Contacts of the helix formed by residues 67 - 98 (chain C) in PDB entry 5TWV
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 LYS 67 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP 3.5 3.4 + - - +
66C LEU* 1.3 73.6 - - - +
68C TRP* 1.3 60.2 - - - +
69C PRO* 3.5 14.8 - - + -
70C HIS* 3.6 22.1 + - + +
71C THR* 2.4 30.9 + - - -
55D SER 5.3 1.4 + - - -
56D SER* 3.8 30.1 - - - +
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Residues in contact with TRP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 5.9 4.9 - - - -
60A PHE* 4.1 32.3 - + - -
162A ILE* 6.2 7.2 - - + -
66C LEU 6.0 0.2 - - - -
67C LYS* 1.3 70.6 - - - +
69C PRO* 1.3 74.7 - - + +
71C THR* 3.7 21.4 - - + -
72C LEU* 3.2 30.6 + - + +
167C ILE* 4.7 17.0 - - + -
170C LYS* 4.0 29.8 - - + -
173C GLN* 5.1 10.8 - - - +
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Residues in contact with PRO 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 3.6 17.9 - - + -
68C TRP* 1.3 96.3 - - + +
70C HIS* 1.3 69.8 + - + +
72C LEU* 3.7 5.7 + - + +
73C LEU* 3.5 18.4 + - - +
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Residues in contact with HIS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.9 18.8 - - + +
67C LYS* 3.6 25.3 + - + +
68C TRP 3.3 0.2 - - - -
69C PRO* 1.3 83.3 - - + +
71C THR* 1.3 61.1 + - - +
73C LEU* 3.0 15.2 + - + +
74C ILE* 2.9 35.7 + - + +
51D TRP* 4.0 28.5 - + + -
52D GLY* 4.1 28.4 + - - -
55D SER* 4.9 10.3 - - - -
56D SER* 6.0 3.0 - - - -
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Residues in contact with THR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU 4.6 8.3 + - - +
66C LEU* 3.0 17.9 + - - +
67C LYS 2.4 25.9 + - - -
68C TRP* 3.7 26.9 - - + -
69C PRO 3.3 0.2 - - - -
70C HIS* 1.3 79.1 - - - +
72C LEU* 1.3 59.3 + - - +
74C ILE* 3.5 12.8 + - + +
75C PHE* 3.1 55.1 + - + -
166C CYS* 6.1 1.6 - - - +
167C ILE* 5.6 1.8 - - + -
170C LYS* 6.1 3.1 - - + -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 4.3 28.0 - - + -
162A ILE* 6.4 0.4 - - + -
68C TRP* 3.2 20.4 + - + +
69C PRO* 3.9 5.8 - - + +
70C HIS 3.2 0.4 - - - -
71C THR* 1.3 79.0 - - - +
73C LEU* 1.3 54.0 + - - +
75C PHE* 3.5 5.6 + - + +
76C THR* 2.7 52.2 + - + +
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO 3.5 11.1 + - - +
70C HIS* 3.0 18.8 + - + +
72C LEU* 1.3 78.8 - - - +
74C ILE* 1.3 62.9 + - + +
76C THR* 3.1 17.7 + - - +
77C MET* 3.1 42.2 + - + +
48D PHE* 5.6 9.9 - - + -
51D TRP* 4.6 22.0 - - + -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 5.0 22.4 - - + +
66C LEU* 4.3 24.5 - - + -
70C HIS* 2.9 22.6 + - + +
71C THR* 3.8 14.8 - - + +
72C LEU 3.3 0.4 - - - -
73C LEU* 1.3 79.3 - - + +
75C PHE* 1.3 73.9 + - + +
77C MET* 4.6 0.8 - - - +
78C SER* 2.8 32.8 + - - +
45D PRO* 5.5 14.4 - - + +
48D PHE* 5.1 16.6 - - + -
49D ILE* 5.1 10.8 - - + +
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Residues in contact with PHE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.6 3.3 - - - +
158A MET* 4.3 14.4 - - + -
63C LEU* 5.5 7.4 - - + -
71C THR* 3.1 39.7 + - + +
