Contacts of the helix formed by residues 108 - 136 (chain C) in PDB entry 2VD0
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 108 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU* 3.1 25.2 + - - +
107C LYS* 1.3 76.0 - - + +
109C GLN* 1.3 66.5 + - - +
110C ASP* 3.4 5.6 - - - +
111C VAL* 3.1 27.7 + - + +
112C LYS* 3.0 18.2 + - - +
115D MET* 6.2 1.8 - - - +
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU 5.2 4.2 + - - -
107C LYS 3.1 16.8 + - - +
108C LYS* 1.3 69.7 - - - +
110C ASP* 1.3 54.0 + - - +
112C LYS* 3.1 21.9 + - - +
113C GLU* 2.7 57.0 + - - +
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LYS* 4.8 3.2 - - - +
109C GLN* 1.3 79.5 + - - +
111C VAL* 1.3 72.3 + - - +
113C GLU* 3.6 18.4 + - - +
114C GLN* 3.3 25.8 + - - +
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PRO* 4.8 0.9 - - - +
106C GLU* 4.0 19.3 - - - +
108C LYS* 3.1 37.1 + - + +
110C ASP* 1.3 90.0 - - - +
112C LYS* 1.3 63.9 + - - +
114C GLN* 4.6 1.9 - - - +
115C MET* 3.2 26.6 + - + +
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PRO* 2.9 25.1 + - - +
104C TRP* 2.8 33.3 + - - +
106C GLU* 3.4 30.7 + - + +
108C LYS 3.0 12.5 + - - +
109C GLN* 3.2 28.0 - - - +
111C VAL* 1.3 74.4 - - - +
113C GLU* 1.3 68.9 + - + +
114C GLN 3.3 0.2 + - - -
115C MET* 3.4 1.9 + - - +
116C PHE* 3.2 50.0 + - + -
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Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLN* 2.7 53.1 + - - +
110C ASP* 3.6 14.1 + - - +
112C LYS* 1.3 76.8 - - + +
114C GLN* 1.3 64.3 + - - +
116C PHE* 3.7 5.1 + - - +
117C ASN* 3.4 25.5 + - - +
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Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP 3.3 16.3 + - - +
111C VAL* 4.6 2.0 - - - +
112C LYS 3.3 0.8 - - - -
113C GLU* 1.3 80.8 - - - +
115C MET* 1.3 64.9 + - - +
117C ASN* 3.1 21.9 + - - +
118C GLU* 2.8 51.3 + - - +
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Residues in contact with MET 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C CYS* 4.5 8.1 - - + +
103C PRO* 3.8 28.7 - - + -
111C VAL* 3.2 22.3 + - + +
114C GLN* 1.3 76.0 - - - +
116C PHE* 1.3 62.2 + - - +
118C GLU* 3.2 21.5 + - + +
119C LEU* 3.1 51.9 + - + +
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Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 3.5 33.7 - + + -
103C PRO* 3.7 26.0 - - + -
104C TRP* 4.0 28.0 - + - -
112C LYS* 3.2 52.7 + - + +
113C GLU* 3.8 7.2 - - - +
115C MET* 1.3 76.9 - - - +
117C ASN* 1.3 66.0 + - - +
119C LEU* 3.4 2.1 + - - +
120C LEU* 3.0 34.5 + - + +
163C PHE* 3.8 43.7 - + + -
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Residues in contact with ASN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLU 3.4 13.8 + - - +
114C GLN* 3.1 26.9 + - - +
116C PHE* 1.3 76.4 - - - +
118C GLU* 1.3 65.6 + - - +
120C LEU* 4.7 5.4 - - - +
121C THR* 2.9 39.0 + - - +
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLN* 2.8 64.5 + - - +
115C MET* 3.2 24.3 + - + +
117C ASN* 1.3 76.1 - - - +
119C LEU* 1.3 58.3 + - + +
121C THR* 3.9 0.6 - - - -
122C TYR* 2.9 40.3 + - + +
