Contacts of the helix formed by residues 113 - 139 (chain B) in PDB entry 1F33
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 ASN 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG 3.4 8.4 - - - +
56B GLY* 5.1 4.7 - - - -
57B ALA 5.6 0.9 + - - -
112B HIS* 1.3 80.2 - - - +
114B VAL* 1.3 69.4 + - - +
115B GLN* 2.7 47.5 - - - +
116B ASP* 3.1 35.2 + - - +
117B HIS* 3.1 11.8 + - - -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 4.3 12.6 - - + -
55B ARG 3.0 31.2 + - - +
56B GLY* 3.8 5.8 - - - +
57B ALA 3.4 27.6 - - - +
58B ASN* 4.6 1.1 - - + +
59B PHE* 4.2 11.9 - - - -
62B VAL* 4.3 22.4 - - + -
112B HIS 4.2 1.1 - - - -
113B ASN* 1.3 73.7 - - - +
115B GLN* 1.3 63.6 + - + +
117B HIS* 3.1 4.2 + - - +
118B LEU* 2.8 46.9 + - + +
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 5.3 4.0 + - + +
58B ASN* 5.9 2.6 - - - +
113B ASN* 2.7 22.8 - - - +
114B VAL* 1.3 78.9 - - + +
116B ASP* 1.3 61.2 + - - +
118B LEU* 3.4 11.6 + - - +
119B LYS* 3.0 42.6 + - - +
165B ASN 3.2 21.8 + - - -
166B ILE* 3.4 13.2 - - - +
167B GLU* 2.8 54.4 + - + +
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 4.2 27.4 - - + +
112B HIS 4.8 0.3 + - - -
113B ASN* 3.1 33.4 + - + +
115B GLN* 1.3 79.5 - - - +
117B HIS* 1.3 58.9 + - - +
119B LYS* 3.3 15.9 + - - +
120B GLU* 3.0 31.8 + - + +
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Residues in contact with HIS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLN* 4.6 1.6 - - - -
50B ALA* 3.4 21.6 - - + -
53B ASN* 3.4 17.9 + - + -
54B MET* 3.6 28.3 - - + -
107B TYR* 2.6 35.5 + + - +
108B PRO 4.9 1.1 - - - -
111B ILE* 3.1 40.3 + - + +
112B HIS 3.4 24.0 - - - -
113B ASN 3.1 9.4 + - - -
114B VAL 3.1 6.3 + - - +
116B ASP* 1.3 75.5 - - - +
118B LEU* 1.3 56.1 + - - +
121B LEU* 2.7 41.6 + - - +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 5.0 0.9 - - + -
58B ASN* 5.8 0.4 - - - +
62B VAL* 3.8 28.7 - - + -
65B MET* 5.1 3.8 - - + -
114B VAL* 2.8 33.7 + - + +
115B GLN* 3.5 14.6 - - - +
117B HIS* 1.3 78.1 - - - +
119B LYS* 1.3 56.9 + - - +
121B LEU* 4.4 10.1 - - + -
122B ALA* 2.8 26.3 + - - +
162B ILE* 3.3 39.3 - - + +
165B ASN* 3.7 34.5 - - + +
166B ILE* 3.9 10.3 - - + -
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 3.0 34.2 + - - +
116B ASP* 3.7 13.2 + - - +
118B LEU* 1.3 73.7 - - - +
120B GLU* 1.3 67.6 + - + +
122B ALA* 3.3 3.5 + - - +
123B ASP* 3.1 30.0 + - - +
166B ILE* 4.0 37.2 - - + -
167B GLU 5.8 0.9 - - - -
18C ARG* 4.4 9.9 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.5 25.4 - - + +
108B PRO* 3.9 11.5 - - + +
111B ILE* 3.7 20.2 - - + +
116B ASP* 3.0 19.5 + - + +
119B LYS* 1.3 77.9 - - - +
121B LEU* 1.3 61.8 + - - +
123B ASP* 3.4 12.7 + - - +
124B ARG* 2.9 51.8 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.9 27.8 - - + +
47B THR* 4.2 9.0 - - - -
50B ALA* 3.6 31.4 - - + -
66B LEU* 3.7 32.1 - - + -
107B TYR* 3.9 2.7 - - + +
117B HIS* 2.7 31.5 + - + +
118B LEU* 3.7 12.6 - - + +
120B GLU* 1.3 71.3 - - - +
122B ALA* 1.3 61.4 + - - +
124B ARG* 3.1 4.0 + - - -
125B TYR* 2.8 46.1 + - + -
