Contacts of the helix formed by residues 118 - 152 (chain A) in PDB entry 2G1X
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 GLY 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A CYS* 4.6 13.9 - - - -
115A TRP* 3.1 16.7 + - - +
116A THR 3.0 5.5 - - - -
117A LEU* 1.3 77.1 - - - +
119A GLN* 1.3 61.0 + - - -
120A VAL 3.2 3.4 - - - -
121A VAL* 2.7 28.5 + - - +
122A CYS* 2.9 3.6 + - - +
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Residues in contact with GLN 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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17A GLU* 5.3 24.1 + - - +
33A CYS* 5.4 1.8 - - - +
117A LEU 4.0 0.6 + - - -
118A GLY* 1.3 71.2 - - - -
120A VAL* 1.3 51.9 + - - +
122A CYS* 2.9 13.9 + - + +
123A ASP* 2.6 49.1 + - - +
189A GLN* 3.8 20.2 + - - +
190A ALA 5.1 7.0 + - - +
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Residues in contact with VAL 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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117A LEU* 3.5 26.2 - - + +
119A GLN* 1.3 78.3 - - - +
121A VAL* 1.4 64.2 + - - +
123A ASP* 2.8 14.6 + - + +
124A PHE* 2.8 70.7 + - + -
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Residues in contact with VAL 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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105A ILE* 2.8 58.6 - - + +
108A MET* 3.8 2.5 - - + -
109A TYR* 6.3 0.4 - - - -
115A TRP* 2.9 37.9 - - + -
116A THR 5.4 0.4 - - - +
117A LEU* 2.9 49.4 - - + -
118A GLY 2.7 19.8 + - - +
120A VAL* 1.4 82.7 - - - +
122A CYS* 1.3 62.3 + - - +
125A TRP* 3.2 9.4 + - - +
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Residues in contact with CYS 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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115A TRP* 4.0 7.6 - - + -
118A GLY 2.9 4.7 + - - +
119A GLN* 2.9 21.5 + - + +
121A VAL* 1.3 84.6 - - - +
123A ASP* 1.3 55.9 + - - +
126A LEU* 2.9 32.6 + - - +
190A ALA* 3.2 27.8 - - - -
191A LYS* 3.9 4.9 - - - -
192A ALA* 4.0 1.3 - - - -
199A CYS* 2.0 54.1 - - - +
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Residues in contact with ASP 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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119A GLN* 2.6 40.3 + - - +
120A VAL* 2.8 19.8 + - + +
122A CYS* 1.3 72.3 - - - +
124A PHE* 1.3 57.6 + - + +
126A LEU* 3.8 0.4 - - - +
127A SER* 2.6 42.8 + - - -
185A PHE* 3.4 37.8 - - + -
190A ALA* 4.0 18.8 + - - +
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Residues in contact with PHE 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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101A LEU* 2.7 49.6 - - + +
102A VAL* 2.7 22.9 - - - +
105A ILE* 2.9 28.5 - - + -
117A LEU* 6.1 1.1 - - + -
120A VAL* 2.8 60.2 + - + -
121A VAL* 4.5 0.4 - - - -
123A ASP* 1.3 75.0 - - + +
125A TRP* 1.3 56.6 + - - +
127A SER* 4.4 2.9 - - - -
128A SER 3.2 4.7 + - - -
185A PHE* 6.6 0.2 - + - -
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Residues in contact with TRP 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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53A VAL* 5.4 0.2 - - + -
98A VAL* 5.6 0.2 - - + -
102A VAL* 2.7 67.2 - - + +
103A MET* 3.3 13.0 - - + -
105A ILE* 3.7 4.4 - - + +
