Contacts of the helix formed by residues 113 - 145 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N ASP* 5.9 1.0 + - + +
7N VAL* 3.4 26.0 - - + +
61N ARG* 3.0 15.6 + - - -
65N LEU* 4.2 6.6 - - - +
108N CYS* 3.0 24.4 + - + +
111N VAL* 3.3 5.2 - - + +
112N HIS* 1.3 73.8 - - - +
114N TYR* 1.3 56.8 + - - +
115N VAL* 3.6 2.1 + - - +
116N SER* 2.6 41.2 + - - -
117N ARG* 3.0 20.4 + - - +
102X ARG* 4.2 5.7 + - - +
128X GLU* 4.8 2.4 - - - +
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Residues in contact with TYR 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109N GLU* 3.5 34.7 + - - -
112N HIS* 3.0 59.4 + - + -
113N ASP* 1.3 72.0 - - - +
115N VAL* 1.3 61.0 + - - +
117N ARG* 3.3 7.1 + - - +
118N ASP* 3.0 27.4 + - - +
102X ARG* 4.0 12.4 - - + +
105X ILE* 3.6 39.9 - - + +
106X VAL* 3.3 16.8 + - - +
117X ARG* 3.6 21.1 - - - +
121X LYS* 4.5 17.8 - - + +
124X LEU* 4.1 17.3 - - + -
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Residues in contact with VAL 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N ARG* 3.8 16.8 - - - +
113N ASP* 3.2 1.2 + - - -
114N TYR* 1.3 76.9 - - + +
116N SER* 1.3 65.4 + - - +
118N ASP* 3.2 6.3 + - + +
119N LEU* 3.1 22.0 + - + +
121X LYS* 5.2 3.4 - - + +
124X LEU* 4.0 13.5 - - + -
125X GLU* 3.9 44.2 - - + +
128X GLU* 3.3 43.3 + - + +
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Residues in contact with SER 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL* 4.0 8.4 - - - +
11N LEU* 4.1 9.8 - - - +
61N ARG* 3.0 25.3 + - - +
65N LEU* 4.0 3.1 - - - +
108N CYS* 3.7 15.3 - - - -
113N ASP* 2.6 37.2 + - - -
115N VAL* 1.3 76.5 - - - +
117N ARG* 1.3 63.9 + - - +
119N LEU* 3.3 7.9 + - - +
120N LEU* 3.1 25.5 + - - +
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Residues in contact with ARG 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105N ILE* 4.0 18.5 - - + +
108N CYS* 3.9 16.7 - - + +
109N GLU* 3.1 40.0 + - - +
113N ASP 3.0 15.7 + - - +
114N TYR* 3.6 11.0 - - - +
115N VAL 3.1 0.2 - - - -
116N SER* 1.3 80.0 - - - +
118N ASP* 1.3 59.8 + - - +
120N LEU* 3.2 6.9 + - - +
121N LYS* 2.9 33.3 + - + +
109O GLU* 2.9 42.8 + - - -
114O TYR* 3.7 22.9 - - - +
117O ARG* 3.8 19.4 - - - +
117X ARG* 3.8 13.6 - - - +
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Residues in contact with ASP 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N TYR 3.0 16.6 + - - +
115N VAL* 3.2 8.7 + - + +
117N ARG* 1.3 77.6 - - - +
119N LEU* 1.3 63.4 + - - +
121N LYS* 3.2 11.2 + - - +
122N ASP* 3.1 40.2 + - - +
121X LYS* 3.6 37.8 + - + +
125X GLU* 4.1 16.6 - - - +
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Residues in contact with LEU 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LEU* 5.4 2.2 - - + -
57N LYS* 3.8 26.2 - - + +
58N LEU* 4.1 15.5 - - + -
61N ARG* 3.7 37.7 - - + -
115N VAL* 3.1 12.1 + - + +
116N SER* 3.5 8.7 - - - +
118N ASP* 1.3 79.1 - - - +
120N LEU* 1.3 64.7 + - + +
122N ASP* 3.4 8.6 + - - +
123N ILE* 3.2 45.9 + - + +
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Residues in contact with LEU 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N HIS* 6.0 0.2 - - + -
11N LEU* 3.8 26.2 - - + -
14N ILE* 4.0 9.9 - - + -
58N LEU* 4.3 11.0 - - + -
101N LEU* 3.7 26.1 - - + +
104N ALA* 3.6 26.0 - - + -
105N ILE* 3.6 22.9 - - + -
108N CYS* 4.0 19.1 - - - -
116N SER 3.1 20.8 + - - +
117N ARG* 3.7 1.1 - - - +
119N LEU* 1.3 78.8 - - + +