162B ILE* 4.0 12.1 - - + -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU 2.8 18.7 + - - +
119B LYS* 3.5 4.0 - - - +
121B LEU* 1.3 75.8 - - - +
123B ASP* 1.3 57.6 + - - +
125B TYR* 4.5 1.3 - - - -
126B ALA* 2.8 31.9 + - - +
159B LEU* 3.4 9.4 - - - +
162B ILE* 3.8 15.8 - - + +
163B GLU* 4.3 8.5 - - + -
166B ILE* 4.3 2.0 - - + -
18C ARG* 3.4 34.7 - - - +
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 3.1 13.9 + - - +
120B GLU* 3.6 16.5 - - - +
121B LEU 3.1 0.4 - - - -
122B ALA* 1.3 77.9 - - - +
124B ARG* 1.3 68.5 + - - +
126B ALA* 3.3 4.1 + - - +
127B ILE* 3.1 29.7 + - + +
18C ARG* 2.8 29.4 + - - +
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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
----------------------------------------------------------
43B LEU* 3.8 18.8 - - + -
46B ILE* 4.2 15.2 - - + +
104B LEU* 3.8 18.2 - - + +
105B LYS* 2.8 53.8 + - - +
106B SER 3.7 3.8 + - - -
107B TYR* 2.9 35.2 - - - +
108B PRO* 3.5 15.2 - - - +
120B GLU* 2.9 42.5 + - - +
121B LEU* 3.1 4.6 + - - +
123B ASP* 1.3 77.8 - - - +
125B TYR* 1.3 67.5 + - - +
127B ILE* 3.3 9.2 + - - +
128B VAL* 3.1 26.2 + - - +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.5 35.2 - - + -
47B THR* 2.7 31.4 + - + +
66B LEU* 5.5 0.2 - - + -
69B PHE* 3.6 18.2 - + - +
73B LEU* 3.5 11.8 - - + +
121B LEU* 2.8 41.9 + - + +
122B ALA 3.9 2.9 - - - +
124B ARG* 1.3 69.3 - - - +
126B ALA* 1.3 55.9 + - - +
128B VAL* 3.3 1.2 + - - +
129B ALA* 2.6 40.3 + - - +
155B LEU* 4.2 9.5 - - + +
158B PHE* 3.7 37.0 - + + -
159B LEU* 4.2 16.4 - - + -
162B ILE* 3.6 23.6 - - + -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA 2.8 19.0 + - - +
123B ASP* 3.4 6.5 - - - +
124B ARG 3.2 0.2 - - - -
125B TYR* 1.3 77.1 - - - +
127B ILE* 1.3 57.2 + - + +
129B ALA* 4.2 0.2 - - - -
130B ASN* 2.8 45.8 + - - +
159B LEU* 3.9 13.0 - - + +
18C ARG* 3.4 32.8 - - + +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 4.3 11.0 - - - +
103B PRO* 4.4 17.5 - - + +
104B LEU* 3.8 24.7 - - + -
105B LYS* 5.5 3.1 - - + +
123B ASP* 3.1 18.1 + - + +
124B ARG* 3.5 13.7 - - - +
126B ALA* 1.3 77.3 - - + +
128B VAL* 1.3 64.3 + - - +
130B ASN* 4.1 4.1 - - - +
131B ASP* 3.0 27.3 + - + +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 3.3 36.5 - - + +
40B PHE* 3.6 27.8 - - + -
43B LEU* 4.0 17.3 - - + -
104B LEU* 3.9 17.5 - - + -
124B ARG 3.1 13.7 + - - +
125B TYR 3.9 2.7 - - - +
127B ILE* 1.3 75.5 - - - +
129B ALA* 1.3 64.9 + - - +
131B ASP* 3.8 0.2 - - - +
132B VAL* 2.9 25.1 + - - +
155B LEU* 3.5 22.9 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TYR 2.6 25.4 + - - +
126B ALA* 3.7 6.1 - - - +
128B VAL* 1.3 73.2 - - - +
130B ASN* 1.3 63.2 + - - +
132B VAL* 3.2 9.5 - - - +
133B ARG* 3.0 30.6 + - - +
155B LEU* 3.9 21.2 - - + +
156B ASP* 3.7 17.6 - - - +
159B LEU* 4.4 12.6 - - + -
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Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA* 2.8 31.3 + - - +
127B ILE* 4.1 3.3 - - - +
129B ALA* 1.3 72.3 - - - +
131B ASP* 1.3 63.9 + - - +
133B ARG* 2.4 36.0 + - - +
