Contacts of the helix formed by residues 113 - 147 (chain A) in PDB entry 3V2W
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 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.8 27.6 - - + +
21A ASN 4.6 0.9 - - - -
22A TYR* 3.5 36.6 - - + +
25A ILE* 4.1 1.6 - - - -
112A LEU* 1.3 73.9 - - - +
114A PRO* 1.4 76.6 - - + +
115A ALA* 4.2 1.2 - - - +
116A GLN* 3.0 38.2 + - - +
117A TRP* 2.9 20.3 + - - +
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Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR 3.4 24.2 - - - +
20A VAL* 3.5 7.9 - - + -
21A ASN 3.0 37.9 - - - +
24A ILE* 3.8 21.3 - - + -
25A ILE* 3.7 15.2 - - + -
113A THR* 1.4 76.7 - - - +
115A ALA* 1.4 54.8 + - - +
117A TRP* 3.2 3.5 + - - +
118A PHE* 2.9 42.8 + - + -
185A ILE* 4.8 2.0 - - + -
197A LEU* 3.9 13.9 - - + -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.7 29.6 - - + +
113A THR* 3.2 2.6 - - - +
114A PRO* 1.4 76.1 - - - +
116A GLN* 1.4 59.1 + - + +
118A PHE* 3.3 10.5 + - - +
119A LEU* 3.0 32.3 + - - +
179A ILE* 5.0 9.4 - - + +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 4.5 4.6 + - - -
104A LEU* 6.1 0.2 - - - +
111A LYS 4.1 3.8 - - - +
112A LEU* 3.5 28.0 - - + +
113A THR* 3.0 45.6 + - - +
115A ALA* 1.4 78.4 - - + +
117A TRP* 1.4 52.0 + - - +
119A LEU* 3.3 11.8 + - + +
120A ARG* 2.7 35.0 + - - +
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Residues in contact with TRP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.9 25.4 - - + -
29A TYR* 2.8 38.4 + + - -
109A THR* 4.3 9.6 - - + -
112A LEU* 4.6 7.1 - - + +
113A THR 2.9 12.2 + - - +
114A PRO* 3.2 10.1 - - + +
116A GLN* 1.4 70.8 - - - +
118A PHE* 1.4 61.8 + + - +
119A LEU 3.0 4.3 - - - -
120A ARG* 2.9 44.8 + - - +
121A GLU* 3.0 31.0 + - + -
195A LEU* 3.9 12.6 - - + -
196A PRO* 3.9 13.7 - - + -
197A LEU* 3.7 31.2 - - + -
198A TYR* 3.2 37.9 - + - -
1201A ML5 4.1 2.9 - - - -
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO* 2.9 35.7 + - + +
115A ALA* 3.8 7.0 - - - +
117A TRP* 1.4 75.7 - + - +
119A LEU* 1.3 56.3 + - - +
122A GLY* 3.1 23.8 + - - -
178A PRO* 3.9 16.8 - - + -
179A ILE* 3.4 33.3 - - + +
183A ASN* 3.2 40.2 - - + -
185A ILE* 3.7 17.9 - - + -
197A LEU* 3.5 43.1 - - + -
198A TYR* 3.8 21.0 + + - -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ALA 3.0 17.9 + - - +
116A GLN* 3.4 11.7 - - + +
118A PHE* 1.3 76.8 - - - +
120A ARG* 1.4 62.8 + - - +
121A GLU 3.3 0.4 - - - -
122A GLY* 4.0 0.9 - - - +
123A SER* 3.5 24.5 + - - -
179A ILE* 4.5 12.8 - - + -
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.3 2.2 + - - -
97A ALA 4.6 4.3 - - - +
100A ALA* 5.3 0.7 - - + -
101A ASN* 4.1 24.1 + - - +
104A LEU* 2.5 62.5 + - + -
105A SER* 3.6 8.8 + - - +
109A THR* 3.2 23.8 + - - +
112A LEU* 3.7 11.1 - - + +
116A GLN 2.7 17.6 + - - +
117A TRP* 2.9 38.7 + - - +
119A LEU* 1.4 76.4 - - - +
121A GLU* 1.4 74.4 + - - +
123A SER* 3.3 13.7 + - - -
124A MET* 4.3 4.3 - - - +
1201A ML5 3.0 28.7 + - - -
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASN* 2.9 24.7 + - - -
117A TRP* 3.0 45.4 + - + +
120A ARG* 1.4 98.3 + - - +
122A GLY* 1.3 65.4 + - - +
123A SER 3.2 2.7 - - - -
124A MET* 3.1 16.3 + - - +