106A SER* 2.8 35.7 - - - -
115A TRP* 3.6 15.5 - + + -
121A VAL 3.2 17.8 + - - +
122A CYS 4.0 0.4 - - - +
124A PHE* 1.3 80.2 - - - +
126A LEU* 1.3 53.2 + - - +
129A ASP* 2.5 49.2 + - - +
198A GLU* 3.0 23.9 + - - +
199A CYS 2.8 28.5 - - - +
359A TYR* 2.9 47.5 - + - -
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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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122A CYS 2.9 19.1 + - - +
123A ASP 3.8 0.4 - - - +
125A TRP* 1.3 76.7 - - - +
127A SER* 1.3 76.3 + - - +
129A ASP* 3.3 1.5 + - - +
130A ILE* 2.7 56.6 + - + +
181A SER* 5.2 2.9 - - - +
184A PRO* 4.6 19.3 - - + -
185A PHE* 6.0 0.7 - - + -
190A ALA* 3.0 30.7 - - + -
199A CYS* 2.8 33.4 - - + +
200A VAL* 2.9 20.9 - - - -
201A VAL* 4.1 3.4 - - + +
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Residues in contact with SER 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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101A LEU* 4.9 1.3 - - - -
123A ASP 2.6 29.3 + - - -
124A PHE* 4.1 4.5 - - - -
126A LEU* 1.3 82.9 - - - +
128A SER* 1.3 62.3 + - - +
130A ILE* 3.1 2.9 + - - -
131A THR* 2.8 26.2 + - - +
181A SER* 3.4 17.7 + - - -
185A PHE* 3.0 32.1 - - - -
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Residues in contact with SER 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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97A LEU* 4.0 11.7 + - - +
98A VAL* 3.7 2.8 - - - +
101A LEU* 2.8 38.7 - - - +
102A VAL* 2.9 24.5 - - - +
124A PHE 3.2 1.0 + - - -
127A SER* 1.3 78.7 - - - +
129A ASP* 1.3 59.4 + - - +
131A THR* 3.0 18.1 - - - +
132A CYS* 2.9 31.4 - - - -
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Residues in contact with ASP 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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98A VAL* 3.5 9.2 - - - +
102A VAL* 2.7 25.9 - - - +
125A TRP* 2.5 57.9 + - - +
126A LEU* 3.3 5.9 + - - +
127A SER 3.1 1.2 - - - -
128A SER* 1.3 78.1 - - - +
130A ILE* 1.3 67.6 + - + +
132A CYS* 3.9 2.7 - - - +
133A CYS* 3.0 26.2 + - - +
198A GLU* 4.8 0.7 - - - +
199A CYS 4.5 1.9 - - - +
327A TRP* 4.2 11.6 - - + -
355A THR* 5.6 1.4 - - - +
359A TYR* 5.3 7.8 - - - -
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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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126A LEU* 2.7 50.7 - - + +
127A SER* 3.1 6.4 + - - +
129A ASP* 1.3 82.5 - - + +
131A THR* 1.3 67.2 + - - +
132A CYS 3.2 0.2 - - - -
133A CYS* 2.9 14.3 - - - -
134A THR* 2.8 26.2 + - - +
180A ILE* 3.4 29.6 - - + +
181A SER* 3.7 20.6 - - - +
184A PRO* 6.3 1.3 - - + -
199A CYS 4.6 0.4 - - - +
200A VAL* 5.0 4.7 - - + -
201A VAL* 5.3 10.3 - - + -
327A TRP* 6.1 2.2 - - + -
330A PHE* 6.3 2.5 - - + -
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Residues in contact with THR 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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94A THR* 4.2 4.3 + - - +
97A LEU* 5.4 4.7 - - + -
127A SER 2.8 14.0 + - - -
128A SER* 3.0 37.2 - - - +
130A ILE* 1.3 74.3 - - - +
132A CYS* 1.3 69.7 + - - +
134A THR* 2.7 10.4 - - - +
135A ALA* 2.7 35.9 + - - +
174A TRP* 5.8 3.1 - - - -
177A SER* 4.0 9.0 + - - -
178A ILE* 5.5 4.2 - - - +
181A SER* 4.2 10.7 + - - -
