Contacts of the helix formed by residues 112 - 143 (chain D) in PDB entry 5IXM
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 THR 112 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ILE* 6.5 1.6 - - + -
305C THR 5.9 1.3 - - - +
306C THR* 4.8 6.1 + - - +
109D ASN* 3.0 38.3 + - - +
111D LEU* 1.3 87.4 - - + +
113D ALA* 1.3 64.1 + - - +
114D LEU 3.3 2.5 - - - -
115D ALA* 3.0 25.6 + - - +
116D LYS* 3.0 16.8 + - - +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C TYR* 4.0 22.4 + - + -
151C PHE* 3.7 37.2 - - + -
153C VAL* 5.1 2.9 - - + -
162C ALA* 5.7 4.5 - - + +
109D ASN 3.4 7.7 + - - -
110D PRO 4.0 10.5 + - - +
111D LEU 3.7 1.4 - - - -
112D THR* 1.3 74.9 - - - +
114D LEU* 1.3 64.7 + - - +
116D LYS* 2.9 9.5 + - - +
117D GLU* 2.9 20.6 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS* 4.0 26.0 - - + -
151C PHE* 3.5 23.5 - - + -
163C TYR* 3.7 32.3 + - + +
164C ARG 4.1 2.0 - - - -
165C ALA* 4.1 11.9 - - + +
168C GLN* 5.4 1.1 - - - +
192C PHE* 3.8 31.4 - - + -
303C TYR 3.5 21.3 - - - +
304C ASP* 3.9 8.7 - - + -
112D THR 3.3 0.4 - - - -
113D ALA* 1.3 76.5 - - - +
115D ALA* 1.3 64.4 + - - +
117D GLU* 3.0 14.4 + - - +
118D ALA* 3.1 12.0 + - - +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ILE* 5.9 0.4 - - + -
303C TYR 4.4 2.2 + - - +
304C ASP* 3.4 32.3 - - - +
305C THR 3.6 17.5 - - - +
306C THR* 3.8 12.8 - - - -
322C SER* 3.6 4.7 + - - -
112D THR* 3.0 19.1 + - - +
114D LEU* 1.3 78.0 - - - +
116D LYS* 1.3 63.3 + - - +
118D ALA* 3.0 6.9 + - - +
119D GLU* 2.9 19.1 + - - +
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Residues in contact with LYS 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C TYR* 4.6 9.2 - - - +
306C THR* 4.0 15.7 + - + -
307C LEU 4.7 4.2 + - - -
442C VAL* 3.8 17.4 - - - +
106D PHE* 4.2 12.7 - - + -
107D PHE* 2.9 31.1 + - - +
108D ASP* 4.3 3.8 - - - +
109D ASN* 4.0 35.0 - - - +
112D THR* 3.0 18.5 + - - +
113D ALA* 2.9 11.7 + - - +
115D ALA* 1.3 75.0 - - - +
117D GLU* 1.3 53.2 + - - +
119D GLU* 2.9 30.9 + - - +
120D ALA* 2.7 35.5 + - - +
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR* 5.0 3.3 + - - +
132C ILE* 3.6 32.5 - - + +
149C LYS* 4.2 22.4 - - + +
151C PHE* 4.1 14.7 - - + -
113D ALA 2.9 10.2 + - - +
114D LEU* 3.0 9.6 + - - +
116D LYS* 1.3 76.5 - - - +
118D ALA* 1.3 64.0 + - - +
120D ALA* 3.0 10.9 + - - +
121D GLU* 2.9 29.7 + - - +
124D ARG* 3.6 26.0 + - - -
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS* 5.7 1.6 - - - +
304C ASP* 3.6 26.2 - - + +
322C SER* 4.1 2.2 - - - +
323C GLY* 4.1 16.4 - - - +
114D LEU 3.1 8.4 + - - +
115D ALA 3.0 10.6 + - - +
117D GLU* 1.3 75.4 - - - +
119D GLU* 1.3 64.5 + - - +
121D GLU* 3.0 25.4 + - - +
122D VAL* 3.1 15.8 + - + +
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Residues in contact with GLU 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C THR* 3.7 6.1 - - + +
307C LEU 4.0 9.0 - - - +
308C MET* 3.5 23.5 - - + +
309C GLN* 3.5 23.9 + - - +
322C SER* 3.8 12.9 - - - -
106D PHE* 3.6 24.9 - - + +
115D ALA 2.9 11.9 + - - +
