Contacts of the helix formed by residues 113 - 142 (chain C) in PDB entry 5A63
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 SER 113 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C SER* 4.4 5.8 + - - -
111C PRO 4.2 1.0 + - - -
112C ILE* 1.3 76.3 - - - +
114C ILE* 1.3 66.8 + - - +
115C ARG* 3.9 14.8 - - - -
116C GLN* 2.6 49.8 + - - +
117C MET* 3.1 12.1 + - - +
1245C PC1 4.0 19.6 + - - -
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Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 4.6 12.3 - - + -
94C LEU* 5.6 0.9 - - + -
95C LYS* 5.2 8.5 - - + +
98C ASP* 4.8 6.3 + - - +
110C SER* 5.2 0.4 + - - -
112C ILE 3.5 1.6 + - - -
113C SER* 1.3 73.2 - - - +
115C ARG* 1.3 72.5 + - + +
117C MET* 3.5 24.9 + - + -
118C ALA* 3.3 17.2 + - - +
179C PHE* 4.0 26.2 - - + -
183C GLU* 4.2 31.0 - - + +
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Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A PHE* 5.8 3.6 - - - +
113C SER* 3.0 6.9 - - - -
114C ILE* 1.3 92.9 - - + +
116C GLN* 1.3 61.0 + - - +
118C ALA* 3.8 6.6 + - - +
119C TYR* 3.6 14.0 + - - +
176C VAL* 5.5 1.7 - - - +
180C ASP* 5.8 4.5 - - - +
231C THR 5.0 2.2 - - - -
232C ALA* 3.7 38.3 + - + +
1245C PC1 2.5 67.1 + - - +
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 3.6 26.0 + - + +
111C PRO 5.0 1.4 - - - +
112C ILE* 4.2 10.7 - - + +
113C SER* 2.6 35.1 + - - +
115C ARG* 1.3 73.7 - - - +
117C MET* 1.3 67.2 + - - +
119C TYR* 2.9 16.8 + - + +
120C VAL* 3.0 18.9 + - + +
1245C PC1 3.0 70.4 + - - +
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Residues in contact with MET 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 3.4 29.6 - - + +
94C LEU* 3.6 58.3 - - + +
95C LYS* 5.2 0.2 - - - -
97C ALA* 5.8 1.8 - - - -
98C ASP* 4.0 21.5 - - + +
101C LEU* 6.3 1.1 - - - -
112C ILE* 3.1 35.4 - - + -
113C SER 3.1 4.6 + - - +
114C ILE* 3.7 27.6 - - + +
116C GLN* 1.3 77.8 - - - +
118C ALA* 1.3 56.2 + - - +
120C VAL* 3.2 1.6 + - - -
121C SER* 2.9 28.2 + - - -
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Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ILE 3.3 10.7 + - - +
115C ARG* 3.8 8.3 - - - +
116C GLN 3.2 0.2 - - - -
117C MET* 1.3 77.6 - - - +
119C TYR* 1.3 58.0 - - - +
121C SER* 3.2 4.5 + - - -
122C GLY* 2.9 26.0 + - - -
175C GLY* 3.6 16.4 - - - +
176C VAL* 4.6 5.2 - - - +
179C PHE* 3.2 49.2 - - + -
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Residues in contact with TYR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.1 28.8 - - + +
24C THR* 3.2 40.6 + - + -
25C VAL* 4.5 5.2 - - + -
115C ARG 3.6 7.2 + - - +
116C GLN* 2.9 11.1 + - + +
118C ALA* 1.3 80.2 - - - +
120C VAL* 1.3 66.3 + - + +
122C GLY* 3.2 2.9 + - - -
123C LEU* 2.9 34.7 + - + +
172C THR* 3.6 27.1 - - + +
176C VAL* 4.0 13.6 - - + +
1245C PC1 3.1 68.4 - - + +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL* 4.3 11.0 - - + -
