Contacts of the helix formed by residues 117 - 156 (chain A) in PDB entry 4LDR
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.7 5.4 - - - -
110A GLU* 5.4 0.8 + - - -
115A GLY 3.4 13.6 + - - -
116A ALA* 1.3 73.3 + - - +
118A GLU* 1.3 76.9 + - + +
119A GLU* 3.1 26.9 - - + +
120A ALA* 3.5 16.7 + - + +
121A VAL* 3.0 27.3 + - - +
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Residues in contact with GLU 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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68A GLY 3.9 6.9 - - - +
69A GLY* 4.4 0.2 - - - -
70A PRO* 4.4 3.1 - - - +
71A GLY* 3.3 40.8 + - - +
72A LEU* 4.9 0.6 - - - +
75A LEU* 3.1 35.1 - - + +
117A THR* 1.3 77.0 - - + +
119A GLU* 1.3 74.4 + - + +
121A VAL* 3.1 21.9 - - - +
122A ARG* 3.1 17.5 + - - +
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Residues in contact with GLU 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.1 20.5 - - + +
118A GLU* 1.3 82.6 - - + +
120A ALA* 1.3 68.5 + - - +
122A ARG* 3.1 8.3 + - - +
123A GLU* 3.0 25.9 + - - +
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Residues in contact with ALA 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 3.6 17.9 - - - +
113A ARG* 5.9 1.1 - - - +
117A THR* 3.5 21.3 + - - +
118A GLU 3.4 0.4 - - - -
119A GLU* 1.3 79.4 - - - +
121A VAL* 1.3 58.1 + - - +
123A GLU* 4.1 4.4 - - - +
124A ARG* 3.1 30.3 + - - +
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Residues in contact with VAL 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.6 26.9 - - + -
75A LEU* 4.6 14.6 - - + -
76A VAL* 4.7 5.4 - - + -
107A ALA* 4.0 25.8 - - + +
110A GLU* 3.0 26.7 - - + +
111A ALA* 4.3 3.4 - - + +
117A THR 3.0 16.7 + - - +
118A GLU* 3.1 19.5 - - - +
120A ALA* 1.3 75.0 - - - +
122A ARG* 1.3 61.9 + - - +
124A ARG* 3.9 2.3 - - + +
125A VAL* 3.1 33.9 + - + +
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Residues in contact with ARG 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.2 49.3 + - + +
66A GLY* 3.4 16.2 + - - -
67A ALA 2.7 23.4 + - - -
68A GLY* 2.5 39.2 + - - -
75A LEU* 3.4 21.2 - - + +
118A GLU* 3.1 23.1 + - - +
119A GLU* 3.1 9.3 + - - +
121A VAL* 1.3 76.6 - - - +
123A GLU* 1.3 66.6 + - - +
125A VAL* 2.9 8.8 + - - +
126A ILE* 2.9 27.9 + - + +
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Residues in contact with GLU 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.3 38.2 + - - -
64A GLN* 4.9 1.2 - - - +
119A GLU 3.0 12.6 + - - +
120A ALA* 4.1 5.6 - - - +
122A ARG* 1.3 78.2 - - - +
124A ARG* 1.3 52.8 + - - +
126A ILE* 3.2 10.3 + - - +
127A CYS* 2.6 50.6 + - - +
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Residues in contact with ARG 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 4.0 32.0 - - + +
110A GLU* 3.8 30.4 - - + +
113A ARG* 6.1 1.3 - - - +
120A ALA 3.1 22.0 + - - +
121A VAL* 3.9 6.7 - - + +
123A GLU* 1.3 78.8 - - - +
125A VAL* 1.3 57.8 + - + +
127A CYS* 3.8 9.4 - - - +
128A CYS* 2.9 42.2 + - - +
131A ASP* 5.7 2.6 + - - -
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Residues in contact with VAL 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 5.0 1.8 - - + -
63A LEU* 3.1 27.4 - - + -
79A VAL* 4.5 13.5 - - + -
103A LEU* 4.2 24.2 - - + +
106A VAL* 5.0 4.3 - - + -
107A ALA* 4.1 31.6 - - + +
121A VAL* 3.1 21.3 + - + +
122A ARG* 2.9 8.9 + - - +
124A ARG* 1.3 76.2 - - + +
126A ILE* 1.3 66.3 + - - +
128A CYS* 3.1 15.9 + - - +
129A THR* 3.1 16.6 + - + +
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Residues in contact with ILE 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 4.3 6.1 - - - +
10A ARG* 3.1 36.6 - - - +
60A ALA* 3.9 13.2 - - + +
63A LEU* 3.5 24.0 - - + +
64A GLN* 3.4 41.3 - - - +
122A ARG* 2.9 23.3 + - + +
123A GLU* 3.5 13.9 - - - +
