Contacts of the helix formed by residues 113 - 145 (chain T) 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 T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K ARG* 4.2 3.8 + - - +
128K GLU* 4.6 3.3 - - - +
4T ASP* 5.7 2.4 + - + +
7T VAL* 3.4 18.8 - - + +
61T ARG* 2.9 24.1 + - - -
65T LEU* 4.0 8.0 - - - +
108T CYS* 2.8 30.2 + - + +
111T VAL* 3.4 10.8 - - + +
112T HIS* 1.3 72.0 - - - +
114T TYR* 1.3 60.1 + - - +
115T VAL* 3.7 2.1 + - - +
116T SER* 2.6 28.7 + - - -
117T ARG* 3.1 17.4 + - - -
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Residues in contact with TYR 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K ARG* 4.0 13.2 - - - +
105K ILE* 3.4 41.7 - - + -
106K VAL* 3.0 34.8 + - - +
117K ARG* 3.9 14.0 + - - +
121K LYS* 4.1 22.2 - - + +
124K LEU* 4.2 12.8 - - + -
109T GLU* 3.7 37.8 + - - -
112T HIS* 3.2 39.2 + - + -
113T ASP* 1.3 72.7 - - - +
115T VAL* 1.3 58.0 + - - +
117T ARG* 3.4 9.3 + - - +
118T ASP* 2.9 29.3 + - - +
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Residues in contact with VAL 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K LYS* 5.0 4.7 - - + +
124K LEU* 4.0 13.0 - - + -
125K GLU* 3.9 44.4 - - + +
128K GLU* 3.2 35.2 + - + +
61T ARG* 3.6 22.0 - - - +
113T ASP* 3.3 1.4 + - - -
114T TYR* 1.3 71.9 - - - +
116T SER* 1.3 66.2 + - - +
118T ASP* 3.2 7.5 + - - +
119T LEU* 3.1 21.5 + - - +
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Residues in contact with SER 116 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T VAL* 4.1 4.7 - - - +
11T LEU* 4.2 10.9 - - - +
61T ARG* 2.9 27.4 + - - +
65T LEU* 3.8 6.9 - - - +
108T CYS* 3.9 14.1 - - - -
113T ASP* 2.6 33.2 + - - -
115T VAL* 1.3 75.7 - - - +
117T ARG* 1.3 65.7 + - - +
119T LEU* 3.3 8.1 + - - +
120T LEU* 3.0 26.7 + - - +
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Residues in contact with ARG 117 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K ARG* 4.1 16.0 - - - +
109M GLU* 2.4 43.6 + - - -
114M TYR* 3.9 17.8 + - - +
117M ARG* 4.1 17.4 - - - +
105T ILE* 3.9 27.2 - - + +
108T CYS* 4.0 15.5 - - + -
109T GLU* 2.7 40.9 + - - +
113T ASP 3.1 15.5 + - - +
114T TYR* 3.4 13.9 - - - +
115T VAL 3.3 0.2 - - - -
116T SER* 1.3 76.2 - - - +
118T ASP* 1.3 60.8 + - - +
120T LEU* 3.1 6.7 + - - +
121T LYS* 2.9 34.5 + - + +
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Residues in contact with ASP 118 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K ASP* 5.5 0.3 - - - +
121K LYS* 3.2 38.3 + - + +
125K GLU* 4.3 9.5 - - - +
118M ASP* 5.6 2.1 - - - +
114T TYR 2.9 17.2 + - - +
115T VAL* 3.5 7.0 - - - +
116T SER 3.2 0.2 - - - -
117T ARG* 1.3 79.9 - - - +
119T LEU* 1.3 61.7 + - - +
121T LYS* 3.3 9.5 + - - +
122T ASP* 3.1 35.2 + - - +
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Residues in contact with LEU 119 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T LEU* 5.5 1.3 - - + -
57T LYS* 3.9 30.1 - - + +
58T LEU* 4.3 12.8 - - + -
61T ARG* 3.7 37.7 - - + -
115T VAL* 3.1 13.4 + - + +
116T SER* 3.4 10.3 - - - +
118T ASP* 1.3 76.3 - - - +
120T LEU* 1.3 64.7 + - + +
122T ASP* 3.3 8.6 + - - +
123T ILE* 3.1 43.1 + - + +
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Residues in contact with LEU 120 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T HIS* 5.8 0.4 - - + -
11T LEU* 3.9 30.5 - - + -
