Contacts of the helix formed by residues 113 - 145 (chain X) in PDB entry 3IS7
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 X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ARG* 4.2 4.2 + - - +
128O GLU* 4.7 3.1 - - - +
4X ASP* 6.0 1.1 - - + +
7X VAL* 3.3 20.9 - - + +
61X ARG* 2.9 25.9 + - - -
65X LEU* 4.0 7.7 - - - +
108X CYS* 2.8 25.2 + - + +
111X VAL* 3.3 14.8 - - + +
112X HIS* 1.3 69.9 - - - +
114X TYR* 1.3 55.6 + - - +
115X VAL* 3.6 1.4 + - - +
116X SER* 2.6 31.2 + - - -
117X ARG* 3.1 18.7 + - - +
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Residues in contact with TYR 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O ARG* 3.8 16.7 - - + +
105O ILE* 3.5 42.6 - - + -
106O VAL* 2.9 31.9 + - - +
109O GLU* 6.0 0.2 - - - +
117O ARG* 3.4 20.6 + - - +
121O LYS* 4.3 18.7 - - + +
124O LEU* 4.2 14.8 - - + -
109X GLU* 3.5 31.8 + - - -
112X HIS* 3.0 44.2 + + + -
113X ASP* 1.3 71.8 - - - +
115X VAL* 1.3 61.6 + - - +
117X ARG* 3.5 6.3 + - - +
118X ASP* 3.0 28.1 + - - +
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Residues in contact with VAL 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121O LYS* 4.7 5.2 - - + +
124O LEU* 3.9 14.6 - - + -
125O GLU* 3.8 44.0 - - + +
128O GLU* 3.7 22.6 + - + +
61X ARG* 3.6 34.3 - - - +
113X ASP* 3.3 1.0 + - - -
114X TYR* 1.3 76.2 - - - +
116X SER* 1.3 67.5 + - - +
118X ASP* 3.2 7.2 + - + +
119X LEU* 3.0 22.8 + - + +
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Residues in contact with SER 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X VAL* 4.4 3.8 - - - -
11X LEU* 4.1 11.0 - - - +
61X ARG* 2.9 29.4 + - - +
65X LEU* 4.0 3.8 - - - +
108X CYS* 3.9 13.5 - - - -
113X ASP* 2.6 34.9 + - - -
115X VAL* 1.3 76.5 - - - +
117X ARG* 1.3 63.8 + - - +
119X LEU* 3.4 7.7 + - - +
120X LEU* 2.9 29.6 + - - +
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Residues in contact with ARG 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109N GLU* 2.8 44.0 + - - -
114N TYR* 3.6 14.3 + - - +
117N ARG* 3.8 17.2 - - - +
117O ARG* 3.6 17.0 - - - +
105X ILE* 4.0 28.9 - - + +
108X CYS* 3.9 16.5 - - + +
109X GLU* 3.0 41.0 + - - +
113X ASP 3.1 16.3 + - - +
114X TYR* 3.7 8.1 - - - +
116X SER* 1.3 77.6 - - - +
118X ASP* 1.3 55.5 + - - +
120X LEU* 3.1 7.2 + - - +
121X LYS* 2.8 38.6 + - + +
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Residues in contact with ASP 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121O LYS* 3.5 37.6 + - + +
125O GLU* 4.5 8.7 - - - +
114X TYR 3.0 19.1 + - - +
115X VAL* 3.2 6.3 + - + +
117X ARG* 1.3 75.5 - - - +
119X LEU* 1.3 64.3 + - - +
121X LYS* 3.1 28.5 + - - +
122X ASP* 3.1 33.7 + - - +
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Residues in contact with LEU 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X LEU* 5.7 1.1 - - + -
57X LYS* 3.9 28.0 - - + +
58X LEU* 3.8 16.8 - - + -
61X ARG* 3.9 37.0 - - + -
115X VAL* 3.0 14.7 + - + +
116X SER* 3.5 8.3 - - - +
118X ASP* 1.3 74.4 - - - +
120X LEU* 1.3 68.9 + - + +
122X ASP* 3.2 10.5 + - - +
123X ILE* 3.1 44.1 + - + +
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Residues in contact with LEU 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X LEU* 3.8 26.0 - - + -
14X ILE* 3.9 22.0 - - + -
58X LEU* 4.2 13.5 - - + -
101X LEU* 4.1 14.9 - - + +
104X ALA* 3.5 30.5 - - + -