125A PHE* 3.3 16.0 - - + -
195A LEU* 4.6 8.7 - - + +
198A TYR* 3.7 13.5 - - + +
1201A ML5 2.7 44.9 + - - +
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE 3.1 22.8 + - - -
119A LEU 4.4 0.4 - - - -
120A ARG 3.7 0.4 - - - -
121A GLU* 1.3 77.7 - - - +
123A SER* 1.3 55.6 + - - +
125A PHE* 3.4 5.0 + - - +
126A VAL* 3.1 36.2 + - - +
175A GLY 3.9 11.7 - - - +
179A ILE* 4.8 4.9 - - - -
198A TYR* 3.4 12.7 + - - -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA* 3.4 28.7 + - - +
119A LEU* 3.5 16.4 + - - -
120A ARG* 3.3 17.8 + - - -
122A GLY* 1.3 77.0 - - - +
124A MET* 1.4 57.2 + - - +
126A VAL* 3.8 8.0 + - - +
127A ALA* 3.2 26.2 + - - +
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Residues in contact with MET 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 4.3 11.4 - - + +
97A ALA* 3.8 36.6 - - - +
98A TYR* 3.8 25.4 - - + -
101A ASN* 4.9 2.5 - - - +
120A ARG 4.3 11.4 - - - +
121A GLU* 3.1 12.5 + - - +
123A SER* 1.4 75.7 + - - +
125A PHE* 1.4 53.8 + - - +
127A ALA* 3.3 5.5 + - - +
128A LEU* 2.8 32.6 + - - +
269A TRP* 5.3 2.9 - - + -
301A VAL* 4.1 6.7 - - + -
1201A ML5 3.6 59.0 - - + +
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU 3.3 16.8 - - - -
122A GLY* 3.4 7.8 + - - +
124A MET* 1.4 73.1 - - - +
126A VAL* 1.4 55.5 + - - +
128A LEU* 3.6 6.6 - - - +
129A SER* 2.8 36.1 + - - -
175A GLY* 4.0 15.7 - - - -
195A LEU* 3.7 22.7 - - + -
198A TYR* 3.6 27.6 - + - -
202A TYR* 3.6 30.1 - + - -
203A ILE* 4.9 7.4 - - + -
206A CYS* 4.2 9.4 - - + -
210A PHE* 4.7 6.0 - + + -
276A LEU* 6.2 0.9 - - + -
1201A ML5 3.4 56.1 - + + -
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLY 3.1 20.2 + - - +
123A SER* 4.0 7.6 - - - +
125A PHE* 1.4 74.9 - - - +
127A ALA* 1.4 56.8 + - - +
129A SER* 4.4 0.2 - - - -
130A ALA* 3.1 30.3 + - - +
168A TRP* 4.1 17.3 - - + -
171A SER* 3.8 33.7 - - - +
172A LEU* 4.1 31.0 - - + +
175A GLY* 3.9 12.6 - - - -
176A GLY 4.7 0.2 - - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 3.8 23.7 - - - +
93A LEU* 4.8 3.8 - - + -
94A ALA* 3.8 24.5 - - + +
123A SER 3.2 20.6 + - - +
124A MET* 3.3 8.3 + - + +
126A VAL* 1.4 75.4 - - - +
128A LEU* 1.4 54.3 + - - +
130A ALA* 4.8 2.7 - - - -
131A SER* 2.7 32.7 + - - -
168A TRP* 5.1 5.2 - - - -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A MET 2.8 17.2 + - - +
125A PHE* 3.3 5.4 + - - +
126A VAL 3.3 0.2 - - - -
127A ALA* 1.4 75.1 - - - +
129A SER* 1.4 65.8 + - - +
131A SER* 3.0 6.5 + - - -
132A VAL* 3.0 29.8 + - + +
210A PHE* 3.8 19.3 - - + -
265A PHE* 3.8 19.7 - - + -
269A TRP* 3.6 45.1 - - + -
273A PHE* 4.2 5.8 - - + -
1201A ML5 3.5 42.6 - - + -
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A PHE 2.8 21.8 + - - -
128A LEU* 1.4 72.3 - - - +
130A ALA* 1.4 60.8 + - - +
132A VAL* 3.3 2.1 + - - +
133A PHE* 3.0 48.7 + - - -
171A SER* 3.3 30.1 - - - -
174A LEU* 3.7 12.9 - - - +
210A PHE* 3.6 21.7 - - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 3.3 18.8 - - - +
126A VAL 3.1 18.9 + - - +
127A ALA 4.3 0.7 - - - +
129A SER* 1.4 74.9 - - - +
131A SER* 1.4 52.8 + - - +
133A PHE 3.5 0.9 + - - -
134A SER* 2.7 36.2 + - - -
167A CYS* 3.7 11.7 - - - -