14T ILE* 4.1 11.4 - - + -
58T LEU* 4.2 12.8 - - + -
101T LEU* 3.6 25.9 - - + +
104T ALA* 3.6 28.3 - - + -
105T ILE* 3.7 18.6 - - + -
108T CYS* 4.1 17.5 - - - -
116T SER 3.0 20.7 + - - +
117T ARG 3.1 0.4 + - - +
119T LEU* 1.3 78.6 - - + +
121T LYS* 1.3 58.0 + - - +
123T ILE* 3.2 7.4 + - + +
124T LEU* 2.8 28.9 + - - +
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Residues in contact with LYS 121 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M TYR* 4.1 28.3 - - + +
115M VAL* 4.7 3.5 - - + +
118M ASP* 3.7 26.2 - - + +
105T ILE* 3.9 7.8 - - + +
117T ARG* 2.9 23.8 + - + +
118T ASP* 3.5 10.1 - - - +
120T LEU* 1.3 74.5 - - - +
122T ASP* 1.3 67.6 + - - +
124T LEU* 3.1 9.2 + - + +
125T GLU* 2.9 23.6 + - - +
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Residues in contact with ASP 122 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M ASP* 5.4 3.6 - - - +
54T HIS* 4.9 1.3 + - + -
118T ASP* 3.1 27.9 + - - +
119T LEU* 3.3 9.3 + - - +
121T LYS* 1.3 76.6 - - - +
123T ILE* 1.3 63.5 + - + +
125T GLU* 3.3 15.0 + - - +
126T SER* 3.2 22.2 + - - -
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Residues in contact with ILE 123 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T ILE* 4.8 1.1 - - + -
18T GLU* 3.5 21.3 - - - +
54T HIS* 3.7 34.5 - - + +
57T LYS* 5.8 0.7 - - + -
58T LEU* 3.8 31.9 - - + -
101T LEU* 4.4 11.4 - - + -
119T LEU* 3.1 34.2 + - + +
120T LEU* 3.2 14.1 + - + +
122T ASP* 1.3 75.5 - - + +
124T LEU* 1.3 57.9 + - - +
126T SER* 3.3 4.2 + - - -
127T GLU* 2.9 43.0 + - + +
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Residues in contact with LEU 124 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M TYR* 4.0 30.1 - - + -
115M VAL* 3.9 13.9 - - + -
98T THR* 3.6 25.1 - - - +
101T LEU* 4.2 23.6 - - + -
102T ARG* 3.8 29.8 - - + +
105T ILE* 4.0 10.8 - - + -
120T LEU 2.8 13.9 + - - +
121T LYS* 3.3 9.2 - - - +
123T ILE* 1.3 75.9 - - - +
125T GLU* 1.3 64.7 + - - +
127T GLU* 3.1 3.1 + - + +
128T GLU* 2.9 32.9 + - + +
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Residues in contact with GLU 125 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M VAL* 3.8 32.5 - - + +
118M ASP* 5.1 8.4 - - - +
121T LYS 2.9 12.8 + - - +
122T ASP* 3.3 17.5 + - - +
124T LEU* 1.3 76.6 - - - +
126T SER* 1.3 62.8 - - - +
128T GLU* 3.3 3.0 + - - +
129T GLU* 3.1 40.2 + - + +
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Residues in contact with SER 126 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50T ASP* 5.2 5.2 + - - +
54T HIS* 2.9 32.9 - - - -
122T ASP 3.2 10.8 + - - -
123T ILE 3.5 7.6 - - - -
124T LEU 3.2 0.4 - - - -
125T GLU* 1.3 82.2 - - - +
127T GLU* 1.3 61.8 + - - +
129T GLU* 3.3 14.4 + - - +
130T HIS* 3.2 19.9 + - - +
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Residues in contact with GLU 127 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T GLU* 2.7 18.1 - - - +
51T GLU* 2.5 38.1 - - - +
54T HIS* 3.8 4.3 + - - -
94T GLU* 2.8 32.8 - - - +
97T ALA* 5.0 7.1 - - + +
98T THR* 4.3 13.7 - - - +
101T LEU* 4.2 13.2 - - + -
123T ILE* 2.9 35.7 + - + +
124T LEU* 3.1 4.5 + - - +
126T SER* 1.3 75.8 + - - +
128T GLU* 1.3 64.0 + - - +
130T HIS* 3.2 6.4 + - - +
131T ILE* 3.0 27.6 + - - +
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Residues in contact with GLU 128 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M ARG* 2.9 37.5 + - - +