121N LYS* 1.3 58.2 + - - +
123N ILE* 3.4 5.6 + - + +
124N LEU* 2.9 28.6 + - - +
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Residues in contact with LYS 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105N ILE* 4.0 8.5 - - + +
117N ARG* 2.9 22.9 + - + +
118N ASP* 3.6 12.8 - - - +
120N LEU* 1.3 74.9 - - - +
122N ASP* 1.3 68.0 + - - +
124N LEU* 3.2 8.1 + - + +
125N GLU* 2.9 45.1 + - - -
114O TYR* 4.4 20.4 - - + +
115O VAL* 4.2 15.5 - - - +
118O ASP* 3.5 42.2 - - + +
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Residues in contact with ASP 122 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N HIS* 4.9 1.7 + - - -
118N ASP* 3.1 27.6 + - - +
119N LEU* 3.7 9.8 - - - +
121N LYS* 1.3 85.8 - - - +
123N ILE* 1.3 64.6 + - + +
125N GLU* 3.4 10.9 + - - +
126N SER* 3.3 20.4 + - - -
118O ASP* 5.6 0.3 - - - +
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Residues in contact with ILE 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N ILE* 4.9 1.3 - - + -
18N GLU* 3.7 20.2 - - - +
54N HIS* 3.8 36.3 - - + +
57N LYS* 5.7 1.3 - - + -
58N LEU* 4.0 28.0 - - + -
101N LEU* 4.0 17.5 - - + -
119N LEU* 3.2 35.3 + - + +
120N LEU* 3.6 12.1 - - + +
122N ASP* 1.3 78.2 - - + +
124N LEU* 1.3 58.4 + - - +
126N SER* 3.1 3.3 + - - -
127N GLU* 2.8 35.2 + - - +
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Residues in contact with LEU 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N THR* 3.5 27.1 - - - +
101N LEU* 4.2 25.1 - - + -
102N ARG* 3.8 28.7 - - + +
105N ILE* 4.2 8.3 - - + -
120N LEU 2.9 18.0 + - - +
121N LYS* 3.2 6.7 + - - +
123N ILE* 1.3 75.3 - - - +
125N GLU* 1.3 64.1 + - - +
127N GLU* 3.1 2.4 + - - +
128N GLU* 2.9 38.2 + - - +
114O TYR* 4.0 31.9 - - + -
115O VAL* 4.0 7.6 - - + -
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Residues in contact with GLU 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121N LYS* 2.9 33.0 + - - +
122N ASP* 3.8 11.0 - - - +
124N LEU* 1.3 79.1 - - - +
126N SER* 1.3 56.4 + - - +
128N GLU* 3.4 3.0 + - - +
129N GLU* 3.1 46.2 + - + +
115O VAL* 3.9 27.2 - - + +
118O ASP* 4.6 6.2 - - - +
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Residues in contact with SER 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N ASP* 5.1 6.9 + - - +
54N HIS* 3.1 30.8 - - - -
122N ASP 3.3 10.4 + - - -
123N ILE 3.1 8.1 + - - -
125N GLU* 1.3 76.1 - - - +
127N GLU* 1.3 66.8 + - - +
129N GLU* 3.3 15.1 + - - +
130N HIS* 3.1 21.1 + - - +
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Residues in contact with GLU 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N GLU* 3.0 16.1 - - - +
51N GLU* 2.4 33.0 - - - +
54N HIS* 3.8 6.1 + - - -
94N GLU* 2.8 33.5 - - - +
97N ALA* 5.1 7.0 - - + +
98N THR* 4.2 14.6 - - - +
101N LEU* 4.0 19.3 - - + -
123N ILE* 2.8 20.8 + - + +
124N LEU* 3.1 5.6 + - - +
126N SER* 1.3 82.2 + - - +
128N GLU* 1.3 56.6 + - - +
130N HIS* 3.1 8.3 + - - +
131N ILE* 2.9 31.1 + - + +
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Residues in contact with GLU 128 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N THR* 4.4 5.2 - - - +
102N ARG* 2.6 40.0 + - - +
124N LEU* 2.9 22.5 + - + +
125N GLU* 3.4 6.0 + - - +
126N SER 3.3 0.2 - - - -
127N GLU* 1.3 73.6 - - - +
129N GLU* 1.3 60.0 + - - +
131N ILE* 3.3 10.3 + - + -
132N ASP* 2.9 27.2 + - - +
61O ARG* 2.9 39.6 + - - +
64O PHE* 3.6 22.2 - - + -
65O LEU* 6.2 0.2 - - - -
113O ASP* 4.8 0.3 - - - +
