Contacts of the helix formed by residues 122 - 157 (chain A) in PDB entry 6TPN
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 PHE 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PRO 5.4 0.4 - - - -
110A ALA* 3.9 35.2 - - + -
113A VAL* 4.2 26.9 - - + -
114A VAL* 4.8 2.0 - - + -
120A TRP* 3.5 45.1 - + + -
121A PHE* 1.3 95.0 - + + +
123A GLY* 1.3 62.7 + - - +
126A LEU* 3.4 35.9 + - + +
130A ILE* 5.0 3.4 - - + -
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Residues in contact with GLY 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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120A TRP* 2.8 32.8 + - - +
121A PHE 3.7 1.8 - - - -
122A PHE* 1.3 78.4 - - - +
124A GLN* 1.3 66.1 + - - -
125A SER 3.3 2.7 - - - -
126A LEU 3.5 0.2 + - - -
127A CYS* 3.1 8.3 + - - +
193A CYS* 4.3 3.6 - - - -
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Residues in contact with GLN 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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123A GLY* 1.3 73.3 - - - -
125A SER* 1.3 64.4 + - - +
127A CYS* 3.2 15.2 + - - +
128A LYS* 3.5 21.7 - - + +
192A GLU* 3.7 23.0 + - - +
193A CYS* 3.2 53.2 + - + +
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Residues in contact with SER 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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123A GLY 3.3 0.6 - - - -
124A GLN* 1.3 80.5 - - - +
126A LEU* 1.3 60.4 + - - +
128A LYS* 3.3 9.7 + - - +
129A VAL* 3.1 32.2 + - - +
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Residues in contact with LEU 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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120A TRP* 3.3 5.4 - - - -
122A PHE* 3.4 45.2 + - + +
123A GLY 3.5 2.2 + - - -
124A GLN 3.4 0.4 - - - -
125A SER* 1.3 79.1 - - - +
127A CYS* 1.3 59.0 + - - +
128A LYS 3.2 0.4 - - - -
129A VAL* 3.9 15.9 - - + +
130A ILE* 3.2 54.6 + - + +
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Residues in contact with CYS 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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120A TRP* 3.6 11.0 - - - +
123A GLY 3.1 14.6 + - - +
124A GLN* 3.2 12.9 + - - +
126A LEU* 1.3 76.9 - - - +
128A LYS* 1.3 56.7 + - - +
131A PRO* 3.2 22.0 - - - +
191A MET* 3.4 6.6 - - - +
192A GLU* 3.7 33.4 - - - -
193A CYS* 3.7 7.9 - - + -
210A CYS* 2.0 49.2 - - - -
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Residues in contact with LYS 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 GLN* 3.5 25.4 - - + +
125A SER* 3.3 7.4 + - - +
126A LEU 3.2 0.2 - - - -
127A CYS* 1.3 79.0 - - - +
129A VAL* 1.3 65.1 + - + +
130A ILE 3.5 0.2 - - - -
131A PRO* 3.6 1.4 - - - +
132A TYR* 3.2 25.4 + - - +
188A ALA* 2.9 37.6 + - + +
189A ILE* 3.1 22.0 + - - +
191A MET* 3.1 30.6 + - - +
192A GLU* 3.9 11.0 + - - -
1207A OLA 3.9 21.8 - - + +
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Residues in contact with VAL 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 SER* 3.1 20.3 + - - +
126A LEU* 4.4 16.6 - - + -
128A LYS* 1.3 76.8 - - + +
130A ILE* 1.3 61.2 + - - +
132A TYR* 3.2 8.9 + - + +
133A LEU* 2.8 55.4 + - + +
1207A OLA 6.0 4.9 - - + +
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Residues in contact with ILE 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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106A THR* 4.3 12.8 - - - +