134B LYS* 3.3 31.9 + - - +
18C ARG 3.1 20.4 + - - -
19C ASN* 3.6 4.2 - - - -
20C ASP* 2.7 37.1 + - - +
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 2.8 41.1 + - - -
36B GLN* 3.7 2.7 - - - +
39B GLN* 3.1 26.8 + - - +
103B PRO* 5.8 0.2 - - - +
127B ILE* 3.0 20.7 + - + +
128B VAL 3.8 2.5 - - - +
130B ASN* 1.3 75.1 - - - +
132B VAL* 1.3 67.0 + - - +
134B LYS* 3.0 12.4 + - - +
135B ALA* 3.0 16.8 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 3.6 30.9 + - - +
40B PHE* 4.3 19.7 - - + -
128B VAL 2.9 19.6 + - - +
129B ALA* 3.2 16.8 - - - +
131B ASP* 1.3 73.4 - - - +
133B ARG* 1.3 66.4 + - - +
135B ALA* 3.2 9.2 + - - +
136B ILE* 3.4 14.3 + - - +
148B LEU* 3.9 35.2 - - + +
151B ALA* 4.7 0.7 - - + -
152B SER* 4.0 21.3 - - - +
155B LEU* 4.8 2.9 - - + -
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 3.0 18.0 + - - +
130B ASN* 2.4 35.3 + - - +
131B ASP 3.1 0.6 - - - -
132B VAL* 1.3 77.9 - - - +
134B LYS* 1.3 61.6 + - + +
136B ILE* 3.4 23.0 - - + +
137B GLY 4.4 0.5 + - - -
152B SER* 3.6 15.3 - - - +
156B ASP* 2.6 43.8 + - - -
19C ASN* 3.0 21.1 + - - +
20C ASP* 3.0 14.5 + - - -
21C VAL* 3.3 22.3 - - - +
83C ARG* 4.0 5.4 - - - +
141C ASP* 4.2 7.9 - - - +
142C ASP* 4.3 7.7 - - + +
143C ASP* 4.0 8.3 - - - +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASN* 3.3 20.1 + - - +
131B ASP* 3.0 10.5 + - - +
133B ARG* 1.3 78.0 - - + +
135B ALA* 1.3 65.1 + - - +
136B ILE 3.0 3.3 + - - -
137B GLY* 3.1 12.1 + - - -
138B GLU* 3.3 14.4 + - - +
20C ASP* 2.4 42.5 + - - -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.9 16.0 - - + +
35B ARG* 4.3 4.0 - - - +
36B GLN* 3.5 22.9 - - - +
131B ASP 3.0 8.3 + - - +
132B VAL* 3.2 11.2 + - - +
134B LYS* 1.3 76.3 - - - +
136B ILE* 1.3 62.5 + - - +
138B GLU* 3.2 14.1 + - - +
139B ALA* 2.9 25.3 + - - +
148B LEU* 3.7 15.9 - - + +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL 3.5 8.7 - - - +
133B ARG* 3.4 19.1 - - + +
134B LYS 3.0 0.6 - - - -
135B ALA* 1.3 77.5 - - - +
137B GLY* 1.3 62.6 + - - +
139B ALA* 3.2 20.5 + - - +
145B ALA* 4.0 14.9 - - + +
148B LEU* 3.9 21.5 - - + -
149B THR* 3.4 30.3 - - - +
152B SER* 3.7 11.9 - - - +
142C ASP* 3.7 27.8 - - + +
143C ASP* 3.5 25.1 - - - +
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG 4.4 0.4 + - - -
134B LYS 3.1 6.7 + - - -
136B ILE* 1.3 82.5 - - - +
138B GLU* 1.3 60.3 + - - +
139B ALA 3.4 5.1 + - - +
142C ASP* 4.3 9.4 + - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.6 30.0 - - + +
35B ARG* 3.8 12.9 + - - -
134B LYS* 3.3 12.6 + - - +
135B ALA* 3.2 13.2 + - - +
137B GLY* 1.3 76.8 - - - +
139B ALA* 1.3 60.3 + - - +
140B LYS* 3.5 11.3 + - - +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.0 15.5 - - + -
135B ALA 2.9 10.7 + - - +
136B ILE 3.4 16.1 - - - +
137B GLY* 3.2 5.4 - - - +
138B GLU* 1.3 77.8 - - - +
140B LYS* 1.3 65.2 + - - +
141B ASP 4.4 2.5 - - - +
144B THR* 4.4 5.8 - - + -
145B ALA* 4.0 31.0 - - - +
148B LEU* 4.2 5.4 - - + -
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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