123C ASN* 4.4 1.8 - - - +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.6 9.7 - - + -
101C CYS* 3.7 25.6 - - + +
102C PHE* 3.6 59.7 - - + +
103C PRO* 4.2 3.1 - - + -
115C MET* 3.1 37.9 + - + +
116C PHE 3.8 2.7 - - - +
118C GLU* 1.3 75.0 - - + +
120C LEU* 1.3 58.0 + - - +
123C ASN* 3.0 31.9 + - - +
124C ALA 2.9 25.8 + - - -
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 3.7 24.7 - - + -
116C PHE* 3.0 28.5 + - + +
117C ASN* 4.1 6.1 - - - +
119C LEU* 1.3 75.9 - - - +
121C THR* 1.3 63.1 + - - +
124C ALA* 3.4 8.1 - - + +
125C PRO* 3.3 19.8 - - - +
160C LEU* 4.3 17.3 - - + +
163C PHE* 3.4 44.6 - - + +
164C LYS* 3.3 39.8 - - + +
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Residues in contact with THR 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASN* 2.9 25.7 + - - +
118C GLU* 4.6 0.7 - - - -
120C LEU* 1.3 80.3 - - - +
122C TYR* 1.3 60.1 + - - +
125C PRO* 4.0 11.9 - - - +
164C LYS* 4.8 11.8 + - - +
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Residues in contact with TYR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU* 2.9 21.4 + - + +
121C THR* 1.3 82.3 - - - +
123C ASN* 1.3 75.7 + - - +
125C PRO* 3.8 6.1 - - - +
126C HIS* 3.3 35.3 + + - -
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Residues in contact with ASN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.5 19.9 - - + -
101C CYS* 5.7 3.2 - - - -
118C GLU* 3.9 6.2 - - - +
119C LEU* 3.0 29.3 + - - +
122C TYR* 1.3 96.1 - - - +
124C ALA* 1.3 67.1 + - - +
126C HIS* 3.2 9.5 + - - +
127C LEU* 3.2 19.8 + - - +
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.7 27.3 - - + -
119C LEU 2.9 6.9 + - - +
120C LEU* 3.4 24.7 - - + +
123C ASN* 1.3 74.3 - - - +
125C PRO* 1.4 64.1 - - + +
127C LEU* 3.1 6.6 + - - +
128C MET* 3.0 29.2 + - + +
160C LEU* 5.4 0.4 - - + -
164C LYS* 4.5 1.1 - - + -
167C LEU* 3.9 20.9 - - + -
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Residues in contact with PRO 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LEU 3.3 18.4 - - - +
121C THR 4.0 11.7 - - - +
122C TYR 3.8 11.4 - - - +
123C ASN 3.6 3.6 - - - -
124C ALA* 1.4 88.9 - - + +
126C HIS* 1.3 57.9 + - + +
128C MET* 3.3 8.7 + - + +
129C GLN* 3.0 30.6 + - - +
164C LYS* 4.3 14.6 - - - +
167C LEU* 5.7 0.4 - - + -
171C HIS* 4.7 2.8 + - - +
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Residues in contact with HIS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 3.3 33.5 + + - +
123C ASN* 3.2 10.0 + - - +
125C PRO* 1.3 78.8 - - + +
127C LEU* 1.3 60.4 + - - +
129C GLN* 3.5 7.2 + - + +
130C ASP* 3.0 39.1 + - - +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C THR* 3.7 32.3 - - + +
95C LEU* 4.7 11.2 - - + -
98C PHE* 3.6 40.8 - - + -
123C ASN 3.2 11.2 + - - +
124C ALA* 3.1 10.4 + - - +
126C HIS* 1.3 75.4 - - - +
128C MET* 1.3 72.8 + - + +
130C ASP* 3.2 4.7 + - - +
131C LEU* 2.8 54.5 + - + +
160C LEU* 5.0 2.0 - - + -
48D PHE* 4.6 7.2 - - + -
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Residues in contact with MET 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA* 3.0 22.8 + - - +
125C PRO* 3.6 8.7 - - + +
127C LEU* 1.3 102.0 - - + +
129C GLN* 1.3 58.2 + - - +
