Contacts of the helix formed by residues 113 - 145 (chain C) in PDB entry 2VE7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 113 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PRO* 3.9 1.8 - - - -
105C GLU* 5.5 1.4 + - - -
107C ALA* 3.8 23.4 + - - +
108C ASP* 5.0 8.1 + - - +
111C CYS* 2.6 36.7 + - - +
112C PRO* 1.3 73.7 - - - +
114C ALA* 1.3 65.1 - - - +
115C LYS 3.6 0.9 - - - +
116C ARG* 4.5 22.9 - - + +
117C THR* 2.9 27.8 + - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU 4.8 4.6 - - - +
37C TYR* 4.2 22.3 - - + -
38C PRO* 3.5 28.0 + - + +
40C PRO* 3.9 14.5 - - - +
113C LYS* 1.3 75.3 - - - +
115C LYS* 1.3 64.1 + - - +
117C THR* 3.5 2.1 + - - -
118C SER* 3.1 22.6 + - - -
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 6.1 2.5 - - - +
113C LYS* 3.6 0.8 - - - +
114C ALA* 1.3 79.2 - - + +
116C ARG* 1.3 63.9 + - + +
118C SER* 3.7 6.9 + - - -
119C ARG* 3.3 23.8 + - + +
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Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASP* 2.6 50.3 + - - +
105C GLU* 4.1 14.5 + - - +
108C ASP* 2.6 39.9 + - - +
113C LYS* 3.5 24.2 + - + +
114C ALA 3.3 0.4 - - - -
115C LYS* 1.3 79.4 - - + +
117C THR* 1.3 58.9 + - - +
119C ARG* 3.1 19.8 + - - +
120C PHE* 2.9 46.3 + - + -
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 4.6 6.4 + - - +
40C PRO* 3.5 16.6 - - - +
45C LEU* 3.9 20.4 - - + +
49C TYR* 4.1 9.0 - - - +
108C ASP* 4.5 5.2 - - - +
112C PRO* 3.5 30.7 - - + -
113C LYS 2.9 25.1 + - - +
114C ALA 3.5 2.3 + - - -
116C ARG* 1.3 76.9 - - + +
118C SER* 1.3 59.4 + - - +
120C PHE* 3.7 13.1 - - + +
121C LEU* 2.8 38.0 + - - +
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR 4.1 7.3 + - - -
11C VAL* 5.0 12.4 + - - +
14C ILE* 3.6 23.5 - - - +
114C ALA 3.1 17.8 + - - -
115C LYS* 3.7 9.0 - - - -
116C ARG 3.2 0.2 - - - -
117C THR* 1.3 79.0 + - - +
119C ARG* 1.3 61.1 + - - +
121C LEU* 3.4 3.5 + - - -
122C SER* 3.1 25.5 + - - -
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.4 18.1 - - + -
8C ARG* 3.4 46.0 - - - +
101C VAL* 4.0 7.7 - - - +
102C ASN 5.0 1.4 - - - +
103C ASP* 2.3 47.0 + - - -
115C LYS* 3.3 13.3 + - + +
116C ARG* 3.1 25.8 + - - +
118C SER* 1.3 76.6 - - - +
120C PHE* 1.3 89.5 + - + +
122C SER* 3.6 3.3 + - - -
123C GLY 3.2 16.3 + - - -
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Residues in contact with PHE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR* 4.1 13.2 - - + +
96C LEU* 4.2 14.0 - - + +
101C VAL* 3.4 37.7 - - + -
103C ASP* 4.0 1.1 - - - -
104C PHE* 3.5 33.9 - + - -
108C ASP* 3.5 20.0 - - + -
116C ARG* 2.9 56.6 + - + -
117C THR* 3.3 12.1 + - + +
119C ARG* 1.3 99.2 - - - +
121C LEU* 1.3 56.5 - - - +
123C GLY* 3.1 2.9 + - - -
124C ILE* 2.9 33.4 + - - +
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.9 28.0 - - + -
18C ILE* 3.9 11.0 - - + -
22C ILE* 6.2 0.7 - - + -
36C LEU* 3.6 31.4 - - + -
45C LEU* 4.1 18.6 - - + -
48C ILE* 3.9 26.7 - - + -
49C TYR* 4.4 12.1 - - + -
117C THR 2.8 26.5 + - - +
118C SER* 3.8 6.5 - - - +
120C PHE* 1.3 76.6 - - - +
122C SER* 1.3 55.9 + - - +