125A VAL* 1.3 77.2 - - - +
127A CYS* 1.3 60.4 + - - +
129A THR* 2.8 23.8 + - - -
130A GLU* 3.1 11.7 + - - +
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Residues in contact with CYS 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.8 17.9 - - - -
123A GLU* 2.6 39.1 + - - +
124A ARG* 3.8 12.3 - - - +
126A ILE* 1.3 73.2 - - - +
128A CYS* 1.3 63.6 + - - +
130A GLU* 3.3 12.2 + - - +
131A ASP* 2.9 30.4 + - - +
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Residues in contact with CYS 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.8 22.0 - - + -
106A VAL* 3.9 26.7 - - + -
124A ARG* 2.9 33.3 + - - +
125A VAL 3.1 6.7 + - - +
127A CYS* 1.3 77.4 - - - +
129A THR* 1.3 57.8 + - - +
131A ASP* 2.9 23.9 + - - +
132A MET* 2.9 25.3 + - - +
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Residues in contact with THR 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.7 2.3 - - - +
56A CYS* 3.6 34.1 - - + +
57A LEU* 4.0 11.6 - - - +
59A LEU* 5.8 0.4 - - + -
60A ALA* 3.4 19.2 - - + +
103A LEU* 3.8 27.8 - - + -
125A VAL* 3.4 16.2 - - + +
126A ILE 2.8 15.1 + - - -
128A CYS* 1.3 75.1 - - - +
130A GLU* 1.3 62.2 + - - +
132A MET* 3.3 13.9 + - - +
133A LEU* 3.2 21.3 + - - +
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Residues in contact with GLU 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 3.0 37.0 + - + +
10A ARG* 2.7 51.3 + - - +
57A LEU* 4.7 2.7 - - - -
126A ILE 3.1 11.3 + - - +
127A CYS* 3.4 14.4 - - - +
128A CYS 3.1 0.2 - - - -
129A THR* 1.3 82.9 + - - +
131A ASP* 1.3 64.5 + - - +
133A LEU* 3.4 9.6 + - - +
134A GLU* 3.2 21.7 + - - +
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Residues in contact with ASP 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ARG* 5.7 2.3 + - - -
127A CYS* 2.9 18.7 + - - +
128A CYS* 2.9 14.2 + - - +
130A GLU* 1.3 78.1 - - - +
132A MET* 1.3 60.0 + - + +
134A GLU* 3.9 6.7 - - - +
135A LYS* 2.9 30.8 + - - +
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Residues in contact with MET 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 6.0 0.9 - - + -
53A LEU* 3.9 18.2 - - + +
56A CYS* 4.2 17.7 - - - -
98A ARG* 5.6 5.6 - - - +
99A ALA* 3.8 33.2 - - + +
103A LEU* 4.6 14.1 - - - -
128A CYS* 2.9 23.8 + - - +
129A THR* 3.3 22.0 + - - +
131A ASP* 1.3 76.3 - - + +
133A LEU* 1.3 64.0 + - - +
135A LYS* 3.4 5.9 + - - +
136A ASP* 3.0 25.8 + - - +
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Residues in contact with LEU 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 5.1 8.3 - - + +
8A TYR* 4.1 28.0 - - + +
53A LEU* 3.9 21.0 - - + +
57A LEU* 4.0 23.6 - - + -
129A THR 3.2 9.2 + - - +
130A GLU* 3.5 11.0 - - - +
132A MET* 1.3 80.5 - - - +
134A GLU* 1.3 57.4 + - - +
136A ASP* 3.7 2.0 - - - +
137A LEU* 3.0 56.4 + - + +
176A ALA* 4.1 18.6 - - + +
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Residues in contact with GLU 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU 3.2 13.1 + - - +
131A ASP* 3.9 7.9 - - - +
133A LEU* 1.3 78.3 - - - +
135A LYS* 1.3 59.1 + - - +
137A LEU* 3.3 14.5 + - - +
138A ARG* 2.8 57.1 + - + +
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Residues in contact with LYS 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASP 2.9 19.2 + - - +
132A MET* 3.7 6.7 - - - +
134A GLU* 1.3 78.1 - - - +
136A ASP* 1.3 59.1 + - - +
138A ARG* 3.2 5.7 + - - +
139A ASP* 2.8 59.3 + - - +
283A TYR* 6.3 1.2 - - - -
340A GLU* 5.3 5.0 + - - +
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Residues in contact with ASP 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PRO* 3.8 14.4 - - - +
53A LEU* 4.1 15.0 - - + -
132A MET 3.0 18.5 + - - +
133A LEU 3.7 3.8 - - - +
135A LYS* 1.3 79.0 - - - +
137A LEU* 1.3 62.1 + - - +
139A ASP* 3.5 7.2 + - - +