31C ARG* 3.2 42.2 - - + +
34C ILE* 2.8 45.5 - - + -
35C LEU* 3.6 12.6 - - + +
116C GLN* 3.0 20.3 + - + +
119C TYR* 1.3 86.5 - - + +
121C SER* 1.3 55.5 + - - +
123C LEU* 3.2 6.7 + - - +
124C SER* 2.9 26.5 + - - -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 4.2 0.4 - - - +
38C GLY* 5.2 0.4 - - - -
87C ARG* 4.7 5.2 + - - +
90C TYR* 3.1 43.8 - - - -
117C MET 2.9 10.9 + - - -
118C ALA 3.3 9.4 - - - -
120C VAL* 1.3 77.7 - - - +
122C GLY* 1.3 56.6 + - - +
124C SER* 3.2 9.2 + - - -
125C PHE* 2.9 39.7 + - - -
179C PHE* 3.7 17.0 - - - -
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 3.7 8.7 - - - -
118C ALA 2.9 13.6 + - - -
119C TYR 3.2 2.4 + - - -
121C SER* 1.3 75.9 + - - +
123C LEU* 1.3 56.8 - - - +
125C PHE* 3.2 1.7 + - - +
126C GLY 2.9 24.1 + - - -
171C HIS* 3.4 28.5 - - - +
172C THR* 3.4 16.8 + - - -
175C GLY* 4.3 2.0 - - - -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ALA* 4.4 1.1 - - - -
20C LEU* 3.5 42.8 - - + -
21C PHE* 3.9 10.3 - - - +
25C VAL* 3.7 23.3 - - + -
35C LEU* 4.2 6.1 - - + -
119C TYR* 2.9 19.7 + - + +
120C VAL* 3.5 11.9 - - - +
122C GLY* 1.3 76.9 - - - +
124C SER* 1.3 57.2 + - - +
126C GLY* 3.2 1.6 + - - -
127C ILE* 2.9 65.8 + - + +
168C ILE* 4.2 11.9 - - + -
172C THR* 3.2 17.6 + - - +
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 2.5 47.0 + - - +
38C GLY* 3.0 6.1 - - - -
39C ALA* 2.5 23.0 + - - +
120C VAL 2.9 13.2 + - - -
121C SER* 3.2 11.2 - - - -
123C LEU* 1.3 77.3 - - - +
125C PHE* 1.3 62.6 + - - -
127C ILE* 3.2 5.7 + - - +
128C ILE* 3.2 26.0 + - - +
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLY* 3.3 33.2 - - - -
41C PHE* 4.5 4.9 - - + -
42C TRP* 3.7 34.1 - + + -
83C GLN* 3.6 23.8 - - + -
86C PHE* 4.5 4.0 - - + -
87C ARG* 3.4 58.3 - - + +
90C TYR* 5.2 2.2 - - + -
121C SER* 2.9 24.8 + - - +
122C GLY 3.5 2.7 - - - +
124C SER* 1.3 76.5 + - - +
126C GLY* 1.3 62.8 + - - +
128C ILE* 3.7 5.1 - - - +
129C SER* 3.2 28.8 + - - -
171C HIS* 3.5 18.1 + + - +
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Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLY 2.9 11.2 + - - -
123C LEU 3.6 3.6 - - - -
125C PHE* 1.3 76.6 - - - +
127C ILE* 1.3 56.8 + - - +
129C SER* 4.1 0.3 - - - -
130C GLY 2.9 25.5 + - - -
167C ILE* 5.0 0.3 - - - +
168C ILE* 3.0 35.2 + - - +
171C HIS* 3.4 20.1 - - - +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1468B PC1 4.6 20.6 - - + -
14C PHE* 4.4 5.0 - - + -
17C ALA* 3.7 26.0 - - + +
21C PHE* 5.5 5.2 - - + -
35C LEU* 4.8 13.7 - - + -
39C ALA* 5.9 2.7 - - + -
123C LEU* 2.9 59.5 + - + +
124C SER* 3.2 9.4 + - - +
126C GLY* 1.3 77.0 - - - +
128C ILE* 1.3 66.2 + - + +
130C GLY* 4.0 0.7 - - - -
131C VAL* 3.1 29.7 + - + +
168C ILE* 4.2 4.7 - - + -
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 3.7 28.9 - - + -
412B VAL* 4.3 16.4 - - + -
1468B PC1 5.9 2.5 - - + -
39C ALA* 4.0 16.6 - - + +
42C TRP* 3.3 50.7 - - + -