72C LEU* 4.1 3.8 - - - +
73C LEU 3.4 0.2 - - - -
74C ILE* 1.3 90.5 - - + +
76C THR* 1.3 63.2 + - - +
78C SER* 3.5 7.7 + - - -
79C PHE* 3.2 28.9 - + - +
162C ILE* 6.3 1.6 - - + -
163C MET* 3.8 37.0 - - + +
166C CYS* 3.8 36.3 - - + -
167C ILE* 3.8 22.0 - - + -
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.1 27.7 - - + +
158A MET* 5.6 2.9 - - + -
72C LEU* 2.7 42.3 + - + +
73C LEU* 3.1 15.8 + - - +
75C PHE* 1.3 79.8 - - + +
77C MET* 1.3 68.0 + - - +
79C PHE* 3.6 5.0 + - - +
80C LEU* 3.2 32.1 + - - +
83C TRP* 6.0 0.2 - - - -
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Residues in contact with MET 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 3.1 37.0 + - + +
74C ILE* 4.6 1.3 - - - +
76C THR* 1.3 79.2 + - - +
78C SER* 1.3 55.1 + - - +
79C PHE 3.1 1.6 - - - -
80C LEU* 3.5 17.5 - - - +
81C CYS* 2.6 38.5 + - - +
44D PHE* 5.2 24.5 - - + -
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Residues in contact with SER 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 2.8 25.7 + - - -
75C PHE* 3.5 14.2 + - - -
77C MET* 1.3 78.0 - - - +
79C PHE* 1.3 68.4 + - - +
81C CYS* 3.8 8.0 - - - +
82C SER* 2.9 27.7 + - - -
159C ILE* 5.0 1.4 - - - +
44D PHE* 6.0 0.2 - - - +
45D PRO* 4.6 22.2 - - - -
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.3 12.6 - - + -
157A LEU* 4.5 15.9 - - + -
75C PHE* 3.2 24.6 + + + +
76C THR* 3.6 5.8 + - - +
77C MET 3.1 0.2 - - - -
78C SER* 1.3 88.0 + - - +
80C LEU* 1.3 59.5 + - - +
82C SER* 3.1 5.0 + - - -
83C TRP* 2.8 71.4 + + + +
129C VAL* 6.1 2.7 - - + -
156C GLY 5.7 0.9 - - - -
159C ILE* 3.9 31.2 - - + -
160C ASN* 4.0 30.5 - - + -
163C MET* 3.8 25.6 - - + -
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 4.7 15.0 - - + -
76C THR* 3.2 23.0 + - - +
77C MET* 3.6 18.6 - - - +
79C PHE* 1.3 76.5 - - - +
81C CYS* 1.3 66.3 + - - +
83C TRP* 3.2 28.6 + - + +
84C LEU* 3.1 24.3 + - - +
121C PHE* 4.8 14.0 - - + -
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Residues in contact with CYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C MET 2.6 23.7 + - - +
78C SER* 3.9 8.3 - - - +
80C LEU* 1.3 73.5 - - - +
82C SER* 1.3 60.3 + - - +
84C LEU* 3.9 0.4 + - - -
85C LEU* 3.8 4.0 + - - +
41D PHE* 3.3 68.6 - - + +
44D PHE* 4.4 12.8 - - + -
45D PRO* 5.7 0.2 - - + -
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Residues in contact with SER 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C SER 2.9 17.4 + - - -
79C PHE 3.1 8.9 + - - -
80C LEU 3.1 0.2 - - - -
81C CYS* 1.3 75.5 - - - +
83C TRP* 1.3 66.2 + - - +
84C LEU 3.1 1.8 - - - -
85C LEU* 3.0 20.1 + - - +
86C PHE* 2.9 39.3 + - - -
155C VAL* 6.2 0.3 - - - +
159C ILE* 4.1 19.3 - - - +
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Residues in contact with TRP 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.6 36.8 - - + -
153A ASN* 5.5 4.9 - - + -
154A ILE* 4.8 16.2 - - + -
79C PHE* 2.8 61.6 + + + +
80C LEU* 3.2 28.5 + - + +
82C SER* 1.3 81.7 - - - +
84C LEU* 1.3 59.3 + - - +
86C PHE* 4.0 4.3 - + - -
87C ALA* 3.4 21.0 + - - +
121C PHE* 3.8 11.9 - + + +