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Residues in contact with CYS 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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94A THR* 2.8 46.4 + - - +
95A ASP* 4.6 8.9 - - - +
97A LEU* 4.5 0.4 - - - -
98A VAL* 3.1 26.2 - - + -
128A SER 2.9 23.5 + - - +
129A ASP 3.9 3.8 - - - +
130A ILE 3.2 0.6 - - - -
131A THR* 1.3 84.0 - - - +
133A CYS* 1.3 65.2 + - - +
135A ALA* 3.8 1.9 - - - +
136A SER* 3.2 20.6 + - - -
361A ASN* 5.9 6.5 - - + +
362A SER* 5.9 2.2 - - - +
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Residues in contact with CYS 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP 3.0 6.3 + - - +
130A ILE* 2.9 41.7 + - - -
132A CYS* 1.3 76.9 - - - +
134A THR* 1.3 66.1 + - - +
136A SER* 3.2 7.8 - - - -
137A ILE* 2.9 23.8 + - - +
180A ILE* 4.6 3.6 - - - -
323A PHE* 3.7 7.9 - - + -
327A TRP* 2.9 51.4 - - + +
361A ASN* 5.6 1.8 - - - -
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Residues in contact with THR 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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130A ILE 2.8 17.3 + - - +
131A THR* 2.7 30.1 - - - +
133A CYS* 1.3 75.3 - - - +
135A ALA* 1.3 63.1 + - - +
136A SER 3.0 1.8 - - - -
137A ILE* 2.9 30.0 - - - +
138A LEU* 3.0 10.0 + - - +
176A PHE* 3.8 3.1 + - - +
177A SER* 2.9 48.4 + - - +
180A ILE* 2.9 27.4 - - + +
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Residues in contact with ALA 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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90A SER* 5.2 5.1 + - - +
91A LEU* 4.1 4.9 - - + +
94A THR* 3.5 29.2 - - + +
131A THR* 2.7 24.1 + - - +
132A CYS 3.8 2.2 - - - +
134A THR* 1.3 71.7 - - - +
136A SER* 1.3 61.5 + - - +
139A HIS* 3.2 13.2 + - - +
173A VAL* 2.9 26.0 - - + +
174A TRP* 6.3 0.2 - - - -
177A SER* 3.0 14.1 + - - +
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Residues in contact with SER 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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91A LEU* 3.9 7.2 - - - +
132A CYS 3.2 11.5 + - - -
133A CYS* 3.2 11.4 - - - -
134A THR 3.0 0.2 - - - -
135A ALA* 1.3 78.2 - - - +
137A ILE* 1.3 65.4 - - - +
139A HIS* 2.8 32.8 + - - -
140A LEU* 2.7 21.0 - - - +
319A ILE* 5.3 2.9 - - - +
323A PHE* 3.5 21.3 - - - -
327A TRP* 5.4 1.3 - - - -
361A ASN* 5.6 3.9 + - - -
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Residues in contact with ILE 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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133A CYS* 2.9 6.0 + - - +
134A THR* 2.9 35.2 - - - +
136A SER* 1.3 74.6 - - - +
138A LEU* 1.3 75.9 + - + +
140A LEU* 3.0 27.6 + - + +
141A CYS* 3.4 4.7 + - - +
180A ILE* 5.7 0.4 - - + -
216A ALA* 4.4 18.4 - - - +
217A PHE* 5.3 4.5 - - + +
220A PRO* 4.2 25.7 - - + +
221A THR* 5.0 12.3 - - - +
224A LEU* 5.5 4.9 - - + -
320A LEU* 5.6 2.2 - - + -
323A PHE* 3.3 43.5 - - + -
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Residues in contact with LEU 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A THR* 3.0 6.5 + - - +
137A ILE* 1.3 83.0 - - + +
139A HIS* 1.3 58.0 + - - +
141A CYS* 2.7 30.7 + - + +
142A VAL* 2.9 24.1 + - + +
172A LEU* 2.9 43.7 - - + +
173A VAL* 2.9 38.6 - - + +
176A PHE* 2.9 31.0 - - + -
220A PRO* 5.7 3.1 - - - -