124C ILE* 3.4 9.4 + - + +
125C ILE* 2.8 38.5 + - + +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.8 8.7 - - - -
7C PRO 3.5 20.0 - - - -
8C ARG* 3.9 5.9 - - - +
9C TYR* 3.1 38.3 + - - +
14C ILE* 3.9 4.5 - - - +
118C SER 3.1 17.2 + - - -
119C ARG* 4.0 1.3 - - - -
121C LEU* 1.3 72.5 - - - +
123C GLY* 1.3 59.3 + - - +
125C ILE* 4.5 1.6 - - - -
126C ASN* 2.7 40.9 + - - +
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Residues in contact with GLY 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 4.9 1.0 + - - -
6C PHE* 3.3 26.3 - - - -
99C CYS* 3.5 26.0 - - - +
101C VAL* 4.6 2.2 - - - -
119C ARG 3.2 7.9 + - - -
120C PHE 3.1 7.0 + - - -
122C SER* 1.3 77.5 - - - +
124C ILE* 1.3 61.0 + - - +
126C ASN* 3.9 1.9 - - - +
127C PHE* 3.1 17.8 + - - +
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 4.0 9.6 - - + -
48C ILE* 5.7 1.3 - - + -
49C TYR* 3.8 35.9 - - + -
52C ALA* 4.0 19.5 - - + -
95C PHE* 3.7 24.5 - - + -
96C LEU* 4.0 17.0 - - + -
99C CYS* 3.8 8.2 - - - +
120C PHE 2.9 17.4 + - - +
121C LEU* 3.7 16.4 - - + +
123C GLY* 1.3 75.8 - - - +
125C ILE* 1.3 65.5 + - - +
127C PHE* 3.1 6.9 + - - +
128C ILE* 3.0 39.0 + - + +
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Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 4.1 11.2 - - + -
14C ILE* 3.9 33.0 - - + +
17C HIS* 3.6 33.2 - - + -
18C ILE* 4.1 16.2 - - + +
21C LYS* 5.8 3.6 - - + -
22C ILE* 4.8 9.6 - - + -
121C LEU* 2.8 28.1 + - + +
122C SER* 4.0 5.4 - - - +
124C ILE* 1.3 72.1 - - + +
126C ASN* 1.3 63.8 + - - +
128C ILE* 3.0 19.4 + - + +
129C HIS* 3.1 38.5 + - + +
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Residues in contact with ASN 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 3.9 15.1 + - - +
6C PHE* 3.2 18.1 - - + +
7C PRO* 2.9 50.4 + - + +
9C TYR* 3.6 19.5 + - - -
122C SER 2.7 28.8 + - - +
123C GLY 3.9 2.7 - - - +
125C ILE* 1.3 71.0 - - - +
127C PHE* 1.3 63.4 + - - +
129C HIS* 3.2 10.6 + - - +
130C PHE* 3.1 21.1 + - - +
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Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 4.4 10.3 - - + -
229A THR* 3.9 29.6 - - + -
230A ILE* 5.0 3.1 - - + -
233A TYR* 3.8 36.2 + + + -
56C VAL* 3.7 35.2 - - + -
95C PHE* 4.1 14.4 - + - -
98C ILE* 3.4 30.1 - - + -
99C CYS* 3.7 12.1 - - - -
123C GLY 3.1 12.2 + - - +
124C ILE 3.1 9.4 + - - +
126C ASN* 1.3 76.5 - - - +
128C ILE* 1.3 66.4 + - + +
130C PHE* 3.1 3.3 + - + +
131C ARG* 2.9 38.2 + - + +
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LYS* 3.9 40.6 - - + +
22C ILE* 3.8 35.2 - - + -
52C ALA* 4.9 7.4 - - + -
55C ILE* 5.0 17.5 - - + -
56C VAL* 4.8 9.9 - - + -
124C ILE* 3.0 23.9 + - + +
125C ILE* 3.0 10.9 + - - +
127C PHE* 1.3 84.8 - - + +
129C HIS* 1.3 62.3 + - + +
131C ARG* 3.4 13.5 - - + +
132C GLU* 3.1 23.8 + - - +
----------------------------------------------------------
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Residues in contact with HIS 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 4.1 11.2 + - - -
17C HIS* 3.2 36.9 + + - -