64M PHE* 3.6 19.6 - - + -
113M ASP* 4.7 0.9 - - - +
115M VAL* 3.4 24.3 - - + +
98T THR* 4.4 6.3 - - - +
102T ARG* 2.9 34.6 + - - +
124T LEU* 2.9 27.6 + - + +
125T GLU* 3.8 5.2 - - - +
127T GLU* 1.3 73.5 - - - +
129T GLU* 1.3 56.5 + - - +
131T ILE* 3.2 12.6 + - + +
132T ASP* 2.8 28.5 + - - +
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Residues in contact with GLU 129 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125T GLU* 3.1 41.9 + - + +
126T SER* 3.3 13.9 + - - +
128T GLU* 1.3 75.7 - - - +
130T HIS* 1.3 58.7 + - - +
132T ASP* 3.3 9.4 + - - +
133T TYR* 3.0 26.5 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T TYR* 3.4 38.6 - + - -
44T GLU* 4.3 4.6 + - - -
47T GLU* 3.2 48.2 + - + +
51T GLU* 4.8 0.8 + - - -
90T ASP* 4.7 2.0 - - + -
94T GLU* 2.9 24.4 + - - +
126T SER 3.2 11.5 + - - +
127T GLU* 3.2 11.7 + - - +
129T GLU* 1.3 74.3 - - - +
131T ILE* 1.3 60.9 + - - +
133T TYR* 3.3 11.9 + + - -
134T LEU* 2.9 57.7 + - + +
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Residues in contact with ILE 131 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M PHE* 4.2 11.7 - - + -
91T LEU* 4.2 10.5 - - + -
94T GLU* 3.7 26.5 - - + +
95T LEU* 3.9 24.5 - - + -
98T THR* 4.2 20.0 - - + +
127T GLU 3.0 18.1 + - - +
128T GLU* 3.5 15.3 - - + +
130T HIS* 1.3 76.7 - - - +
132T ASP* 1.3 62.7 + - - +
134T LEU* 3.2 7.0 + - - +
135T GLU* 3.0 48.1 + - - +
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Residues in contact with ASP 132 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M PHE* 3.4 36.3 - - + +
34N ASP* 4.3 14.4 - - - +
128T GLU 2.8 12.2 + - - +
129T GLU* 3.5 10.8 - - - +
130T HIS 3.2 0.2 - - - -
131T ILE* 1.3 76.0 - - - +
133T TYR* 1.3 63.5 + - - +
135T GLU* 4.0 4.0 - - - +
136T THR* 2.9 35.3 + - - -
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Residues in contact with TYR 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40T LEU* 3.6 25.3 + - - +
43T HIS* 3.3 57.4 - + + +
44T GLU* 5.3 3.8 - - - -
47T GLU* 4.8 0.4 - - - +
87T LEU* 4.5 4.5 - - + -
129T GLU 3.0 14.1 + - - +
130T HIS* 3.3 16.1 + + + +
132T ASP* 1.3 75.9 - - - +
134T LEU* 1.3 80.6 + - + +
136T THR* 3.2 5.4 + - - -
137T GLN* 2.9 68.8 + - + +
153T HIS* 5.1 2.8 + - - -
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Residues in contact with LEU 134 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T GLU* 5.6 0.4 - - - +
87T LEU* 3.9 35.7 - - + +
90T ASP* 4.1 9.6 - - + +
91T LEU* 4.0 30.1 - - + +
94T GLU* 4.2 8.3 - - + -
130T HIS* 2.9 52.9 + - + +
131T ILE* 3.2 6.0 + - - +
133T TYR* 1.3 97.5 - - + +
135T GLU* 1.3 66.2 + - - +
137T GLN* 3.1 4.3 + - - +
138T LEU* 3.1 30.2 + - + +
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Residues in contact with GLU 135 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M PHE* 4.4 16.1 - - - +
66M GLU* 4.2 19.0 - - - +
91T LEU* 4.2 21.5 - - + +
95T LEU* 5.6 3.1 - - - +
131T ILE* 3.0 34.3 + - + +
132T ASP* 4.0 2.8 - - - +
134T LEU* 1.3 80.1 - - - +
136T THR* 1.3 62.3 + - - +
138T LEU* 3.5 8.0 + - - +
139T GLY* 3.0 20.3 + - - -
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Residues in contact with THR 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N ASN 5.1 1.1 + - - +
34N ASP 3.2 14.8 + - - +
35N TRP* 3.6 5.4 - - - +
36N GLY* 3.5 37.5 - - - +