107A CYS* 3.5 26.7 - - - -
110A ALA* 4.0 21.1 - - + -
120A TRP* 3.8 19.5 - - + -
122A PHE* 4.9 4.3 - - + -
126A LEU* 3.2 45.4 + - + +
129A VAL* 1.3 77.3 - - + +
131A PRO* 1.3 62.1 - - + +
133A LEU* 3.0 25.8 + - + +
134A GLN* 3.2 8.7 + - - +
1201A NU8 4.4 13.9 - - - +
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Residues in contact with PRO 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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120A TRP* 5.3 0.7 - - + -
126A LEU 3.8 0.4 - - - +
127A CYS* 3.2 29.6 - - - +
128A LYS 3.6 4.0 - - - +
130A ILE* 1.3 94.9 - - + +
132A TYR* 1.3 58.0 + - - +
134A GLN* 3.3 2.9 + - + +
135A THR* 3.0 31.0 + - - +
187A GLN* 5.0 2.2 - - + -
191A MET* 3.8 28.9 - - + -
1201A NU8 3.6 47.0 + - + +
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Residues in contact with TYR 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 LYS 3.2 21.8 + - - +
129A VAL* 3.2 9.4 + - + +
131A PRO* 1.3 76.9 - - - +
133A LEU* 1.3 70.5 + - + +
135A THR* 3.3 4.7 + - - -
136A VAL* 3.1 51.9 + - + +
181A CYS* 2.7 42.9 + - - +
184A MET* 3.3 37.2 - - + -
185A ILE* 3.9 9.8 - - + +
187A GLN* 5.2 3.9 - - - +
188A ALA* 3.7 18.6 - - + +
191A MET* 5.7 0.2 - - - +
1207A OLA 4.0 31.8 + - + +
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Residues in contact with LEU 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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102A LEU* 4.4 30.2 - - + +
103A VAL* 4.1 1.6 - - - +
106A THR* 4.0 29.6 - - + +
107A CYS* 4.1 10.8 - - - -
129A VAL* 2.8 38.1 + - + +
130A ILE* 3.0 11.1 + - + +
132A TYR* 1.3 90.7 - - + +
134A GLN* 1.3 58.6 + - - +
136A VAL* 3.9 5.6 + - + +
137A SER* 3.1 26.5 + - - -
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Residues in contact with GLN 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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103A VAL* 4.0 18.6 - - + +
107A CYS* 3.8 12.6 - - - -
130A ILE 3.2 8.3 + - - +
131A PRO 3.3 1.8 + - - +
132A TYR 3.3 0.2 - - - -
133A LEU* 1.3 77.4 - - - +
135A THR* 1.3 62.1 + - - +
136A VAL 3.4 0.2 - - - -
137A SER* 3.8 1.3 - - - -
138A VAL* 3.2 25.5 + - + +
350A HIS* 5.8 0.7 + - - -
353A VAL* 3.4 25.7 - - - +
354A TYR* 3.3 20.9 + - - -
1201A NU8 2.8 66.8 + - - +
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Residues in contact with THR 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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131A PRO 3.0 14.5 + - - +
132A TYR* 3.3 10.0 + - - -
134A GLN* 1.3 76.7 - - - +
136A VAL* 1.3 63.1 + - - +
138A VAL* 3.3 5.4 + - - +
139A SER* 3.0 28.1 + - - -
184A MET* 3.7 31.9 - - - +
187A GLN* 4.2 11.1 - - + +
227A PHE* 3.8 10.3 - - + -
1201A NU8 3.2 48.5 - - + +
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Residues in contact with VAL 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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102A LEU* 5.9 1.8 - - + -
132A TYR* 3.1 48.9 + - + +
133A LEU* 4.1 7.2 - - + +
135A THR* 1.3 78.1 + - - +
137A SER* 1.3 57.5 + - - +
139A SER* 3.2 1.7 + - - -
140A VAL* 2.8 28.4 + - - +
177A TRP* 3.8 30.7 - - + -
180A SER* 3.8 28.0 - - - +
181A CYS* 4.1 10.8 - - - -
184A MET* 3.9 8.7 - - + -