168A TRP* 3.7 28.3 - - + -
171A SER* 3.1 13.8 + - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.4 7.1 - - - +
90A SER* 3.4 12.5 + - - -
91A ASP* 3.1 24.9 + - - -
127A ALA 2.7 19.7 + - - -
128A LEU* 3.0 11.6 + - - -
130A ALA* 1.4 77.1 - - - +
132A VAL* 1.4 60.3 + - - +
134A SER* 3.3 7.7 + - - -
135A LEU* 3.2 27.5 + - - +
265A PHE* 4.1 18.6 - - - -
269A TRP* 6.5 0.2 - - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.0 24.2 + - + +
129A SER 3.3 6.7 + - - +
131A SER* 1.4 73.4 - - - +
133A PHE* 1.4 61.7 + - + +
135A LEU* 3.2 14.1 + - - +
136A LEU* 3.1 20.1 + - + +
210A PHE* 3.8 29.4 - - + +
213A LEU* 3.8 38.6 - - + -
214A LEU* 4.5 12.8 - - + -
217A ILE* 5.4 2.5 - - + +
265A PHE* 3.7 23.8 - - + -
273A PHE* 5.8 0.2 - - + -
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A SER* 3.0 45.3 + - - -
132A VAL* 1.4 72.0 - - - +
134A SER* 1.4 59.5 + - - +
136A LEU* 3.4 29.2 - - + +
137A ALA* 3.0 28.4 + - - +
167A CYS* 3.6 27.1 - - + -
170A ILE* 4.0 31.4 - - + -
171A SER* 4.3 6.7 - - - -
174A LEU* 4.3 10.5 - - + -
209A VAL* 5.6 2.7 - - + -
210A PHE* 5.0 3.4 - + - -
213A LEU* 3.6 30.7 - - + -
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 4.1 5.5 - - - +
86A ASN* 3.5 22.1 + - - +
87A LEU* 3.6 34.2 - - - -
90A SER* 3.9 1.0 + - - -
130A ALA 2.7 20.8 + - - -
131A SER 3.3 11.4 - - - -
132A VAL 3.1 0.4 - - - -
133A PHE* 1.4 74.1 - - - +
135A LEU* 1.4 57.8 + - - +
137A ALA* 3.2 8.1 + - - +
138A ILE* 2.9 36.3 + - - +
167A CYS* 5.3 0.2 - - - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.7 20.8 - - + +
131A SER 3.2 14.3 + - - +
132A VAL* 3.2 7.5 + - - +
134A SER* 1.4 73.6 - - - +
136A LEU* 1.4 54.2 - - - +
138A ILE* 3.2 10.0 + - + +
139A ALA* 2.8 36.8 + - - +
214A LEU* 4.4 4.3 - - + -
217A ILE* 4.6 7.2 - - + -
221A TYR* 3.8 7.7 + - - +
258A VAL 5.3 1.1 - - - +
261A VAL* 4.2 18.8 - - + +
262A LEU* 3.8 34.1 - - + +
265A PHE* 3.7 44.4 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.1 13.0 + - + +
133A PHE* 3.4 36.8 - - + +
135A LEU* 1.4 73.8 - - - +
137A ALA* 1.4 53.3 + - - +
139A ALA* 3.3 2.0 + - - +
140A ILE* 2.8 48.1 + - + +
213A LEU* 5.1 13.7 - - + -
217A ILE* 3.6 31.3 - - + +
220A LEU* 5.7 4.3 - - + -
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Residues in contact with ALA 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 3.5 36.1 - - + -
133A PHE 3.0 17.9 + - - +
134A SER* 3.5 8.5 - - - +
136A LEU* 1.4 76.5 - - + +
138A ILE* 1.4 57.5 + - - +
140A ILE* 3.5 12.3 - - - +
141A GLU* 3.1 27.2 + - - +
163A LEU* 6.2 2.2 - - + -
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Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET* 4.3 14.8 - - + +
83A PHE* 3.6 21.3 - - + +
84A ILE* 3.8 32.1 - - + +
87A LEU* 3.9 20.9 - - + -
134A SER 2.9 19.8 + - - +
135A LEU* 3.2 11.4 + - + +
137A ALA* 1.4 74.7 - - - +
139A ALA* 1.4 63.8 + - - +
141A GLU* 3.2 15.2 + - - +
142A ARG* 3.3 14.9 + - - +
221A TYR* 4.2 1.6 - - - +
258A VAL* 3.5 36.1 - - + -
261A VAL* 6.0 1.8 - - + -
311A TYR* 5.5 1.8 - - - +
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Residues in contact with ALA 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU 2.8 20.6 + - - +