105X ILE* 3.7 18.2 - - + +
108X CYS* 3.8 21.1 - - - -
116X SER 2.9 21.3 + - - +
117X ARG 3.7 0.4 - - - +
119X LEU* 1.3 77.9 - - + +
121X LYS* 1.3 58.6 + - - +
123X ILE* 3.2 7.4 + - + +
124X LEU* 2.9 26.9 + - - +
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Residues in contact with LYS 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N TYR* 4.5 24.0 - - + +
115N VAL* 5.2 2.8 - - + +
118N ASP* 3.6 43.6 + - + +
105X ILE* 4.1 12.1 - - + +
117X ARG* 2.8 22.2 + - + +
118X ASP* 3.1 30.0 + - - +
120X LEU* 1.3 76.6 - - - +
122X ASP* 1.3 89.6 + - - +
124X LEU* 3.2 4.7 + - + +
125X GLU* 3.0 27.7 + - + +
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Residues in contact with ASP 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X HIS* 5.0 1.1 + - - -
118X ASP* 3.1 27.5 + - - +
119X LEU* 3.2 9.6 + - - +
121X LYS* 1.3 98.1 + - - +
123X ILE* 1.3 62.7 + - + +
125X GLU* 3.4 13.2 + - - +
126X SER* 3.2 21.5 + - - -
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Residues in contact with ILE 123 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X ILE* 4.8 1.1 - - + -
18X GLU* 3.5 21.3 - - - +
54X HIS* 3.7 37.5 - - + +
57X LYS* 5.6 1.6 - - + -
58X LEU* 4.0 24.0 - - + -
101X LEU* 3.9 17.0 - - + -
119X LEU* 3.1 36.0 + - + +
120X LEU* 3.5 13.0 - - + +
121X LYS 3.2 0.2 - - - -
122X ASP* 1.3 76.4 - - + +
124X LEU* 1.3 63.6 + - - +
126X SER* 3.1 4.5 + - - -
127X GLU* 2.9 28.6 + - - +
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Residues in contact with LEU 124 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N TYR* 4.1 18.8 - - + -
115N VAL* 4.0 7.4 - - + -
98X THR* 3.6 24.7 - - - +
101X LEU* 3.9 26.5 - - + -
102X ARG* 3.6 37.7 - - + +
105X ILE* 4.1 20.4 - - + -
120X LEU 2.9 13.8 + - - +
121X LYS* 3.2 8.9 + - - +
123X ILE* 1.3 78.0 - - - +
125X GLU* 1.3 63.1 + - - +
127X GLU* 3.1 1.7 + - - +
128X GLU* 2.9 30.7 + - - +
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Residues in contact with GLU 125 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N VAL* 3.9 31.9 - - + +
118N ASP* 4.1 16.1 - - - +
121X LYS* 3.0 14.2 + - + +
122X ASP* 3.6 19.0 - - - +
124X LEU* 1.3 78.8 - - - +
126X SER* 1.3 62.2 + - - +
128X GLU* 3.4 3.7 + - - +
129X GLU* 2.8 40.5 + - + +
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Residues in contact with SER 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X ASP* 5.2 5.9 + - - +
51X GLU* 5.3 0.2 + - - -
54X HIS* 3.2 30.8 + - - -
122X ASP 3.2 9.3 + - - -
123X ILE 3.1 8.0 + - - -
125X GLU* 1.3 81.5 - - - +
127X GLU* 1.3 62.6 + - - +
129X GLU* 3.3 15.8 + - - +
130X HIS* 3.1 20.1 + - - +
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Residues in contact with GLU 127 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18X GLU* 3.2 15.4 - - - +
51X GLU* 2.6 34.1 - - - +
54X HIS* 4.0 1.9 + - - -
94X GLU* 2.7 41.3 - - - +
97X ALA* 5.0 6.8 - - + +
98X THR* 4.0 14.8 - - - +
101X LEU* 3.8 19.7 - - + -
123X ILE* 2.9 22.2 + - + +
124X LEU 3.1 5.3 + - - +
126X SER* 1.3 79.0 + - - +
128X GLU* 1.3 57.2 + - - +
130X HIS* 3.1 6.9 + - - +
131X ILE* 2.8 32.4 + - - +
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Residues in contact with GLU 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N ARG* 2.9 38.8 + - - +
64N PHE* 3.5 22.3 - - + -
113N ASP* 4.8 1.0 - - - +
115N VAL* 3.3 26.3 - - + +
98X THR* 4.6 3.6 - - - +