131C LEU* 3.4 1.3 + - + -
132C ASP* 3.0 31.2 + - - +
153C TRP* 3.6 37.9 - - + -
160C LEU* 4.3 15.7 - - + -
167C LEU* 3.7 39.9 - - + +
168C LEU* 3.8 3.8 - - + -
171C HIS* 3.6 22.0 - - + +
174C LEU* 3.4 7.7 - - + +
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Residues in contact with GLN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PRO 3.0 16.8 + - - +
126C HIS* 3.8 7.6 - - + +
128C MET* 1.3 76.1 - - - +
130C ASP* 1.3 58.9 + - - +
132C ASP* 3.4 6.0 + - - +
133C THR* 2.9 48.7 + - - +
171C HIS* 3.2 26.1 + - + +
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C HIS* 3.0 25.7 + - - +
127C LEU* 3.7 4.9 - - - +
129C GLN* 1.3 78.3 - - - +
131C LEU* 1.3 57.5 + - - +
133C THR* 3.3 6.4 + - - -
134C TYR* 2.7 31.0 + - - +
46D LEU 5.4 1.1 - - - +
47D PRO 3.6 15.1 - - - +
48D PHE* 3.4 46.8 - - + +
49D GLY 4.4 0.2 + - - -
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ILE* 4.5 16.2 - - + -
94C THR* 5.5 1.8 - - + -
95C LEU* 4.2 17.9 - - + -
127C LEU* 2.8 56.7 + - + +
128C MET* 3.9 4.5 - - + +
130C ASP* 1.3 72.1 - - - +
132C ASP* 1.3 53.7 + - - +
134C TYR* 3.5 4.1 - - + +
135C LEU* 2.6 37.1 + - - +
141C LEU* 4.5 22.1 - - + +
153C TRP* 4.3 22.0 - - + -
174C LEU* 4.1 15.5 - - + -
48D PHE* 3.9 19.4 - - + -
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C MET 3.0 17.8 + - - +
129C GLN* 3.6 9.7 - - - +
131C LEU* 1.3 72.0 - - - +
133C THR* 1.3 57.9 + - - +
135C LEU* 3.8 1.2 - - - +
136C GLY 2.9 16.6 + - - -
170C ASN 4.5 1.2 - - - +
171C HIS* 2.8 37.5 + - + +
172C PRO* 5.0 1.2 - - - +
173C ARG* 2.6 71.4 + - - +
174C LEU* 3.9 19.0 - - + +
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Residues in contact with THR 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLN* 2.9 33.8 + - - -
130C ASP* 3.7 6.7 + - - -
132C ASP* 1.3 76.0 - - - +
134C TYR* 1.3 64.5 + - - +
136C GLY* 3.1 13.3 + - - -
173C ARG* 4.2 6.1 - - - +
47D PRO 6.2 0.2 - - - +
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Residues in contact with TYR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 4.3 17.5 + + - +
91C ILE* 3.6 33.6 - - + +
130C ASP 2.7 21.7 + - - +
131C LEU* 3.5 4.7 - - + +
133C THR* 1.3 77.3 - - - +
135C LEU* 1.3 54.2 + - - +
138C ARG* 2.5 58.9 + - - -
141C LEU* 3.5 26.1 + - + -
142C ILE* 4.2 8.0 - - - +
47D PRO* 5.3 8.1 - - + +
48D PHE* 3.6 26.7 - + + -
62D HIS* 5.0 6.0 + + - -
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU 2.6 21.0 + - - +
132C ASP 3.8 4.3 - - - +
134C TYR* 1.3 76.2 - - - +
136C GLY* 1.3 74.3 + - - +
137C GLY 3.3 0.2 + - - -
138C ARG* 3.0 47.5 + - - +
139C GLU 4.7 1.6 - - - +
140C TRP* 4.0 28.9 - - - +
141C LEU* 4.1 15.0 - - + +
173C ARG* 3.5 34.3 - - + +
174C LEU* 3.8 17.9 - - + -
177C LEU* 4.1 15.9 - - + -
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Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP 2.9 17.0 + - - -
133C THR 3.1 10.9 + - - -
134C TYR 4.6 0.2 - - - -
135C LEU* 1.3 83.2 - - - +
137C GLY* 1.3 60.0 + - - -
138C ARG 3.3 3.6 + - - +
173C ARG* 3.5 35.4 + - - +
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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