* 4.9 3.6 - - - +
54B ILE* 5.8 2.4 - - - +
55B PHE* 5.8 1.6 - - - -
118B ARG 2.9 17.7 + - - +
119B ALA* 3.5 21.5 + - - +
121B VAL* 1.3 78.0 - - - +
123B LEU* 1.3 68.7 + - - +
125B ASP* 3.3 6.8 + - - +
126B GLN* 3.1 62.1 + - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.8 26.0 - - + +
49B LYS* 4.0 23.1 - - + +
50B ASP* 4.8 5.4 - - + -
55B PHE* 3.3 36.1 - - + -
77B PHE* 3.7 21.1 - - + -
99B PHE* 3.5 21.4 - - + -
102B ILE* 5.3 0.4 - - + -
103B ILE* 3.9 12.6 - - + -
119B ALA 2.9 16.0 + - - +
122B ARG* 1.3 78.8 - - - +
124B ARG* 1.3 57.2 + - - +
126B GLN* 4.0 4.3 - - - +
127B GLY* 2.7 33.7 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASP 3.1 26.3 + - - -
70A HIS* 2.8 24.9 + - - +
71A ILE* 4.8 0.2 - - - +
72A LYS* 3.3 35.8 - - - +
99B PHE* 4.5 5.2 - - + -
103B ILE* 3.8 29.3 - - + +
104B ASP* 6.0 0.7 - - - -
107B MET* 3.8 18.4 - - - +
120B ALA 2.8 19.7 + - - +
121B VAL* 3.6 19.0 + - - +
123B LEU* 1.3 76.8 - - - +
125B ASP* 1.3 58.2 + - - +
128B GLY* 2.8 28.4 + - - -
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 3.1 15.6 + - + +
122B ARG* 3.6 8.7 - - - +
124B ARG* 1.3 80.9 - - - +
126B GLN* 1.3 74.3 + - - +
128B GLY* 3.9 1.3 - - - -
129B VAL* 3.4 26.1 + - - +
132B ARG* 4.8 1.9 + - - -
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 3.8 36.5 - - + +
122B ARG* 3.1 57.8 + - + +
123B LEU* 4.0 4.0 - - - +
125B ASP* 1.3 87.1 - - - +
127B GLY* 1.3 62.2 + - - +
129B VAL* 3.3 9.1 + - - +
130B VAL* 3.2 26.2 + - - +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.6 26.4 - - - +
99B PHE* 4.0 6.7 - - - -
123B LEU* 2.7 23.7 + - - +
126B GLN* 1.3 70.6 - - - +
128B GLY* 1.3 57.8 + - - +
130B VAL* 3.2 1.9 + - - +
131B LEU* 2.8 40.8 + - - +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 4.7 1.4 - - - -
124B ARG 2.8 18.5 + - - -
125B ASP 3.9 1.8 - - - -
126B GLN 3.3 0.2 - - - -
127B GLY* 1.3 76.5 - - - +
129B VAL* 1.3 55.6 + - - +
131B LEU* 3.4 7.0 + - - +
132B ARG* 2.9 52.5 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP* 3.4 18.5 + - - +
126B GLN* 3.3 10.2 + - - +
127B GLY 3.2 0.4 - - - -
128B GLY* 1.3 76.0 - - - +
130B VAL* 1.3 64.8 + - + +
132B ARG* 3.3 23.6 + - - +
133B GLN* 3.1 23.8 + - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.8 36.1 - - + +
45B GLN* 3.9 31.2 - - + +
46B LEU* 4.4 10.1 - - + -
49B LYS* 4.4 18.8 - - - +
126B GLN 3.2 14.3 + - - +
127B GLY 3.2 8.6 + - - +
129B VAL* 1.3 78.7 - - + +
131B LEU* 1.3 58.2 + - - +
133B GLN* 3.3 7.9 + - - +
134B ALA* 2.8 25.5 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.0 24.2 - - + -
46B LEU* 5.4 2.7 - - + -
92B LEU* 4.1 14.1 - - + +
95B PHE* 4.1 13.9 - - + -
96B GLU* 3.9 40.3 - - + +
99B PHE* 3.7 34.5 - - + -
100B ASP* 5.4 2.0 - - - +
127B GLY 2.8 19.7 + - - +
128B GLY* 4.0 6.3 - - - +
130B VAL* 1.3 74.8 - - + +
132B ARG* 1.3 61.7 + - + +
134B ALA* 3.3 5.2 + - + +
135B ARG* 3.0 26.3 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP* 4.8 1.8 + - - -