124C SER* 3.5 8.8 + - - -
125C ILE* 3.1 39.7 - - + -
128C GLN* 4.3 26.8 - - + +
129C VAL* 4.5 18.1 - - + +
159C ILE* 5.7 2.4 - - - +
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 3.1 13.7 + - - +
81C CYS* 4.2 0.4 - - - +
82C SER 3.0 1.2 + - - -
83C TRP* 1.3 75.2 - - - +
85C LEU* 1.3 60.8 - - - +
87C ALA* 3.7 6.7 - - - +
88C MET* 3.2 28.2 + - - +
121C PHE* 4.3 10.1 - - + -
41D PHE* 3.7 29.4 - - + -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C CYS 3.8 4.4 + - - +
82C SER* 3.0 13.8 + - - +
84C LEU* 1.3 79.6 - - - +
86C PHE* 1.3 72.5 + - + +
87C ALA 3.1 2.0 + - - -
88C MET* 3.6 5.0 + - + +
89C VAL* 3.6 22.2 + - - +
34D VAL* 5.0 6.3 - - + +
37D VAL* 5.3 0.9 - - + -
38D PHE* 4.4 36.8 - - + +
41D PHE* 3.9 30.5 - - + -
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Residues in contact with PHE 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 2.9 45.2 + - - +
83C TRP* 4.1 2.0 - + - -
85C LEU* 1.3 88.1 - - + +
87C ALA* 1.3 56.8 + - - +
89C VAL* 3.8 13.6 - - + +
90C TRP* 3.5 24.0 - - + +
124C SER* 2.8 22.9 + - - +
128C GLN* 3.1 39.0 - - + +
148C ILE* 6.6 0.2 - - + -
151C VAL* 4.6 4.0 - - + -
152C GLN* 3.8 30.1 - - + -
155C VAL* 4.5 20.0 - - + -
156C GLY* 4.9 4.0 - - - -
159C ILE* 5.8 1.1 - - + -
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TRP 3.4 16.5 + - - +
84C LEU 3.8 4.5 - - - +
85C LEU 3.1 0.4 - - - -
86C PHE* 1.3 79.9 - - - +
88C MET* 1.3 64.6 + - - +
89C VAL 3.4 0.7 - - - -
90C TRP* 3.4 5.2 + - - +
91C TRP* 3.1 23.7 + - - +
117C PHE* 5.7 5.2 - - + -
120C ALA* 3.9 4.4 - - - +
121C PHE* 3.3 42.6 - - + +
124C SER* 3.9 5.2 - - - -
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Residues in contact with MET 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU 3.2 17.7 + - - +
85C LEU* 3.6 7.6 + - + +
87C ALA* 1.3 73.6 - - - +
89C VAL* 1.3 57.9 - - - +
90C TRP 3.1 4.5 - - - -
91C TRP* 3.2 35.4 + - + +
92C LEU* 3.1 27.8 + - + +
117C PHE* 4.5 17.9 - - + -
30D ALA* 5.3 4.3 - - - +
33D VAL* 3.7 30.1 - - + -
34D VAL* 4.5 26.0 - - + -
37D VAL* 5.3 11.0 - - + -
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU 3.6 17.0 + - - +
86C PHE* 3.8 16.6 - - + +
88C MET* 1.3 78.2 - - - +
90C TRP* 1.3 70.7 + - + +
92C LEU* 3.7 19.8 - - + +
93C ILE* 3.0 29.6 + - + +
148C ILE* 4.4 25.1 - - + -
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Residues in contact with TRP 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.5 21.8 - - + +
87C ALA* 3.4 6.5 + - - +
88C MET 3.1 0.4 - - - -
89C VAL* 1.3 83.4 - - + +
91C TRP* 1.3 58.9 + - - +
92C LEU 3.0 5.4 - - - -
93C ILE* 3.1 37.2 + - + +
94C ALA* 3.8 8.3 + - - +
111C VAL* 3.8 22.8 - - + +
114C ILE* 5.5 5.5 - - + +
120C ALA* 4.1 17.6 - - + +
123C PHE* 2.8 55.3 - + + -
127C VAL* 6.0 0.2 - - + -
138C VAL* 5.8 1.6 - - + -
145C ALA* 3.4 23.1 - - + -
148C ILE* 3.6 31.6 - - + -
149C LEU* 3.5 28.0 - - + -
152C GLN* 5.1 7.4 - - + -
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Residues in contact with TRP 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ALA 3.1 16.5 + - - +
88C MET* 3.2 24.2 + - - +