116D LYS* 2.9 42.5 + - - +
118D ALA* 1.3 74.0 - - - +
120D ALA* 1.3 65.3 + - - +
122D VAL* 3.0 7.2 + - - +
123D LEU* 2.9 28.5 + - + +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLN* 5.9 0.7 - - - +
80D LEU* 4.1 16.6 - - + +
106D PHE* 4.6 12.8 - - + -
116D LYS 2.7 16.5 + - - +
117D GLU* 3.0 16.4 + - - +
119D GLU* 1.3 73.5 - - - +
121D GLU* 1.3 62.9 + - - +
123D LEU* 3.0 8.3 + - - +
124D ARG* 2.8 48.3 + - - +
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS* 2.7 36.6 + - - -
168C GLN* 5.0 4.7 + - - -
170C ASP* 5.2 2.9 - - - +
117D GLU* 2.9 29.0 + - - +
118D ALA* 3.0 12.9 + - - +
120D ALA* 1.3 75.2 - - - +
122D VAL* 1.3 66.2 + - + +
124D ARG* 3.0 17.1 + - - +
125D GLN* 2.9 23.3 + - - +
128D ARG* 4.5 2.5 + - - +
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Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C MET* 3.7 26.0 - - + -
317C ARG* 4.5 5.4 - - - -
321C TYR 6.0 0.2 - - - +
322C SER* 5.0 7.0 - - - -
323C GLY 5.6 2.0 - - - +
118D ALA* 3.1 15.3 + - + +
119D GLU 3.0 8.1 + - - +
121D GLU* 1.3 74.5 - - + +
123D LEU* 1.3 65.0 + - - +
125D GLN* 3.0 11.7 + - + +
126D GLU* 2.9 42.9 + - + +
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C MET* 4.1 17.7 - - + -
309C GLN* 5.0 7.4 - - + +
317C ARG* 4.4 3.6 - - - +
80D LEU* 3.9 15.5 - - + -
104D ARG* 4.2 29.4 - - + -
105D THR 4.7 3.6 - - - +
106D PHE* 3.7 40.8 - - + -
119D GLU* 2.9 24.6 + - + +
120D ALA* 3.3 7.0 - - - +
122D VAL* 1.3 75.1 - - - +
124D ARG* 1.3 53.3 + - - +
126D GLU* 3.0 19.2 + - - +
127D MET* 2.7 38.9 + - - +
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLU* 3.4 31.8 + - - +
64D GLN* 4.2 17.2 + - - -
80D LEU* 4.4 15.8 - - + +
82D LEU* 5.4 0.2 - - - +
117D GLU* 3.6 25.7 + - - -
120D ALA* 2.8 35.1 + - - +
121D GLU* 3.0 20.2 + - - +
123D LEU* 1.3 75.6 - - - +
125D GLN* 1.3 64.7 + - - +
127D MET* 3.0 13.9 + - - +
128D ARG* 2.8 43.5 + - - +
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Residues in contact with GLN 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PRO* 4.6 6.8 - - - +
31D SER* 4.1 9.9 + - - -
34D GLN* 5.9 1.0 + - - -
121D GLU 2.9 11.7 + - - +
122D VAL* 3.2 12.3 - - - +
124D ARG* 1.3 75.5 - - - +
126D GLU* 1.3 66.7 + - + +
128D ARG* 3.0 40.0 + - - +
129D GLU* 3.0 46.9 + - - +
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ASP* 5.0 3.5 - - - +
313C SER* 5.1 5.9 - - - -
314C GLY 5.2 0.3 + - - -
317C ARG* 2.6 51.6 + - - +
104D ARG* 4.3 24.6 + - - +
122D VAL* 2.9 26.9 + - + +
123D LEU* 3.4 12.5 - - - +
125D GLN* 1.3 77.5 - - + +
127D MET* 1.3 58.1 + - - +
129D GLU* 3.0 19.8 + - - +
130D GLN* 2.8 28.2 + - - +
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Residues in contact with MET 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.4 33.0 - - + +
81D VAL 3.6 3.6 - - - -
82D LEU* 3.3 30.7 - - + +
102D VAL* 3.2 45.2 - - + +
104D ARG* 3.4 31.6 - - + +
123D LEU 2.7 26.6 + - - +
124D ARG* 3.3 13.0 - - - +
126D GLU* 1.3 71.1 - - - +
128D ARG* 1.3 65.4 + - - +
130D GLN* 3.0 5.1 + - - +