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Residues in contact with SER 137 (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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99A ALA* 3.1 37.6 + - - +
102A LEU* 5.0 5.4 - - - +
103A VAL* 3.4 22.9 - - - +
133A LEU 3.1 21.6 + - - -
134A GLN* 4.2 2.9 - - - -
135A THR 3.2 0.2 - - - -
136A VAL* 1.3 77.6 - - - +
138A VAL* 1.3 61.6 + - - +
140A VAL* 3.7 2.7 + - - +
141A SER* 3.2 24.3 + - - -
177A TRP* 5.4 2.0 - - - -
317A TYR* 5.4 0.4 + - - -
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Residues in contact with VAL 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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134A GLN* 3.2 26.3 + - + +
135A THR* 3.3 7.0 + - - +
136A VAL 3.3 0.2 - - - -
137A SER* 1.3 78.9 - - - +
139A SER* 1.3 61.4 + - - +
141A SER* 3.8 6.1 + - - -
142A ALA* 3.4 21.3 + - - +
227A PHE* 4.7 2.2 - - + -
231A THR* 4.0 21.5 - - + +
313A PHE* 5.5 1.1 - - + -
317A TYR* 3.8 23.9 - - + +
353A VAL* 5.1 1.3 - - + -
1201A NU8 3.3 48.7 - - + -
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Residues in contact with SER 139 (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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135A THR 3.0 17.0 + - - -
136A VAL* 3.6 2.5 - - - -
138A VAL* 1.3 76.9 - - - +
140A VAL* 1.3 63.8 + - - +
142A ALA* 3.4 3.2 + - - +
143A LEU* 3.1 33.8 + - - +
180A SER* 2.9 21.7 + - - -
183A ILE* 3.3 20.1 - - - +
184A MET* 3.8 16.6 - - - -
230A VAL* 5.1 2.4 - - - +
231A THR* 4.7 8.0 - - - +
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Residues in contact with VAL 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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95A ASN* 3.6 28.7 - - - +
99A ALA* 4.2 9.2 - - + -
136A VAL 2.8 24.1 + - - +
137A SER* 4.0 5.6 - - - +
139A SER* 1.3 71.6 - - - +
141A SER* 1.3 56.1 + - - +
143A LEU 3.9 0.2 - - - -
144A THR* 2.6 38.4 + - - +
176A ILE* 3.8 13.9 - - + +
177A TRP* 3.6 46.7 - - + -
180A SER* 3.4 17.5 - - - +
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Residues in contact with SER 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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96A LEU* 3.6 23.2 + - - +
99A ALA* 5.6 4.5 - - - -
137A SER 3.2 18.6 + - - -
138A VAL* 3.9 7.4 - - - -
140A VAL* 1.3 75.7 - - - +
142A ALA* 1.3 64.2 + - - +
144A THR 4.0 0.2 - - - -
145A LEU* 3.0 37.9 + - - +
313A PHE* 4.3 10.0 - - - -
317A TYR* 4.4 10.6 + - - -
356A ASN* 5.0 4.7 + - - -
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Residues in contact with ALA 142 (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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138A VAL 3.4 12.1 + - - +
139A SER* 3.4 4.3 + - - +
141A SER* 1.3 80.1 - - - +
143A LEU* 1.3 61.4 + - + +
145A LEU* 3.6 5.0 + - - +
146A SER* 2.9 30.8 + - - -
230A VAL 4.4 1.6 - - - +
231A THR* 3.1 32.8 - - - +
235A PRO* 3.9 17.7 - - + +
239A MET* 5.5 0.4 - - - -
313A PHE* 4.5 11.9 - - + -
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Residues in contact with LEU 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 SER* 3.1 31.8 + - - +
142A ALA* 1.3 77.7 - - + +
144A THR* 1.3 60.2 + - - +
146A SER* 3.5 8.5 + - - +
147A CYS* 3.0 32.8 + - - -
176A ILE* 4.1 22.9 - - + +
179A VAL* 4.3 11.4 - - + -
180A SER* 3.9 9.6 - - - +
183A ILE* 5.2 1.1 - - + -
230A VAL* 5.0 14.4 - - + +