115O VAL* 3.6 22.5 - - + +
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Residues in contact with GLU 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125N GLU* 3.1 37.6 + - + +
126N SER* 3.7 15.2 - - - +
128N GLU* 1.3 75.6 - - - +
130N HIS* 1.3 58.4 + - - +
132N ASP* 3.1 10.7 + - - +
133N TYR* 2.9 26.4 + - - +
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Residues in contact with HIS 130 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N TYR* 3.5 35.4 - + - -
44N GLU* 4.7 1.2 + - - -
47N GLU* 3.4 44.0 + - + +
51N GLU* 5.9 0.4 - - - -
90N ASP* 4.5 4.0 + - + -
94N GLU* 2.9 22.6 + - - +
126N SER 3.1 11.1 + - - +
127N GLU* 3.1 12.6 + - - +
129N GLU* 1.3 74.7 - - - +
131N ILE* 1.3 65.3 + - - +
133N TYR* 3.2 15.4 + + - -
134N LEU* 3.0 47.9 + - + +
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Residues in contact with ILE 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91N LEU* 4.1 14.1 - - + -
94N GLU* 3.5 33.4 - - + +
95N LEU* 4.1 17.3 - - + -
98N THR* 3.8 23.8 - - + +
127N GLU 2.9 15.8 + - - +
128N GLU* 3.3 14.1 + - + +
130N HIS* 1.3 74.8 - - - +
132N ASP* 1.3 64.0 + - - +
134N LEU* 3.7 6.6 - - - +
135N GLU* 3.0 48.3 + - - +
64O PHE* 4.3 11.7 - - + -
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Residues in contact with ASP 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128N GLU 2.9 13.2 + - - +
129N GLU* 3.1 13.6 + - - +
131N ILE* 1.3 77.8 - - - +
133N TYR* 1.3 60.8 + - - +
135N GLU* 3.6 3.9 + - - +
136N THR* 2.8 40.1 + - - -
64O PHE* 3.6 31.4 - - + +
34P ASP* 4.4 12.0 - - - +
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Residues in contact with TYR 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N LEU* 3.7 25.1 - - - +
43N HIS* 3.2 55.8 - + + +
44N GLU* 5.3 3.8 - - - -
47N GLU* 5.0 0.7 - - - +
87N LEU* 4.8 3.8 - - + -
129N GLU 2.9 11.8 + - - +
130N HIS* 3.4 17.5 - + + +
132N ASP* 1.3 77.4 - - - +
134N LEU* 1.3 80.5 + - + +
136N THR* 3.4 3.4 + - - -
137N GLN* 2.9 72.0 + - + +
153N HIS* 5.2 2.3 + - - -
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Residues in contact with LEU 134 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N GLU* 5.5 0.7 - - - +
87N LEU* 4.0 29.4 - - + +
90N ASP* 3.7 21.5 - - + +
91N LEU* 3.6 34.5 - - + +
94N GLU* 4.1 4.9 - - + -
130N HIS* 3.0 50.7 + - + +
131N ILE* 3.7 7.4 - - - +
133N TYR* 1.3 94.7 - - + +
135N GLU* 1.3 58.6 + - - +
137N GLN* 3.2 5.1 + - - +
138N LEU* 3.0 36.3 + - + +
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Residues in contact with GLU 135 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91N LEU* 4.3 21.5 - - + +
95N LEU* 5.8 2.6 - - - +
131N ILE* 3.0 37.7 + - + +
132N ASP* 4.1 2.8 - - - +
134N LEU* 1.3 73.1 - - - +
136N THR* 1.3 61.0 + - - +
138N LEU* 3.3 8.7 + - - +
139N GLY* 2.9 26.9 + - - -
64O PHE* 4.3 14.6 - - - +
66O GLU* 4.0 18.6 - - - +
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Residues in contact with THR 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132N ASP* 2.8 26.9 + - - -
133N TYR* 3.6 5.6 - - - -
135N GLU* 1.3 76.5 - - - +
137N GLN* 1.3 66.2 + - - +
139N GLY* 3.3 2.2 + - - +
140N LEU* 2.8 30.8 + - + +
33P ASN 4.9 0.9 - - - +
34P ASP 3.2 17.4 + - - +
35P TRP* 3.5 10.3 - - - +
36P GLY* 3.4 34.1 - - - +
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Residues in contact with GLN 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N LEU* 4.1 16.2 - - + -