136A LEU* 3.6 5.2 - - - +
138A ILE* 1.4 73.0 - - - +
140A ILE* 1.4 59.2 + - - +
142A ARG* 3.4 4.2 + - - +
217A ILE* 3.6 17.0 - - + -
220A LEU* 3.6 18.8 - - + +
221A TYR* 3.6 31.6 + - + +
224A ILE* 3.3 26.9 - - - +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 6.2 1.1 - - + -
136A LEU* 2.8 33.7 + - + +
137A ALA* 3.5 15.9 - - - +
139A ALA* 1.4 69.0 - - - +
141A GLU* 1.4 58.7 + - + +
142A ARG 3.1 8.5 + - - -
143A TYR* 3.5 18.0 + - + +
144A ILE* 3.2 35.5 + - + +
163A LEU* 6.5 1.3 - - + -
220A LEU* 4.1 20.4 - - + -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PRO* 5.8 1.6 - - + -
80A MET* 4.6 13.1 - - + +
83A PHE* 3.7 26.0 - - + -
137A ALA 3.1 20.9 + - - +
138A ILE* 3.2 8.6 + - - +
140A ILE* 1.4 74.5 - - + +
142A ARG* 1.3 64.5 + - - +
144A ILE* 4.4 13.1 - - - +
145A THR* 3.7 15.9 + - - +
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Residues in contact with ARG 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET* 3.4 34.3 - - - +
138A ILE 3.3 15.0 - - - +
139A ALA 3.5 8.7 - - - +
140A ILE 3.1 0.4 - - - -
141A GLU* 1.3 82.6 + - - +
143A TYR* 1.3 59.9 + - - +
144A ILE 3.1 1.8 - - - -
145A THR* 2.7 58.3 + - - +
146A MET* 4.2 0.7 + - - +
221A TYR* 4.3 16.4 - - + -
224A ILE* 3.8 22.1 - - + +
251A ASN* 3.7 21.2 + - - +
254A LEU* 3.5 33.9 - - - +
255A LEU* 4.2 13.1 - - - +
258A VAL* 4.4 12.8 - - + -
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ALA 3.6 2.9 + - - +
140A ILE* 3.5 18.5 + - + +
142A ARG* 1.3 77.7 - - - +
144A ILE* 1.3 64.4 + - + +
146A MET* 3.5 26.8 - - + +
147A LEU* 3.6 34.3 + - + +
220A LEU* 4.1 19.1 - - + -
223A ARG* 5.2 4.9 - - + -
224A ILE* 3.5 34.3 - - + +
227A LEU* 4.4 23.8 - - + +
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Residues in contact with ILE 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 3.2 31.4 + - + +
141A GLU* 4.6 9.4 - - - +
142A ARG 3.1 1.2 - - - -
143A TYR* 1.3 81.9 - - + +
145A THR* 1.4 63.7 + - - +
146A MET 3.4 0.2 - - - -
147A LEU* 3.0 34.7 - - + +
148A LYS* 3.4 14.9 - - + +
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Residues in contact with THR 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU 3.7 9.6 + - - +
142A ARG* 2.7 55.2 + - - +
144A ILE* 1.4 79.3 - - - +
146A MET* 1.4 70.0 + - - +
148A LYS* 3.9 15.1 - - - +
224A ILE* 5.5 0.7 - - - +
228A VAL* 5.3 4.7 - - - +
251A ASN* 5.5 13.5 - - + +
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Residues in contact with MET 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ARG 4.9 0.4 - - - +
143A TYR* 3.5 25.4 - - + +
145A THR* 1.4 81.3 + - - +
147A LEU* 1.4 63.9 + - + +
148A LYS* 3.3 6.8 + - - +
224A ILE* 4.7 9.4 - - - +
227A LEU* 4.0 38.8 - - + +
228A VAL* 3.6 31.2 - - + -
231A ARG* 4.4 15.9 - - + -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.6 42.1 + - + +
144A ILE* 3.0 25.8 + - + +
145A THR 3.5 0.2 - - - -
146A MET* 1.4 80.5 - - + +
148A LYS* 1.3 61.3 + - - +
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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) + - + + + + + -
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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