21C LYS* 4.3 23.3 - - + +
125C ILE* 3.1 36.5 + - + +
126C ASN* 3.2 9.2 + - - +
128C ILE* 1.3 72.4 - - - +
130C PHE* 1.3 66.1 + - - +
132C GLU* 3.2 32.5 - - - +
133C ALA* 3.3 8.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 4.1 5.6 - - + -
232A CYS* 3.8 5.6 - - + -
233A TYR* 3.4 53.8 - + + -
236A PHE* 3.4 52.0 - + + -
243A PHE* 4.0 14.8 - + - -
126C ASN 3.1 13.0 + - - +
127C PHE* 3.1 7.4 + + - +
129C HIS* 1.3 76.2 - - - +
131C ARG* 1.3 66.6 + - - +
133C ALA* 3.0 20.5 + - + +
134C CYS* 3.0 33.7 + - - -
2194C IPH 5.0 4.5 - + - -
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 4.3 1.4 + - - -
217A ASP* 2.3 36.0 + - - -
219A ILE* 3.8 12.9 - - - +
222A ASN* 4.2 5.1 + - - -
225A PHE* 3.8 21.4 - - + -
226A LEU* 5.7 2.0 - - - +
229A THR* 3.6 23.1 - - + -
55C ILE* 3.4 31.4 + - - +
56C VAL* 3.6 20.3 + - - +
127C PHE* 2.9 37.1 + - + +
128C ILE* 3.4 20.9 - - - +
130C PHE* 1.3 76.9 - - - +
132C GLU* 1.3 54.9 + - - +
134C CYS* 3.0 8.9 + - - +
135C ARG* 2.6 39.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LYS* 2.8 47.4 + - - +
128C ILE* 3.1 17.4 + - - +
129C HIS* 3.2 21.3 - - - +
130C PHE 3.1 0.4 - - - -
131C ARG* 1.3 81.9 - - - +
133C ALA* 1.3 60.2 + - - +
135C ARG* 3.3 38.1 + - - +
136C GLU* 3.4 11.6 + - - +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C HIS 3.3 6.4 + - - +
130C PHE* 3.0 15.6 + - + +
132C GLU* 1.3 79.1 - - - +
134C CYS* 1.3 60.4 + - - +
135C ARG 3.5 0.2 + - - -
136C GLU* 3.5 12.6 + - - +
137C THR* 3.3 20.4 - - - +
2194C IPH 3.8 23.8 + - + +
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Residues in contact with CYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 3.7 2.5 - - + -
228A TYR* 3.9 5.3 - - + -
229A THR* 3.8 24.7 - - - +
232A CYS* 4.0 12.1 - - - -
130C PHE* 3.0 45.0 + - - +
131C ARG* 3.0 8.7 + - - +
133C ALA* 1.3 73.8 - - - +
135C ARG* 1.3 65.6 + - - +
137C THR* 3.4 2.6 + - - -
138C TYR* 3.0 26.5 + - - +
2194C IPH 3.6 24.7 - - + -
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Residues in contact with ARG 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 3.6 35.9 + - - +
219A ILE* 3.4 42.6 - - + -
225A PHE* 3.7 10.3 - - + -
131C ARG* 2.6 21.1 + - - +
132C GLU* 3.4 28.5 + - - +
133C ALA 3.2 0.2 - - - -
134C CYS* 1.3 70.5 - - - +
136C GLU* 1.3 69.2 + - - +
138C TYR* 3.3 0.7 + - - -
139C MET* 2.9 50.0 + - + +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLU 3.4 9.0 + - - +
133C ALA* 3.6 11.9 - - - +
134C CYS 3.3 0.2 - - - -
135C ARG* 1.3 80.9 - - - +
137C THR* 1.3 60.2 + - + +
139C MET* 3.7 4.9 + - - +
140C GLU* 3.1 28.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 2.8 26.5 + - - -
247A ASN* 4.3 2.2 + - - -
133C ALA 3.3 14.4 - - - +
134C CYS 3.4 1.9 + - - +
135C ARG 3.2 0.2 - - - -
136C GLU* 1.3 75.8 - - + +
138C TYR* 1.3 66.2 + - - +
140C GLU* 3.4 12.8 + - - +
141C PHE* 3.1 35.2 + - - -
2194C IPH 3.1 38.8 - - + +
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Residues in contact with TYR 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ILE* 4.0 12.6 - - + -
220A MET 2.6 25.6 + - - -