140A ASN* 3.1 38.9 + - - +
176A ALA* 3.1 24.4 + - + +
283A TYR* 2.9 33.4 + - - -
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Residues in contact with LEU 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.0 43.7 + - + +
134A GLU* 3.6 15.5 - - - +
136A ASP* 1.3 77.0 - - - +
138A ARG* 1.3 57.4 + - + +
140A ASN* 3.3 6.3 + - - +
141A ARG* 3.0 33.9 + - + +
176A ALA* 3.7 9.2 - - + +
177A GLY* 3.5 40.4 - - - +
178A TYR* 5.0 2.8 - - + +
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Residues in contact with ARG 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLU* 2.8 42.0 + - + +
135A LYS* 3.7 6.1 - - - +
137A LEU* 1.3 75.8 - - + +
139A ASP* 1.3 60.5 + - - +
141A ARG* 3.4 25.1 + - - +
142A SER* 2.9 29.6 + - - -
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Residues in contact with ASP 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 2.8 59.2 + - - +
136A ASP* 3.8 8.6 - - - +
137A LEU 3.3 0.2 - - - -
138A ARG* 1.3 77.2 - - - +
140A ASN* 1.3 59.5 + - - +
142A SER* 3.3 5.4 + - - -
143A ILE* 2.9 34.2 + - + +
281A PRO* 6.0 3.4 - - + -
283A TYR* 5.8 4.9 - - + -
340A GLU* 3.6 35.1 - - + +
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Residues in contact with ASN 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASP* 3.1 34.1 + - - +
137A LEU* 3.6 4.5 - - - +
138A ARG 3.3 0.2 - - - -
139A ASP* 1.3 76.3 - - - +
141A ARG* 1.3 65.4 + - - +
143A ILE* 3.1 12.4 + - - +
144A GLY* 2.9 19.6 + - - -
175A THR* 3.8 14.8 + - - +
177A GLY 3.0 27.8 + - - +
178A TYR* 3.9 3.3 - - + -
179A GLY 3.3 26.0 - - - +
180A THR* 3.9 15.9 - - - +
281A PRO* 4.6 6.1 - - - +
283A TYR* 4.9 3.7 + - - -
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Residues in contact with ARG 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.0 19.4 + - + +
138A ARG* 3.5 28.0 - - - +
140A ASN* 1.3 75.5 - - - +
142A SER* 1.3 56.4 + - - +
144A GLY* 3.3 1.6 + - - -
145A ASP* 2.8 68.0 + - - +
178A TYR* 3.8 45.9 + - + -
187A SER* 4.4 0.9 + - - +
190A SER* 5.5 6.1 + - - -
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Residues in contact with SER 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ARG 2.9 17.9 + - - -
139A ASP* 3.5 9.2 - - - -
141A ARG* 1.3 73.9 - - - +
143A ILE* 1.3 66.3 + - - +
145A ASP* 4.4 4.7 - - - +
146A LEU* 2.9 40.8 + - - +
340A GLU 2.7 26.9 + - - -
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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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139A ASP* 2.9 20.7 + - + +
140A ASN* 3.1 13.0 + - - +
142A SER* 1.3 75.4 - - - +
144A GLY* 1.3 58.8 + - - +
147A GLY* 2.9 24.9 + - - -
180A THR* 3.8 31.4 - - + +
184A VAL* 3.7 1.8 - - + +
279A ALA* 4.0 14.1 - - + -
280A ALA 4.3 1.3 - - - -
281A PRO* 3.9 42.0 - - + -
338A ILE* 3.3 20.6 - - + +
339A THR 3.5 10.1 - - - -
340A GLU* 3.4 21.3 - - + +
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Residues in contact with GLY 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN 2.9 12.5 + - - -
141A ARG 3.6 3.1 - - - -
143A ILE* 1.3 78.0 - - - +
145A ASP* 1.3 56.3 + - - +
148A ALA* 2.9 31.9 + - - +
178A TYR* 4.4 0.9 - - - -
183A GLY 3.6 8.5 - - - -
184A VAL* 3.6 28.0 - - - -
187A SER* 3.2 10.0 - - - -
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Residues in contact with ASP 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG* 2.8 53.7 + - - +
142A SER* 4.1 3.5 - - - +
144A GLY* 1.3 70.3 - - - +
146A LEU* 1.3 65.5 + - + +
148A ALA* 3.3 2.8 + - - +
149A ARG* 3.0 29.9 + - - +
187A SER* 2.7 29.8 + - - -
191A LEU* 6.1 1.2 - - - +
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Residues in contact with LEU 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A SER* 2.9 39.0 + - - +
143A ILE* 4.6 0.9 - - - +