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Residues in contact with HIS 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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87A LEU* 2.9 23.5 - - + +
90A SER* 5.8 0.9 - - - +
91A LEU* 2.8 51.3 - - + +
135A ALA 3.2 12.0 + - - +
136A SER* 2.8 26.3 + - - -
138A LEU* 1.3 76.5 - - - +
140A LEU* 1.3 82.0 + - + +
142A VAL* 2.7 27.1 - - - +
143A ILE* 2.8 16.1 + - - +
173A VAL* 3.8 5.8 - - + +
252A THR* 3.6 20.9 - - + -
316A LEU* 4.8 3.1 - - + -
319A ILE* 4.0 17.6 - - + +
365A ASN* 4.6 0.7 - - - -
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Residues in contact with LEU 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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136A SER* 2.7 42.1 + - - +
137A ILE* 3.1 16.2 - - + +
138A LEU 3.0 0.6 - - - -
139A HIS* 1.3 103.4 + - + +
141A CYS* 1.3 50.3 + - - +
143A ILE* 2.7 10.2 - - + +
144A ALA* 2.6 36.0 + - - +
224A LEU* 3.5 29.9 - - + +
316A LEU 4.3 2.7 - - - +
319A ILE* 2.9 39.3 - - + -
320A LEU* 3.8 13.0 - - + +
323A PHE* 4.4 9.4 - - + -
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Residues in contact with CYS 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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137A ILE 3.4 2.7 + - - +
138A LEU* 2.7 27.7 + - + +
140A LEU* 1.3 72.0 - - - +
142A VAL* 1.3 62.1 + - - +
144A ALA* 3.5 5.4 - - - +
145A LEU* 2.8 32.4 + - - +
172A LEU* 6.5 0.7 - - - -
219A PHE* 5.9 1.8 - - - -
220A PRO* 4.9 16.6 - - + +
223A LEU* 3.2 37.9 - - - -
224A LEU* 5.5 3.6 - - - -
227A LEU* 4.7 0.2 - - - +
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Residues in contact with VAL 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 2.9 30.8 + - + -
139A HIS* 2.7 31.6 - - - +
141A CYS* 1.3 74.8 - - + +
143A ILE* 1.3 55.8 + - - +
145A LEU* 3.4 6.8 + - - +
146A ASP* 2.8 24.6 + - - +
169A MET* 3.3 45.1 - - + +
172A LEU* 4.6 4.7 - - + -
251A LEU* 2.7 28.4 - - - +
252A THR* 2.9 17.7 - - - -
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Residues in contact with ILE 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 4.5 0.2 - - - -
87A LEU* 2.9 18.6 - - + -
139A HIS 2.8 17.0 + - - +
140A LEU* 2.7 35.2 - - + +
142A VAL* 1.3 75.4 - - - +
144A ALA* 1.3 54.7 + - - +
145A LEU 3.1 1.3 - - - -
146A ASP 3.0 0.2 + - - -
147A ARG 2.7 31.2 + - - -
250A ARG* 2.8 51.4 + - + +
251A LEU 3.4 8.7 - - - +
308A ARG* 2.9 34.1 - - - +
316A LEU* 2.9 27.1 - - + -
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Residues in contact with ALA 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU 2.6 22.8 + - - +
141A CYS* 3.1 8.7 + - - +
143A ILE* 1.3 74.3 - - - +
145A LEU* 1.3 61.1 + - - +
147A ARG* 3.4 4.0 + - - +
148A TYR* 3.2 14.9 + - - +
223A LEU* 4.3 0.4 - - + -
224A LEU* 4.1 26.0 - - + +
227A LEU* 2.9 32.3 - - + +
250A ARG* 3.5 9.9 - - - +
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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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141A CYS* 2.8 21.2 + - - +
142A VAL* 3.5 6.5 - - - +
144A ALA* 1.3 74.3 - - - +
146A ASP* 1.3 69.6 + - - +
148A TYR* 2.8 18.7 + - + +
149A TRP* 3.0 19.2 + - + +
161A ARG* 5.1 11.0 - - - +
169A MET* 4.4 21.5 - - + -
223A LEU* 5.5 3.4 - - + -
227A LEU* 3.2 12.1 - - + +