221A HIS* 3.4 15.9 + - - +
224A LEU* 4.0 18.6 - - + +
225A PHE* 3.5 44.2 - + + -
228A TYR* 4.2 6.1 - + + -
250A LEU* 4.0 29.4 - - + -
254A LEU* 5.2 2.9 - - + +
134C CYS 3.0 18.7 + - - +
135C ARG* 3.7 1.3 - - - +
137C THR* 1.3 78.5 + - - +
139C MET* 1.3 66.1 + - + +
141C PHE* 3.0 6.2 + - - +
142C LEU* 2.7 61.9 + - + +
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Residues in contact with MET 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP 4.9 0.9 - - - +
218A GLY* 3.5 31.4 - - - +
219A ILE* 4.5 9.9 - - - -
135C ARG* 2.9 48.7 + - - +
136C GLU* 3.9 5.2 - - - +
138C TYR* 1.3 87.7 - - + +
140C GLU* 1.3 64.2 + - - +
142C LEU* 3.2 9.0 + - - -
143C TRP* 2.7 56.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLU* 3.1 19.3 + - - +
137C THR* 3.6 11.9 - - - +
138C TYR 3.2 0.2 - - - -
139C MET* 1.3 75.4 - - - +
141C PHE* 1.3 62.1 + - + +
143C TRP* 3.1 16.7 + - - +
144C GLN* 3.2 35.6 + - + +
----------------------------------------------------------
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Residues in contact with PHE 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 4.1 33.7 - - + -
250A LEU* 3.8 20.6 - - + -
251A GLN* 3.3 45.3 - - + -
254A LEU* 3.5 16.1 - - + +
137C THR* 3.1 23.1 + - - -
138C TYR 3.0 7.9 + - - +
140C GLU* 1.3 78.6 - - + +
142C LEU* 1.3 56.7 + - - +
143C TRP 3.3 0.7 - - - -
144C GLN* 3.5 24.6 + - - +
145C TYR* 3.1 39.7 + + - -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A MET* 3.5 36.3 - - + +
221A HIS* 4.1 10.5 - - - +
254A LEU* 3.9 17.5 - - + +
258A PHE* 3.7 33.9 - - + -
138C TYR* 2.7 50.8 + - + +
139C MET* 3.2 14.3 + - - +
140C GLU 3.2 0.4 - - - -
141C PHE* 1.3 72.1 - - - +
143C TRP* 1.3 67.5 + - + +
144C GLN 3.5 0.2 - - - -
145C TYR* 4.8 0.4 - - - +
146C LYS* 3.3 24.3 - - + +
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Residues in contact with TRP 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLY 5.7 1.8 - - - -
220A MET* 4.8 20.4 - - + -
139C MET* 2.7 54.2 + - + +
140C GLU* 3.1 7.5 + - - +
142C LEU* 1.3 83.4 - - + +
144C GLN* 1.3 61.7 + - - +
145C TYR 3.6 0.2 - - - -
146C LYS* 3.6 41.5 - - + -
147C SER* 2.8 30.4 - - - -
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Residues in contact with GLN 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN* 5.3 1.2 + - - -
140C GLU* 3.2 38.7 + - + +
141C PHE* 3.8 29.1 - - - +
143C TRP* 1.3 81.4 - - - +
145C TYR* 1.3 67.2 + - + +
147C SER* 4.2 1.5 - - - -
148C SER* 3.1 26.3 + - - -
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Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN* 3.4 41.3 + - + +
254A LEU* 3.6 28.9 - - + -
255A LYS* 3.2 45.6 + - + -
258A PHE* 3.7 21.6 - - + -
260A VAL* 4.0 21.0 - - + +
261A ASP* 5.7 0.9 - - - -
141C PHE* 3.1 33.3 + + - +
144C GLN* 1.3 87.6 - - + +
146C LYS* 1.3 58.9 + - - +
147C SER 3.3 0.2 - - - -
148C SER* 3.2 9.2 + - - -
149C ALA* 3.1 24.9 + - - +
----------------------------------------------------------
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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