132T ASP* 2.9 28.3 + - - -
133T TYR* 3.4 7.0 - - - -
135T GLU* 1.3 77.8 - - - +
137T GLN* 1.3 66.6 + - - +
139T GLY* 3.3 1.8 + - - -
140T LEU* 2.8 30.5 + - + +
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Residues in contact with GLN 137 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87T LEU* 4.0 16.2 - - + -
133T TYR* 2.9 67.4 + - + +
134T LEU 3.1 5.3 + - - +
136T THR* 1.3 89.1 - - - +
138T LEU* 1.3 58.7 + - - +
140T LEU* 3.3 13.1 + - - +
141T ILE* 2.9 33.4 + - - +
149T TYR* 2.7 43.5 + - + +
153T HIS* 4.0 10.7 + - - -
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Residues in contact with LEU 138 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84T GLN* 4.0 15.5 - - + +
87T LEU* 3.9 35.2 - - + +
88T GLN* 4.5 13.5 - - + +
91T LEU* 4.2 20.2 - - + -
134T LEU 3.1 30.9 + - - +
135T GLU* 3.9 5.6 - - - +
137T GLN* 1.3 76.4 - - - +
139T GLY* 1.3 64.0 + - - +
141T ILE* 3.2 29.5 + - + +
142T GLN* 3.2 16.0 + - - +
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Residues in contact with GLY 139 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135T GLU 3.0 14.5 + - - -
136T THR* 3.6 3.8 - - - -
138T LEU* 1.3 77.9 - - - +
140T LEU* 1.3 61.1 + - - +
142T GLN* 3.1 12.4 + - - +
143T LYS* 3.0 38.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N TRP 3.0 26.6 + - - +
36N GLY* 4.0 14.4 - - - +
37N LEU* 4.0 24.2 - - + -
154N MET* 3.8 35.9 - - + -
136T THR* 2.8 21.1 + - + +
137T GLN* 3.7 24.0 - - - +
139T GLY* 1.3 68.7 - - - +
141T ILE* 1.3 66.9 + - - +
143T LYS* 4.2 7.4 - - + +
144T VAL* 3.0 33.7 + - + +
149T TYR* 4.0 9.2 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83T THR* 5.0 0.9 - - + -
84T GLN* 4.5 24.0 - - + +
87T LEU* 3.8 26.0 - - + -
137T GLN 2.9 20.1 + - - +
138T LEU* 3.2 22.1 + - + +
140T LEU* 1.3 75.9 - - - +
142T GLN* 1.3 76.0 + - - +
145T GLY* 3.0 23.0 + - - -
146T LEU* 3.7 23.5 + - + +
149T TYR* 3.6 32.3 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147N GLU* 4.2 7.8 - - - +
138T LEU 3.2 10.2 + - - +
139T GLY* 3.1 11.1 + - - +
141T ILE* 1.3 94.8 + - - +
143T LYS* 1.3 65.0 + - + +
144T VAL 3.7 0.2 + - - -
145T GLY* 4.0 2.9 + - - -
----------------------------------------------------------
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Residues in contact with LYS 143 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N TRP* 3.8 54.1 + - + +
37N LEU* 4.7 12.6 - - + -
146N LEU* 5.5 1.2 - - - +
147N GLU* 3.3 16.3 - - - +
150N LEU* 3.8 27.0 - - + +
139T GLY* 3.0 29.9 + - - +
140T LEU* 3.1 10.5 + - + +
142T GLN* 1.3 81.0 - - + +
144T VAL* 1.3 66.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147N GLU* 3.4 25.3 - - - +
150N LEU* 3.6 27.1 - - + -
151N GLN* 3.7 11.9 - - + +
154N MET* 4.3 18.2 - - + -
140T LEU* 3.0 25.3 + - + +
143T LYS* 1.3 82.5 - - + +
145T GLY* 1.3 69.9 + - - +
148T ASN* 3.1 32.2 + - + +
149T TYR* 3.8 20.2 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147N GLU* 4.1 14.3 - - - -
141T ILE 3.0 17.7 + - - -
142T GLN 4.0 2.1 + - - -
143T LYS 3.5 1.6 - - - -
144T VAL* 1.3 81.6 - - - +
146T LEU* 1.3 60.2 + - - -
147T GLU 3.5 2.2 - - - -
148T ASN 3.5 0.8 + - - -
149T TYR* 2.9 29.3 + - - +
----------------------------------------------------------
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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