235A PRO* 5.5 3.1 - - + -
1208A OLA 4.0 47.3 - - + -
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Residues in contact with THR 144 (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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92A PHE* 3.4 48.0 - - + +
95A ASN* 3.2 22.0 + - - +
96A LEU* 4.1 17.9 - - + +
140A VAL* 2.6 25.8 + - - +
143A LEU* 1.3 75.0 - - - +
145A LEU* 1.3 64.5 + - - +
147A CYS* 3.3 3.7 + - - +
148A ILE* 3.0 25.6 + - + +
176A ILE* 3.9 11.8 - - - +
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Residues in contact with LEU 145 (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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96A LEU* 4.1 18.6 - - + -
141A SER* 3.0 27.3 + - - +
142A ALA* 3.9 3.6 - - - +
143A LEU 3.4 0.2 - - - -
144A THR* 1.3 78.9 - - - +
146A SER* 1.3 60.5 + - - +
148A ILE* 3.5 14.1 + - + +
149A ALA* 3.3 16.1 + - - +
239A MET* 3.3 23.9 - - + +
243A TYR* 4.5 2.9 + - - +
306A LEU* 5.4 2.2 - - + +
309A VAL* 3.9 27.1 - - + -
310A VAL* 4.2 18.8 - - + +
313A PHE* 3.7 39.7 - - + -
360A ASN* 6.3 0.4 - - - +
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Residues in contact with SER 146 (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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142A ALA 2.9 18.5 + - - -
143A LEU* 3.8 10.2 - - - +
144A THR 3.2 0.2 - - - -
145A LEU* 1.3 75.5 - - - +
147A CYS* 1.3 60.4 + - - +
149A ALA* 3.3 3.1 + - - +
150A LEU* 2.8 32.1 + - - +
235A PRO* 3.4 25.6 + - - +
238A LEU* 4.0 20.5 - - - +
239A MET* 3.7 12.2 - - - +
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Residues in contact with CYS 147 (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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92A PHE* 3.8 22.5 - - + -
143A LEU 3.0 21.6 + - - +
144A THR* 3.3 4.2 + - - +
146A SER* 1.3 74.9 - - - +
148A ILE* 1.3 61.2 + - - +
150A LEU* 3.7 7.4 - - - +
151A ASP* 2.8 31.0 + - - +
176A ILE* 4.1 12.1 - - - -
1208A OLA 3.6 54.7 - - - +
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Residues in contact with ILE 148 (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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89A THR* 4.2 17.7 - - + +
92A PHE* 3.5 35.9 - - + -
93A ILE* 4.2 15.5 - - + +
96A LEU* 5.2 4.5 - - + -
144A THR* 3.0 23.5 + - + +
145A LEU* 3.7 17.0 - - + +
146A SER 3.2 0.4 - - - -
147A CYS* 1.3 74.3 - - - +
149A ALA* 1.3 60.3 + - - +
151A ASP* 3.4 3.7 + - - +
152A ARG* 2.9 35.0 + - + +
243A TYR* 3.8 6.1 - - - +
306A LEU* 3.6 38.1 - - + -
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Residues in contact with ALA 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU 3.3 3.8 + - - +
146A SER 3.3 7.2 + - - +
148A ILE* 1.3 78.0 - - - +
150A LEU* 1.3 57.7 + - - +
152A ARG* 3.3 2.2 + - - +
153A TRP* 2.9 31.0 + - - +
239A MET* 3.8 18.6 - - + -
242A LEU* 3.7 18.5 - - + +
243A TYR* 3.5 39.2 + - + -
246A ILE* 4.5 1.0 - - - +
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Residues in contact with LEU 150 (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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146A SER 2.8 18.4 + - - +
147A CYS* 3.7 10.1 - - - +
148A ILE 3.3 0.2 - - - -
149A ALA* 1.3 72.3 - - - +
151A ASP* 1.3 63.9 + - - +
153A TRP* 3.2 3.0 + - + -
154A TYR* 3.0 48.3 + - + -
238A LEU* 4.3 21.5 - - + -