131D ALA* 2.8 22.9 + - - +
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Residues in contact with ARG 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PRO* 3.5 26.4 - - - +
28D LEU* 3.8 38.6 - - + +
31D SER* 4.1 13.3 - - - +
62D GLU* 3.4 24.7 + - - +
82D LEU* 3.9 20.2 - - + -
121D GLU* 4.5 2.6 + - - +
124D ARG* 2.8 28.5 + - - +
125D GLN* 3.3 39.7 + - - +
127D MET* 1.3 75.5 - - - +
129D GLU* 1.3 63.3 + - - +
131D ALA* 3.0 5.6 + - - +
132D ALA* 2.9 22.0 + - - +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D SER* 4.0 15.7 + - - +
34D GLN* 5.4 6.9 - - - +
35D GLN* 4.6 7.0 - - - +
125D GLN* 3.0 42.1 + - - +
126D GLU* 3.0 21.6 + - - +
128D ARG* 1.3 75.0 - - - +
130D GLN* 1.3 63.2 + - - +
132D ALA* 3.0 14.1 + - - +
133D GLN* 3.0 24.3 + - - +
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Residues in contact with GLN 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C SER* 4.4 5.9 + - - -
102D VAL* 3.6 16.1 - - + +
103D PHE 5.6 0.4 - - - +
104D ARG* 2.5 43.3 + - - +
126D GLU 2.8 15.3 + - - +
127D MET 3.4 7.0 - - - +
129D GLU* 1.3 71.7 - - - +
131D ALA* 1.3 66.8 + - - +
133D GLN* 3.0 25.3 + - + +
134D GLN* 3.0 39.4 + - + +
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 4.6 4.5 - - + -
82D LEU* 3.9 20.0 - - + -
84D VAL* 4.1 14.6 - - + -
100D VAL* 3.8 22.2 - - + +
102D VAL* 3.8 9.1 - - + +
127D MET 2.8 16.0 + - - +
128D ARG* 3.3 8.7 - - - +
130D GLN* 1.3 73.1 - - - +
132D ALA* 1.3 65.0 + - - +
134D GLN* 3.0 3.5 + - - +
135D LEU* 2.9 24.7 + - + +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 5.2 1.5 - - + +
31D SER* 3.8 23.1 - - - +
32D ILE* 3.9 17.9 - - + +
35D GLN* 3.6 21.5 - - + -
128D ARG 2.9 11.0 + - - +
129D GLU 3.0 9.2 + - - +
131D ALA* 1.3 76.2 - - - +
133D GLN* 1.3 65.5 + - - +
135D LEU* 3.0 18.6 + - - +
136D VAL* 3.1 15.1 + - - +
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Residues in contact with GLN 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LYS* 5.3 6.4 + - - -
35D GLN* 3.5 36.5 - - - +
129D GLU* 3.0 18.9 + - - +
130D GLN* 3.0 18.8 + - + +
132D ALA* 1.3 75.9 - - - +
134D GLN* 1.3 65.1 + - + +
136D VAL* 3.0 16.6 + - - +
137D ARG* 3.1 32.7 + - + +
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Residues in contact with GLN 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D VAL* 3.3 29.6 - - + +
101D ASN 4.3 9.5 + - - +
102D VAL* 4.1 5.8 - - - +
130D GLN* 3.0 44.4 + - + +
131D ALA 3.0 6.3 + - - +
133D GLN* 1.3 78.2 - - + +
135D LEU* 1.3 64.3 + - - +
137D ARG* 3.0 32.7 + - - +
138D GLN* 2.8 34.4 + - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 6.2 0.7 - - + -
32D ILE* 4.0 29.4 - - + -
55D LEU* 5.1 13.2 - - + -
57D ILE* 4.5 6.1 - - + -
84D VAL* 4.4 14.8 - - + -
86D ALA* 4.0 25.8 - - + -
98D LEU* 3.9 28.3 - - + -
99D GLN 5.6 0.2 - - - -
100D VAL* 3.8 19.9 - - + +
131D ALA 2.9 13.0 + - - +
132D ALA* 3.0 11.4 + - - +
134D GLN* 1.3 75.7 - - - +
136D VAL* 1.3 66.7 + - + +
138D GLN* 3.0 16.3 + - - +
139D LEU* 3.4 14.8 - - - +