102X ARG* 2.9 33.7 + - - +
124X LEU* 2.9 23.3 + - + +
125X GLU* 3.7 7.0 - - - +
126X SER 3.3 0.2 - - - -
127X GLU* 1.3 73.0 - - - +
129X GLU* 1.3 58.3 + - - +
131X ILE* 3.2 12.7 + - + +
132X ASP* 2.9 24.6 + - - +
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Residues in contact with GLU 129 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125X GLU* 2.8 46.9 + - + +
126X SER* 3.3 13.5 + - - +
128X GLU* 1.3 75.5 - - - +
130X HIS* 1.3 63.9 + - - +
132X ASP* 3.3 9.5 + - - +
133X TYR* 3.0 21.3 + - - +
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Residues in contact with HIS 130 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25X TYR* 3.4 33.7 - + - -
44X GLU* 4.6 4.6 + - - -
47X GLU* 3.4 42.0 + - + +
51X GLU* 5.9 0.4 - - - -
90X ASP* 4.5 1.6 - - + -
94X GLU* 2.4 33.4 + - - +
126X SER 3.1 11.5 + - - +
127X GLU* 3.1 11.9 + - - +
129X GLU* 1.3 78.1 - - - +
131X ILE* 1.3 62.0 + - - +
133X TYR* 3.2 13.2 + + - -
134X LEU* 3.0 48.0 + - + +
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Residues in contact with ILE 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N PHE* 4.2 11.0 - - + -
91X LEU* 4.1 13.5 - - + -
94X GLU* 3.6 25.6 - - + +
95X LEU* 4.1 22.2 - - + -
98X THR* 3.8 26.5 - - + +
127X GLU 2.8 16.0 + - - +
128X GLU* 3.2 15.0 + - + +
130X HIS* 1.3 77.2 - - - +
132X ASP* 1.3 56.8 + - - +
134X LEU* 3.2 7.8 + - - +
135X GLU* 2.8 53.2 + - - +
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Residues in contact with ASP 132 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M ASP* 4.3 12.6 - - - +
64N PHE* 3.5 36.9 - - + +
128X GLU 2.9 8.8 + - - +
129X GLU* 3.4 13.6 - - - +
130X HIS 3.2 0.2 - - - -
131X ILE* 1.3 77.8 - - - +
133X TYR* 1.3 58.0 + - - +
135X GLU* 3.9 4.4 - - - +
136X THR* 2.7 42.5 + - - -
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Residues in contact with TYR 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X LEU* 3.5 26.6 - - + +
43X HIS* 3.4 54.7 - + + +
44X GLU* 5.3 4.0 - - - -
47X GLU* 4.9 0.7 - - - +
87X LEU* 4.5 3.6 - - + -
129X GLU 3.0 13.1 + - - +
130X HIS* 3.5 18.2 - + + +
132X ASP* 1.3 79.1 - - - +
134X LEU* 1.3 77.9 + - + +
136X THR* 3.2 5.3 + - - -
137X GLN* 2.8 70.5 + - + +
153X HIS* 5.2 2.7 + - - -
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Residues in contact with LEU 134 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X GLU* 5.5 0.9 - - - +
87X LEU* 3.7 39.4 - - + +
90X ASP* 3.8 20.9 - - + +
91X LEU* 3.7 30.5 - - + +
94X GLU* 4.2 3.8 - - + -
130X HIS* 3.0 53.1 + - + +
131X ILE* 3.6 5.8 - - - +
133X TYR* 1.3 84.6 - - + +
135X GLU* 1.3 65.6 + - - +
137X GLN* 3.2 5.5 + - - +
138X LEU* 3.0 30.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N PHE* 4.1 18.4 - - - +
66N GLU* 4.0 19.5 - - - +
91X LEU* 4.3 20.2 - - + +
95X LEU* 6.0 1.2 - - - +
131X ILE* 2.8 40.0 + - + +
132X ASP* 3.9 3.8 - - - +
134X LEU* 1.3 72.9 - - - +
136X THR* 1.3 64.6 + - - +
138X LEU* 3.4 7.6 + - - +
139X GLY* 2.9 21.5 + - - -
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Residues in contact with THR 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ASN 5.0 0.9 - - - +
34M ASP* 3.3 15.0 + - - +
35M TRP* 3.6 6.6 - - - +
36M GLY* 3.4 38.8 - - - +
132X ASP* 2.7 31.5 + - - -
133X TYR* 3.4 7.6 - - - -
135X GLU* 1.3 76.5 - - - +
137X GLN* 1.3 72.8 + - - +
139X GLY* 3.2 2.9 + - - -