43C LEU* 4.1 11.0 - - + -
124C SER 3.2 17.4 + - - +
125C PHE 3.7 2.2 - - - +
127C ILE* 1.3 80.8 - - + +
129C SER* 1.3 62.2 + - - +
131C VAL* 3.2 6.8 + - + +
132C PHE* 2.9 41.4 + - + -
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ILE* 3.3 27.5 - - - +
42C TRP* 3.4 25.6 + - - -
83C GLN* 4.1 0.2 + - - -
125C PHE 3.2 15.8 + - - -
126C GLY 4.1 1.6 - - - -
128C ILE* 1.3 81.8 - - - +
130C GLY* 1.3 57.1 + - - +
132C PHE* 3.2 4.2 + - - +
133C SER* 2.9 28.3 + - - -
167C ILE* 4.0 10.4 - - - +
171C HIS* 3.9 17.5 + - - -
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Residues in contact with GLY 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 3.8 2.5 - - - -
126C GLY 2.9 19.3 + - - -
127C ILE 4.0 0.7 - - - -
129C SER* 1.3 78.3 - - - +
131C VAL* 1.3 56.4 + - - +
133C SER* 3.2 7.2 + - - -
134C VAL* 2.9 25.6 + - - +
164C THR* 3.4 31.6 - - - +
167C ILE* 4.8 4.0 - - - +
168C ILE* 4.1 5.6 - - - -
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 3.3 35.7 - - + -
1468B PC1 3.9 27.8 - - + -
14C PHE* 3.6 25.7 - - + -
127C ILE* 3.1 20.1 + - + +
128C ILE* 3.2 11.4 + - + +
130C GLY* 1.3 75.7 - - - +
132C PHE* 1.3 71.7 + - + +
135C ILE* 2.8 43.8 + - + +
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ASN* 3.1 60.5 + - + +
408B ILE* 4.4 6.3 - - + -
409B ALA* 4.3 4.0 - - + -
449B THR* 4.9 1.3 - - + -
453B VAL* 3.8 14.8 - - + -
457B MET* 3.8 22.2 - - + +
461B ALA* 5.8 2.4 - - - +
42C TRP* 3.6 12.8 - + + -
43C LEU* 3.3 30.3 - - + -
46C LEU* 3.4 31.0 - - + -
128C ILE* 2.9 28.8 + - + +
129C SER 3.2 8.2 + - - +
131C VAL* 1.3 85.2 - - + +
133C SER* 1.3 61.8 + - - +
136C ASN* 4.0 8.7 + - - +
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Residues in contact with SER 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B MET* 4.7 5.7 - - - +
461B ALA* 4.9 8.0 - - - +
466B TYR* 3.0 41.4 + - - -
467B ILE* 6.2 2.2 - - - -
129C SER 2.9 12.7 + - - -
130C GLY* 3.2 10.5 + - - -
132C PHE* 1.3 79.8 - - - +
134C VAL* 1.3 58.2 + - - +
136C ASN* 5.8 0.5 - - - +
137C ILE* 4.1 19.8 - - - +
164C THR* 2.5 26.3 + - - -
167C ILE* 6.4 0.9 - - - -
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 4.2 4.5 - - + -
14C PHE* 3.4 31.4 - - + -
130C GLY 2.9 8.8 + - - +
133C SER* 1.3 79.3 - - - +
135C ILE* 1.3 55.9 + - - +
136C ASN 2.8 2.6 + - - -
137C ILE* 2.7 17.7 + - + -
138C LEU* 2.7 53.7 + - + -
157C PHE 5.7 0.4 - - - +
160C SER* 4.0 18.6 - - - +
161C ALA* 4.1 11.9 - - - +
164C THR* 3.0 28.9 - - + +
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Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B TRP* 3.6 29.2 - - + +
405B ASN* 4.2 4.5 - - - +
408B ILE* 4.1 10.8 - - + -
1468B PC1 3.4 58.2 - - + +
14C PHE* 4.2 17.5 - - + -
131C VAL* 2.8 42.5 + - + +
134C VAL* 1.3 74.1 - - - +
136C ASN* 1.3 75.3 + - - +
138C LEU* 3.9 7.4 - - + +
139C ALA* 3.5 17.0 + - - +