145A ASP* 1.3 75.7 - - + +
147A GLY* 1.3 62.6 + - - +
149A ARG* 3.5 12.4 + - - +
150A HIS* 3.0 25.5 + - - +
338A ILE* 5.3 0.4 - - + -
340A GLU 3.9 0.9 - - - +
341A LEU 3.8 7.6 - - - +
342A GLY* 3.6 37.7 - - - +
343A VAL* 4.0 2.9 - - + +
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Residues in contact with GLY 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE 2.9 20.8 + - - -
144A GLY 3.9 0.2 - - - -
146A LEU* 1.3 78.2 - - - +
148A ALA* 1.3 55.9 + - - +
150A HIS* 3.3 2.8 + - - +
151A LEU* 2.9 30.3 + - - +
184A VAL* 4.0 7.6 - - - -
277A TYR* 5.2 1.0 - - - -
338A ILE* 3.7 29.2 - - - +
343A VAL* 4.2 4.0 - - - -
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Residues in contact with ALA 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLY 2.9 20.3 + - - +
145A ASP 3.6 4.0 - - - +
147A GLY* 1.3 75.9 - - - +
149A ARG* 1.3 58.2 + - - +
151A LEU* 3.2 3.3 + - - +
152A LEU* 2.9 34.9 + - - +
184A VAL* 3.7 8.8 - - - +
187A SER* 3.7 18.2 - - - -
188A LEU* 3.5 28.7 - - + +
191A LEU* 4.6 6.7 - - + -
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Residues in contact with ARG 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ASP 3.0 16.1 + - - +
146A LEU* 3.9 15.0 - - - +
148A ALA* 1.3 76.4 - - - +
150A HIS* 1.3 64.8 - - - +
152A LEU* 3.2 11.4 + - - +
153A GLU* 3.0 43.2 + - + +
191A LEU* 5.4 3.8 - - + +
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Residues in contact with HIS 150 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU 3.0 18.8 + - - +
147A GLY 3.7 2.7 - - - +
149A ARG* 1.3 79.5 - - - +
151A LEU* 1.3 58.4 + - - +
153A GLU* 3.4 6.9 + - - +
154A ARG* 3.0 57.3 + - + +
277A TYR* 2.9 29.4 + + + -
335A GLY 3.6 10.0 + - - -
343A VAL* 3.5 37.4 + - + +
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Residues in contact with LEU 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLY 2.9 16.6 + - - +
148A ALA* 3.5 5.4 - - - +
150A HIS* 1.3 78.5 - - - +
152A LEU* 1.3 58.5 + - - +
154A ARG* 3.3 1.0 + - - +
155A VAL* 2.9 38.2 + - + +
162A VAL* 4.0 34.1 - - + -
164A VAL* 4.3 9.6 - - + -
184A VAL* 4.5 9.2 - - + -
188A LEU* 4.4 5.4 - - + -
242A ALA* 3.7 28.9 - - + -
244A VAL* 3.8 26.0 - - + -
277A TYR* 3.5 25.8 + - + +
338A ILE* 6.2 0.4 - - + -
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Residues in contact with LEU 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA 2.9 20.6 + - - +
149A ARG* 3.7 6.7 - - - +
151A LEU* 1.3 77.9 - - - +
153A GLU* 1.3 56.8 + - - +
156A ALA* 2.8 37.7 + - - +
157A PRO* 3.9 0.4 - - - +
162A VAL* 3.9 22.9 - - + -
188A LEU* 3.6 23.8 - - + -
191A LEU* 4.2 17.0 - - + -
193A ARG* 3.7 58.8 - - + +
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 3.0 39.6 + - + +
150A HIS* 3.7 6.7 - - - +
152A LEU* 1.3 77.2 - - - +
154A ARG* 1.3 63.4 + - - +
157A PRO* 3.5 38.8 - - - +
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A HIS* 3.0 37.9 + - + +
151A LEU 3.7 1.8 - - - +
153A GLU* 1.3 80.7 - - - +
155A VAL* 1.3 69.0 + - + +
157A PRO* 4.2 4.4 - - - +
275A PRO* 4.3 11.3 - - + +
277A TYR* 3.6 14.1 - - - +
334A THR 2.8 25.1 + - - -
335A GLY* 3.4 23.0 + - - -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 2.9 20.0 + - + +
154A ARG* 1.3 82.1 - - + +
156A ALA* 1.3 58.6 + - + +
157A PRO* 3.3 8.8 - - - +
162A VAL* 3.7 17.3 - - + -
241A SER* 3.4 38.4 - - - +
242A ALA* 4.5 5.2 - - + -
275A PRO* 3.4 35.2 - - + -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU 2.8 16.2 + - - +
155A VAL* 1.3 76.5 - - + +
157A PRO* 1.3 59.9 - - - +
158A SER 3.1 3.1 - - - -
159A GLY 2.9 32.2 + - - +
160A GLY* 3.6 16.8 - - - +
161A LYS 4.9 1.1 - - - +
162A VAL* 3.9 17.9 - - + -
193A ARG* 3.1 14.5 + - - +
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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