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PRO* 4.0 7.0 - - + +
12D THR* 4.0 14.6 - - - +
32D ILE* 5.2 3.1 - - + +
35D GLN* 4.1 21.8 - - + +
36D LEU* 3.9 28.9 - - + +
39D ASN* 3.8 30.1 - - + +
41D VAL* 6.1 0.2 - - + -
132D ALA 3.1 11.7 + - - +
133D GLN* 3.0 9.2 + - - +
135D LEU* 1.3 74.8 - - + +
137D ARG* 1.3 66.6 + - + +
139D LEU* 3.0 31.0 + - + +
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Residues in contact with ARG 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLU* 6.0 0.2 - - - -
340C ARG* 3.2 46.2 - - - +
342C TYR* 3.9 22.0 + - + +
348C GLU* 3.9 14.5 + - - -
11D PRO* 4.9 6.1 - - + -
133D GLN* 3.1 32.2 + - - +
134D GLN* 3.0 37.4 + - - +
136D VAL* 1.3 78.4 - - + +
138D GLN* 1.3 64.1 + - + +
140D LEU* 2.9 36.2 + - + +
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 3.2 38.7 - - + +
99D GLN 3.1 25.3 + - - +
100D VAL* 3.5 18.7 - - - +
134D GLN* 2.8 22.4 + - + +
135D LEU* 3.0 10.7 + - - +
137D ARG* 1.3 76.6 - - + +
139D LEU* 1.3 62.8 + - - +
140D LEU 3.0 0.4 - - - -
141D THR* 2.9 29.8 + - - +
142D VAL* 3.4 7.7 + - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PRO 4.7 5.8 - - - +
12D THR* 4.0 28.9 - - + +
13D GLU* 5.8 3.0 + - - +
14D LEU* 4.6 8.5 - - + -
17D LEU* 4.6 19.7 - - + -
36D LEU* 5.0 9.6 - - + -
55D LEU* 5.0 11.4 - - + -
88D VAL* 4.3 13.9 - - + -
98D LEU* 4.2 15.0 - - + -
135D LEU 3.4 18.8 - - - +
136D VAL* 3.0 19.3 + - + +
138D GLN* 1.3 78.5 - - - +
140D LEU* 1.3 61.8 + - - +
142D VAL* 2.9 23.0 + - + +
143D HIS* 3.2 11.1 + - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C TYR* 4.2 32.8 - - + +
346C ARG* 3.9 43.3 + - + +
9D GLN* 4.8 13.0 - - + +
11D PRO* 3.1 47.8 + - + +
12D THR* 6.2 0.4 - - - +
137D ARG* 2.9 30.3 + - + +
139D LEU* 1.3 76.6 - - - +
141D THR* 1.3 58.0 + - - +
143D HIS* 3.0 24.6 + - - +
144D ALA* 3.3 8.7 + - - +
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C ALA* 3.9 15.9 - - + +
346C ARG 3.1 17.3 + - - -
347C VAL* 4.5 13.2 - - + +
96D TYR* 3.2 31.8 - - + +
98D LEU* 5.6 0.9 - - - -
138D GLN* 2.9 19.3 + - - +
140D LEU* 1.3 78.8 - - - +
142D VAL* 1.3 58.6 + - - +
144D ALA* 2.9 27.7 + - + +
145D ALA* 3.4 5.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 3.6 46.9 - - + -
90D ILE* 3.8 21.9 - - + +
96D TYR* 4.0 27.6 - - + -
98D LEU* 4.5 3.1 - - + -
138D GLN 3.8 10.5 - - - +
139D LEU* 2.9 19.9 + - + +
141D THR* 1.3 78.1 - - - +
143D HIS* 1.3 55.2 + - - +
145D ALA* 3.1 27.1 + - + +
146D GLU* 4.3 3.8 + - - -
----------------------------------------------------------
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Residues in contact with HIS 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ARG* 6.1 4.3 - - - -
13D GLU* 4.1 37.9 - - + +
90D ILE* 6.3 0.7 - - - -
139D LEU 3.2 7.8 + - - +
140D LEU* 3.0 14.2 + - - +
142D VAL* 1.3 75.8 - - - +
144D ALA* 1.3 56.7 + - - +
145D ALA 3.2 2.0 - - - -
146D GLU* 2.8 54.6 + - + +
----------------------------------------------------------
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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