128B GLY* 2.9 30.1 + - - +
129B VAL* 3.3 35.3 + - - +
131B LEU* 1.3 77.4 - - - +
133B GLN* 1.3 61.0 + - - +
135B ARG* 3.2 9.0 + - - +
136B ARG* 3.1 25.6 + - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 3.1 14.6 + - + +
130B VAL* 3.5 11.0 - - - +
132B ARG* 1.3 73.4 - - - +
134B ALA* 1.3 66.6 + - - +
136B ARG* 3.2 26.1 + - - +
137B GLU* 3.0 45.4 + - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.6 11.2 - - + +
42B VAL* 3.9 25.6 - - + -
92B LEU* 3.8 18.6 - - + -
130B VAL 2.8 15.3 + - - +
131B LEU* 3.4 12.1 - - - +
133B GLN* 1.3 77.2 - - - +
135B ARG* 1.3 56.1 + - - +
137B GLU* 3.1 9.4 + - - +
138B VAL* 2.9 31.2 + - - +
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.6 27.3 - - + +
93B HIS* 3.9 12.5 - - - +
96B GLU* 3.5 24.9 + - - +
131B LEU 3.0 13.3 + - - +
132B ARG* 3.5 11.9 - - - +
133B GLN 3.2 0.2 - - - -
134B ALA* 1.3 73.2 - - - +
136B ARG* 1.3 66.0 + - + +
138B VAL* 3.2 10.6 + - - +
139B ASP* 3.0 40.9 + - - +
144B GLU* 2.9 35.6 + - - -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG 3.1 18.3 + - - +
133B GLN* 3.5 31.4 - - - +
135B ARG* 1.3 77.0 - - + +
137B GLU* 1.3 58.4 + - - +
139B ASP* 3.4 9.6 + - - +
140B SER* 2.9 28.7 + - - -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.2 22.7 - - + +
133B GLN* 3.0 38.2 + - + +
134B ALA* 3.5 7.9 - - - +
136B ARG* 1.3 75.9 - - - +
138B VAL* 1.3 61.4 + - - +
140B SER* 4.3 10.1 + - - -
141B ILE* 2.8 54.3 + - + +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.9 4.0 - - + -
38B LEU* 3.7 17.2 - - + +
92B LEU* 3.9 23.8 - - + -
134B ALA 2.9 18.1 + - - +
135B ARG* 3.2 16.4 + - - +
137B GLU* 1.3 73.5 - - - +
139B ASP* 1.3 65.0 + - - +
142B GLY* 3.0 22.9 + - - -
143B LEU* 3.0 32.1 + - + -
144B GLU* 3.8 38.1 + - + +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 3.0 32.9 + - - +
136B ARG* 3.7 8.9 - - - +
138B VAL* 1.3 85.5 - - - +
140B SER* 1.3 63.5 + - - +
142B GLY* 3.5 10.7 + - - -
144B GLU* 5.6 1.7 - - - +
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG 2.9 17.9 + - - -
137B GLU* 3.8 14.7 + - - -
139B ASP* 1.3 78.4 - - - +
141B ILE* 1.3 65.5 + - - +
142B GLY* 4.6 0.3 - - - -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 4.3 29.8 - - + +
38B LEU* 5.4 6.3 - - + -
137B GLU* 2.8 45.6 + - + +
140B SER* 1.3 76.6 - - - +
142B GLY* 1.3 57.5 + - - +
143B LEU* 3.5 34.3 - - + +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL 3.0 7.5 + - - -
139B ASP* 3.5 7.6 + - - -
140B SER 3.3 3.0 - - - -
141B ILE* 1.3 79.4 - - - +
143B LEU* 1.3 65.5 + - - +
144B GLU 3.3 12.0 + - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 5.0 5.4 - - - +
32B LEU 5.6 2.7 - - - +
34B GLU* 3.8 20.2 - - + +
35B LEU* 3.8 38.8 - - + +
38B LEU* 4.3 8.3 - - + -
138B VAL* 3.0 38.4 + - + +
141B ILE* 3.5 36.1 - - + +
142B GLY* 1.3 78.9 - - - +
144B GLU* 1.3 62.7 + - + +
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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