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Residues in contact with ASN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.8 17.4 + - - +
402B GLY* 2.8 24.1 - - - +
403B ASP* 3.7 8.7 - - - +
404B TRP* 3.3 9.5 + - - -
405B ASN* 3.0 41.0 + - - +
461B ALA* 6.2 1.8 - - + -
132C PHE 4.0 6.8 + - - +
133C SER 5.8 0.4 - - - +
134C VAL 2.8 5.4 + - - -
135C ILE* 1.3 86.0 - - - +
137C ILE* 1.3 63.3 + - + +
138C LEU 3.3 0.7 - - - -
139C ALA* 3.2 14.7 - - - +
140C ASP* 3.0 19.1 - - - +
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 6.0 1.6 - - + -
36A VAL* 3.4 28.0 - - + +
461B ALA* 4.3 25.1 - - + +
466B TYR* 5.9 1.1 - - + -
133C SER 4.1 13.2 - - - +
134C VAL* 2.7 17.7 + - + +
136C ASN* 1.3 77.2 - - + +
138C LEU* 1.3 64.6 + - - +
139C ALA 3.2 0.7 - - - -
140C ASP* 3.7 8.5 + - - -
141C ALA 3.6 1.9 + - - -
156C TYR* 3.8 22.7 - - + +
157C PHE* 3.1 30.9 - - + -
160C SER* 3.0 36.6 - - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1468B PC1 5.3 1.6 - - + +
6C PHE* 3.3 39.5 - - + +
9C CYS* 3.5 34.5 - - + +
10C THR* 3.1 37.0 - - - +
14C PHE* 3.8 7.6 - - + -
134C VAL* 2.7 47.7 + - + +
135C ILE* 3.9 15.5 - - + +
137C ILE* 1.3 73.0 - - - +
139C ALA* 1.3 63.5 + - - +
141C ALA* 3.3 13.2 + - + +
142C LEU 3.6 1.4 + - - -
157C PHE* 6.0 0.7 - - + +
161C ALA* 5.2 0.2 - - + -
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 4.2 8.5 - - - +
37A GLU* 5.0 0.3 - - - +
403B ASP* 4.5 4.9 - - - +
404B TRP* 4.9 0.7 - - + -
1468B PC1 3.6 47.9 + - - +
135C ILE 3.5 10.0 + - - +
136C ASN* 3.2 16.8 + - - +
138C LEU* 1.3 79.1 - - - +
140C ASP* 1.3 60.3 + - - +
142C LEU* 3.4 19.3 + - - +
143C GLY 4.4 1.4 + - - -
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.0 29.8 - - - +
36A VAL* 3.0 27.8 - - + +
37A GLU* 2.7 50.9 + - - +
40A ILE* 3.8 11.5 - - + +
41A TYR* 4.4 1.4 + - - -
136C ASN 3.0 17.1 + - - +
137C ILE* 3.7 2.9 + - - +
138C LEU 3.3 0.4 - - - -
139C ALA* 1.3 72.6 - - - +
141C ALA* 1.3 63.9 + - - +
142C LEU 3.2 2.7 + - - -
143C GLY* 3.4 12.0 + - - -
145C GLY 4.3 2.4 - - - +
157C PHE* 3.6 6.9 - - + -
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLY* 2.8 23.1 - - - +
5C VAL* 4.5 8.6 - - + +
6C PHE* 4.2 17.4 + - - +
9C CYS* 4.9 4.3 - - + -
137C ILE 3.6 1.5 + - - +
138C LEU* 3.3 13.9 + - + +
139C ALA 3.3 0.4 - - - -
140C ASP* 1.3 77.4 - - - +
142C LEU* 1.3 55.6 + - - +
143C GLY 3.2 8.9 - - - +
145C GLY 5.0 0.3 - - - +
157C PHE* 3.3 43.9 - - + -
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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
----------------------------------------------------------
1468B PC1 3.3 65.3 - - + +
2C GLY* 3.4 15.2 - - - -
3C ALA* 3.8 19.4 + - + +
6C PHE* 3.4 41.3 - - + -
7C PHE* 5.5 1.8 - - + -
138C LEU 3.6 1.0 + - - +
139C ALA 3.4 13.1 + - - +
140C ASP 3.2 1.4 - - - -
141C ALA* 1.3 77.8 - - - +
143C GLY* 1.3 59.0 + - - +
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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