133N TYR* 2.9 66.7 + - + +
134N LEU 3.2 7.8 + - - +
136N THR* 1.3 87.3 - - - +
138N LEU* 1.3 64.2 + - - +
140N LEU* 3.1 14.2 + - - +
141N ILE* 3.0 27.8 + - - +
149N TYR* 2.5 48.2 + - + +
153N HIS* 3.9 11.1 + - - -
154P MET* 5.3 0.2 - - - +
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Residues in contact with LEU 138 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N GLN* 3.7 38.1 + - + +
87N LEU* 3.8 43.5 - - + +
88N GLN* 4.5 12.1 - - + +
91N LEU* 4.4 20.4 - - + -
134N LEU* 3.0 31.7 + - - +
135N GLU* 3.3 5.6 + - - +
137N GLN* 1.3 77.8 - - - +
139N GLY* 1.3 60.8 + - - +
141N ILE* 3.6 7.3 + - + +
142N GLN* 3.5 23.6 + - - +
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Residues in contact with GLY 139 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135N GLU 2.9 14.3 + - - -
136N THR* 3.7 4.5 - - - -
138N LEU* 1.3 78.5 - - - +
140N LEU* 1.3 59.8 + - - +
142N GLN* 3.3 9.4 + - - +
143N LYS* 3.0 39.7 + - - +
35P TRP 5.6 0.7 - - - -
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Residues in contact with LEU 140 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136N THR* 2.8 26.9 + - + +
137N GLN* 3.1 28.9 + - - +
139N GLY* 1.3 72.9 - - - +
141N ILE* 1.3 59.1 + - - +
143N LYS* 2.9 7.6 + - + +
144N VAL* 2.8 44.0 + - + +
149N TYR* 3.9 9.6 - - + -
35P TRP 3.3 20.4 + - - +
36P GLY* 4.1 12.3 - - - +
37P LEU* 4.0 25.4 - - + -
154P MET* 4.0 29.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N THR* 4.7 2.0 - - + -
84N GLN* 3.7 41.1 - - - +
87N LEU* 3.9 28.0 - - + -
137N GLN 3.0 10.9 + - - +
138N LEU* 3.7 10.1 - - + +
140N LEU* 1.3 73.5 - - - +
142N GLN* 1.3 64.4 + - - +
145N GLY* 3.0 28.1 + - - -
146N LEU* 3.6 29.5 + - + +
149N TYR* 3.5 38.1 - - + -
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Residues in contact with GLN 142 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N GLN* 4.0 14.6 + - - +
138N LEU 3.5 10.7 + - - +
139N GLY* 3.3 11.5 + - - +
140N LEU 3.2 0.6 - - - -
141N ILE* 1.3 91.6 - - - +
143N LYS* 1.3 64.1 + - + +
145N GLY* 4.3 2.6 + - - -
147P GLU* 5.0 3.3 - - - +
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Residues in contact with LYS 143 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139N GLY* 3.0 29.1 + - - +
140N LEU* 2.9 11.3 + - + +
142N GLN* 1.3 80.9 - - + +
144N VAL* 1.3 64.9 + - + +
145N GLY 3.6 0.2 - - - -
35P TRP* 3.7 51.1 + - + +
37P LEU* 4.7 17.0 - - + -
82P ASN* 6.6 0.2 - - - -
146P LEU* 5.5 1.7 - - - +
147P GLU* 3.8 13.1 - - - +
150P LEU* 3.5 29.2 - - + +
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Residues in contact with VAL 144 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N LEU* 2.8 29.0 + - + +
143N LYS* 1.3 78.2 - - + +
145N GLY* 1.3 68.3 + - - +
148N ASN* 3.2 30.1 + - + +
149N TYR* 3.8 22.2 - - + +
37P LEU* 5.0 0.2 - - + -
147P GLU* 3.4 25.9 - - - +
150P LEU* 3.8 11.9 - - + -
151P GLN* 3.7 27.4 - - + +
154P MET* 4.3 18.6 - - + -
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Residues in contact with GLY 145 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141N ILE 3.0 15.1 + - - -
142N GLN 4.3 1.9 + - - -
143N LYS 3.6 1.6 - - - -
144N VAL* 1.3 83.1 - - - +
146N LEU* 1.3 67.5 + - - -
147N GLU 3.3 2.6 + - - -
148N ASN 3.6 1.3 + - - -
149N TYR* 2.9 19.8 + - - +
147P GLU* 3.7 17.1 + - - -
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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