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Residues in contact with ASP 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 VAL 2.8 8.7 + - - +
143A ILE 3.0 1.5 + - - +
145A LEU* 1.3 80.7 - - - +
147A ARG* 1.3 65.7 + - - +
149A TRP* 3.4 3.5 + - - +
150A ALA* 3.3 15.4 + - - +
161A ARG* 2.8 38.7 + - - +
249A LYS* 3.3 11.2 - - - +
250A ARG* 2.6 32.1 + - - +
251A LEU* 2.9 39.8 - - + +
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Residues in contact with ARG 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE 2.7 6.4 + - - +
144A ALA 3.6 4.9 - - - +
146A ASP* 1.3 79.7 - - - +
148A TYR* 1.3 54.6 + - - +
150A ALA* 3.2 3.3 + - - +
151A ILE* 2.7 85.0 + - + +
231A ILE* 4.3 5.8 - - + -
248A GLY* 3.5 3.6 - - - -
249A LYS 2.7 49.4 + - - +
250A ARG* 2.8 50.5 - - - +
309A GLU 2.7 19.8 + - - -
312A ALA* 2.9 21.6 - - - +
313A THR* 2.9 24.2 - - + +
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Residues in contact with TYR 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA 3.2 9.4 + - - +
145A LEU* 2.8 15.1 + - + +
147A ARG* 1.3 79.3 - - - +
149A TRP* 1.3 70.2 + - + +
151A ILE* 3.9 7.6 - - - -
152A THR* 2.9 56.6 + - + +
153A ASP 4.5 4.3 + - - -
154A ALA* 3.9 18.2 - - + +
155A VAL* 5.0 8.5 + - + +
227A LEU* 4.2 25.6 - - + +
230A ARG* 4.0 24.2 - - + -
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Residues in contact with TRP 149 (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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145A LEU* 3.0 21.7 + - + +
146A ASP* 4.1 9.4 - - - +
147A ARG 3.3 0.2 - - - -
148A TYR* 1.3 80.1 - - + +
150A ALA* 1.3 81.9 + - + +
154A ALA* 2.7 48.8 + - + +
155A VAL 3.6 5.6 + - - -
157A TYR* 5.6 2.7 - + - -
158A SER* 2.8 41.2 + - - -
159A ALA* 3.0 39.5 - - - -
160A LYS* 3.3 19.5 - - + -
161A ARG* 4.6 18.2 - - + +
249A LYS* 5.0 8.7 - - - -
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Residues in contact with ALA 150 (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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146A ASP 3.3 5.4 + - - +
147A ARG* 3.2 12.8 + - - +
149A TRP* 1.3 95.1 - - + +
151A ILE* 1.4 63.5 + - + +
153A ASP* 4.6 2.9 + - - -
154A ALA 5.1 0.3 + - - -
248A GLY* 5.3 0.4 - - - -
249A LYS* 2.9 49.4 + - + +
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Residues in contact with ILE 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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147A ARG* 2.7 85.8 + - + +
148A TYR* 3.9 5.2 - - - +
150A ALA* 1.4 74.5 - - + +
152A THR* 1.3 71.5 + - + +
153A ASP* 3.2 7.8 + - - +
231A ILE* 2.9 50.0 - - + +
234A GLU* 3.2 39.2 - - + +
235A ALA* 5.7 2.9 - - + -
248A GLY* 5.4 2.9 - - - -
313A THR* 3.8 8.1 - - + -
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Residues in contact with THR 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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148A TYR* 2.9 53.1 + - + +
151A ILE* 1.3 89.3 - - + +
153A ASP* 1.4 70.5 + - - +
154A ALA 3.3 1.5 + - - -
230A ARG* 3.9 13.7 + - + +
231A ILE* 4.8 0.7 - - - +
233A VAL* 3.3 30.2 - - - +
234A GLU* 5.2 3.4 - - - -
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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
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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