140X LEU* 2.9 23.0 + - + +
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Residues in contact with GLN 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X LEU* 4.1 15.0 - - + -
133X TYR* 2.8 70.8 + - + +
134X LEU 3.2 4.2 + - - +
136X THR* 1.3 82.2 - - - +
138X LEU* 1.3 63.0 + - - +
140X LEU* 3.0 23.0 + - - +
141X ILE* 3.0 20.3 + - - +
149X TYR* 2.7 42.9 + - + +
153X HIS* 3.9 10.9 + - - -
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Residues in contact with LEU 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X GLN* 4.1 23.6 - - + +
87X LEU* 4.1 20.2 - - + +
88X GLN* 3.9 33.0 - - + +
91X LEU* 4.0 19.1 - - + -
134X LEU 3.0 22.6 + - - +
135X GLU* 3.8 5.6 - - - +
137X GLN* 1.3 77.6 - - - +
139X GLY* 1.3 61.4 + - - +
141X ILE* 3.5 20.1 + - + +
142X GLN* 3.6 18.6 + - - +
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Residues in contact with GLY 139 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135X GLU 2.9 14.7 + - - -
136X THR* 3.6 4.3 - - - -
138X LEU* 1.3 75.4 - - - +
140X LEU* 1.3 63.4 + - - +
142X GLN* 3.2 9.5 + - - +
143X LYS* 3.0 45.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TRP 3.2 25.8 - - - +
36M GLY* 3.9 19.5 - - - +
37M LEU* 4.1 14.4 - - + -
154M MET* 4.0 37.2 - - + -
136X THR* 2.9 16.2 + - + +
137X GLN* 3.0 25.1 + - - +
139X GLY* 1.3 73.0 - - - +
141X ILE* 1.3 66.9 + - - +
143X LYS* 3.0 8.8 + - + +
144X VAL* 2.8 36.5 + - + +
149X TYR* 3.8 12.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X THR* 4.8 1.3 - - + -
84X GLN* 4.0 31.6 - - + +
87X LEU* 4.2 16.2 - - + -
137X GLN 3.0 17.0 + - - +
138X LEU* 3.6 14.8 - - + +
139X GLY 3.3 0.2 - - - -
140X LEU* 1.3 74.8 - - - +
142X GLN* 1.3 72.5 + - - +
145X GLY* 3.0 27.7 + - - -
146X LEU* 3.7 25.7 + - + +
149X TYR* 3.6 40.8 - - + -
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Residues in contact with GLN 142 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M GLU* 4.8 3.8 - - - +
84X GLN* 5.1 6.1 - - - +
138X LEU 3.6 15.0 + - - +
139X GLY* 3.2 10.0 + - - +
140X LEU 3.0 0.4 - - - -
141X ILE* 1.3 93.9 + - - +
143X LYS* 1.3 62.2 + - + +
145X GLY* 4.3 2.4 + - - -
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Residues in contact with LYS 143 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TRP* 3.8 55.3 - - + +
37M LEU* 5.0 10.8 - - + -
146M LEU* 5.6 1.2 - - - +
147M GLU* 3.7 14.6 - - - +
150M LEU* 3.8 28.6 - - + +
139X GLY* 3.0 36.9 + - - +
140X LEU* 3.0 9.4 + - + +
142X GLN* 1.3 80.3 - - + +
144X VAL* 1.3 64.4 + - + +
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Residues in contact with VAL 144 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M GLU* 3.4 23.3 - - - +
150M LEU* 3.8 15.3 - - + -
151M GLN* 3.4 30.7 - - + +
154M MET* 4.2 18.8 - - + -
140X LEU* 2.8 30.6 + - + +
143X LYS* 1.3 76.1 - - + +
145X GLY* 1.3 66.7 + - - +
148X ASN* 3.2 30.6 + - + +
149X TYR* 3.7 23.1 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M GLU* 3.7 15.9 + - - -
141X ILE 3.0 15.9 + - - -
142X GLN 4.3 1.5 + - - -
143X LYS 3.6 1.6 - - - -
144X VAL* 1.3 79.8 - - - +
146X LEU* 1.3 66.8 + - - -
147X GLU 3.4 2.5 - - - -
148X ASN 3.6 0.8 + - - -
149X TYR* 3.1 23.7 + - - +
----------------------------------------------------------
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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