242A LEU* 3.6 25.0 - - + +
1208A OLA 3.9 28.0 - - + +
1209A OLA 5.7 4.9 - - + -
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Residues in contact with ASP 151 (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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88A VAL* 3.3 30.0 - - - +
89A THR* 4.0 5.5 + - - -
92A PHE* 4.8 9.5 - - + -
147A CYS 2.8 21.7 + - - +
148A ILE* 3.9 5.3 - - - +
150A LEU* 1.3 72.9 - - - +
152A ARG* 1.3 80.5 + - - +
154A TYR* 3.5 6.0 + - - +
155A ALA* 3.2 22.7 + - - +
162A PHE 5.2 1.0 - - - +
164A SER* 3.2 30.0 + - - +
1208A OLA 4.6 7.8 + - - +
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Residues in contact with ARG 152 (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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88A VAL* 4.3 10.3 - - - +
89A THR* 3.4 23.1 + - - +
148A ILE* 2.9 21.7 + - + +
149A ALA* 3.8 4.9 - - - +
150A LEU 3.2 0.2 - - - -
151A ASP* 1.3 92.6 + - - +
153A TRP* 1.3 57.6 + - - +
155A ALA* 3.3 18.4 + - - +
156A ILE* 3.0 61.6 + - + +
243A TYR* 5.1 1.6 - - + +
246A ILE* 3.9 16.4 - - + -
299A ARG* 4.9 13.1 - - - +
302A THR* 5.1 10.0 - - - +
303A ALA* 6.2 2.2 - - - +
306A LEU* 3.9 26.0 - - + -
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Residues in contact with TRP 153 (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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149A ALA 2.9 17.7 + - - +
150A LEU* 3.2 2.7 + - + +
152A ARG* 1.3 75.0 - - - +
154A TYR* 1.3 86.5 + + - +
157A CYS* 2.9 53.6 + - + +
158A HIS* 3.1 26.4 + + + -
159A PRO* 6.1 0.2 - - + -
242A LEU* 3.6 42.5 - - + +
245A GLN* 2.8 29.9 + - + -
246A ILE* 3.9 7.6 - - + +
1209A OLA 3.5 60.6 - - + -
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Residues in contact with TYR 154 (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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150A LEU* 3.0 46.3 + - + +
151A ASP* 4.0 6.1 - - - +
153A TRP* 1.3 98.0 - + - +
155A ALA* 1.3 58.2 + - - +
158A HIS* 3.4 27.5 - + - +
161A MET* 3.7 1.6 - - - -
162A PHE* 3.1 55.7 + + + -
1209A OLA 2.9 43.3 + - + +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ASP* 3.2 17.8 + - - +
152A ARG* 3.3 27.3 + - - +
153A TRP 3.2 0.4 - - - -
154A TYR* 1.3 80.3 - - - +
156A ILE* 1.3 60.4 + - + +
161A MET* 3.4 28.9 - - - +
162A PHE 3.4 21.8 - - - +
163A LYS* 5.7 1.1 - - + -
299A ARG* 3.7 10.9 + - - +
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Residues in contact with ILE 156 (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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152A ARG* 3.0 43.2 + - + +
155A ALA* 1.3 82.2 - - - +
157A CYS* 1.3 58.5 + - - +
158A HIS 3.8 0.2 - - - -
161A MET* 3.9 7.1 - - - +
246A ILE* 4.2 19.5 - - + -
249A LYS* 2.7 51.3 + - + -
250A LEU* 4.0 37.7 - - + -
299A ARG* 3.9 32.8 - - + +
303A ALA* 5.6 2.0 - - + -
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Residues in contact with CYS 157 (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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153A TRP* 2.9 45.6 + - + +
156A ILE* 1.3 80.3 - - - +
158A HIS* 1.3 65.0 + - - +
159A PRO* 3.4 7.4 - - - +
161A MET* 5.3 0.4 - - - +
245A GLN* 3.6 35.0 - - - +
246A ILE* 4.2 9.2 - - - -
249A LYS* 4.5 16.6 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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