90C TRP* 1.3 76.3 - - - +
92C LEU* 1.3 62.4 - - + +
94C ALA* 4.0 6.2 + - + +
95C PHE* 3.3 53.4 + + + +
100C LEU* 5.1 9.8 - - + +
114C ILE* 5.9 1.1 - - + -
116C SER 4.5 4.7 + - - -
117C PHE* 3.1 66.6 - + + +
120C ALA* 4.0 10.1 - - + -
6D CYS* 6.2 2.2 - - + -
30D ALA* 4.3 23.8 - - + -
105D HIS* 5.0 16.6 - - + -
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 3.1 15.8 + - + +
89C VAL* 3.7 21.8 - - + +
91C TRP* 1.3 81.8 - - + +
93C ILE* 1.3 59.9 + - + +
94C ALA 3.1 1.8 - - - -
95C PHE* 4.1 9.0 - - + -
96C ALA* 2.8 36.3 + - + +
27D PHE* 5.8 6.1 - - + +
30D ALA* 4.8 24.7 - - + +
31D LEU* 5.4 15.0 - - + +
34D VAL* 5.7 9.0 - - + -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 3.0 22.0 - - + +
90C TRP* 3.1 52.5 - - + +
92C LEU* 1.3 77.4 - - + +
94C ALA* 1.3 59.7 + - + +
95C PHE 3.3 0.2 - - - -
96C ALA* 3.9 8.2 - - - +
97C HIS* 3.4 24.6 + - - +
110C CYS* 5.5 6.5 - - + +
111C VAL* 4.6 9.2 - - + -
142C CYS* 5.3 6.6 - - - -
144C LEU* 5.3 11.0 - - + -
145C ALA* 3.6 37.5 - - + +
148C ILE* 5.6 4.9 - - + -
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TRP 3.8 12.5 + - - +
91C TRP* 4.2 3.8 - - - +
92C LEU 3.1 0.2 - - - -
93C ILE* 1.3 79.8 - - + +
95C PHE* 1.3 61.2 + - - +
96C ALA 3.3 0.2 - - - -
97C HIS* 4.5 1.3 - - - +
98C GLY* 2.8 28.4 + - - -
99C ASP* 3.8 12.6 + - - +
100C LEU* 3.6 29.2 - - + +
114C ILE* 4.5 16.6 - - + -
----------------------------------------------------------
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TRP* 3.3 50.7 + + + +
92C LEU* 3.3 15.0 + - + +
94C ALA* 1.3 79.9 - - - +
96C ALA* 1.3 62.4 + - - +
97C HIS 3.3 0.2 - - - -
98C GLY* 3.7 10.0 + - - -
100C LEU* 4.7 18.2 - - + -
6D CYS* 4.7 12.3 - - + -
12D SER* 5.3 14.8 - - - -
15D TYR* 5.6 8.8 - - + +
16D ARG* 5.7 2.1 - - - -
21D VAL* 6.0 2.3 - - - +
26D CYS* 3.8 35.0 - - + -
27D PHE* 4.6 15.6 - - + +
30D ALA* 5.4 7.0 - - + -
105D HIS* 6.1 0.2 - - + -
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 2.8 22.1 + - + +
93C ILE* 4.2 7.9 - - - +
95C PHE* 1.3 79.0 - - - +
97C HIS* 1.3 61.2 + - - +
144C LEU* 6.4 2.2 - - + -
21D VAL* 5.7 9.9 - - - +
----------------------------------------------------------
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Residues in contact with HIS 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE 3.4 17.8 + - - +
94C ALA* 4.3 1.3 - - - +
96C ALA* 1.3 79.1 - - - +
98C GLY* 1.3 63.6 + - - +
99C ASP* 3.0 32.3 + - + +
107C ASN* 6.1 2.9 - - - -
108C VAL 4.7 11.1 + - - -
110C CYS* 5.1 6.0 + - + -
141C GLU* 4.8 13.9 - - - +
142C CYS* 4.2 25.6 - - + +
16D ARG* 4.1 11.6 - - - +
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ALA 2.8 15.7 + - - -
95C PHE* 3.7 10.3 - - - -
96C ALA 3.4 1.0 - - - -
97C HIS* 1.3 78.1 - - - +
99C ASP* 1.3 58.1 + - - +
100C LEU* 3.2 5.8 + - - +
101C ALA* 4.0 1.4 + - - +
102C PRO* 3.1 24.3 - - - +
12D SER* 4.5 4.6 - - - +
16D ARG* 3.3 23.4 - - - +
----------------------------------------------------------
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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