Contacts of the helix formed by residues 116 - 153 (chain A) in PDB entry 2YPT
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 PRO 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 1.4 67.6 + - + +
118A TYR* 3.3 5.6 - - - -
119A GLU* 3.4 13.2 + - + +
120A ILE* 3.1 38.8 + - + +
187A TYR* 6.3 1.6 - - + -
190A LYS* 5.0 14.5 - - + +
191A ILE* 4.6 24.0 - - + -
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 1.4 82.9 - - + +
118A TYR* 1.3 52.0 + - - +
120A ILE* 3.5 8.8 + - - +
121A THR* 2.7 46.5 + - - +
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO 3.3 3.0 - - - -
117A GLU* 1.3 77.9 - - - +
119A GLU* 1.4 57.3 + - - +
121A THR* 3.4 6.0 + - - -
122A GLN* 3.0 29.8 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TRP* 4.1 9.7 - - + -
116A PRO* 3.4 14.3 + - + +
118A TYR* 1.4 74.1 - - - +
120A ILE* 1.4 57.7 + - + +
122A GLN* 3.5 9.8 + - - +
123A SER* 2.6 52.1 + - - -
186A LEU* 5.2 1.1 - - - +
190A LYS* 4.3 9.7 - - + +
382A GLN 5.2 0.9 - - - +
383A PRO* 3.7 13.6 - - + +
384A THR* 3.1 43.5 + - - -
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Residues in contact with ILE 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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116A PRO* 3.1 29.5 + - + +
117A GLU* 3.9 7.2 - - + +
119A GLU* 1.4 74.3 - - + +
121A THR* 1.4 60.7 + - - +
123A SER* 3.4 7.9 + - - -
124A LEU* 2.9 30.4 + - + +
183A SER* 4.0 34.5 - - - +
186A LEU* 4.0 20.4 - - + +
187A TYR* 4.0 38.1 - - + -
190A LYS* 5.2 7.2 - - + -
191A ILE* 6.3 0.2 - - + -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 2.7 33.0 + - - +
118A TYR* 3.7 7.1 - - - -
120A ILE* 1.4 74.8 - - - +
122A GLN* 1.4 58.8 + - - +
124A LEU* 3.1 12.2 + - + +
125A VAL* 2.9 36.3 + - + +
107B ARG* 6.3 3.1 - - + -
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Residues in contact with GLN 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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102A TRP* 2.8 63.6 + - + +
103A ARG* 4.7 2.4 + - - +
105A SER 3.2 20.6 - - - +
106A GLY* 3.7 16.6 - - - -
118A TYR 3.0 18.2 + - - +
119A GLU* 3.7 10.7 - - - +
121A THR* 1.4 73.9 - - - +
123A SER* 1.4 57.4 + - - +
125A VAL* 3.4 5.0 - - - +
126A PHE* 3.0 31.0 + - - +
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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
----------------------------------------------------------
102A TRP* 3.3 22.7 - - - -
119A GLU* 2.6 33.8 + - - -
120A ILE* 3.4 7.2 - - - -
122A GLN* 1.4 75.5 - - - +
124A LEU* 1.4 56.6 + - - +
126A PHE* 3.4 0.7 + - - +
127A LEU* 2.9 30.1 + - - +
186A LEU* 3.8 24.2 - - - +
385A LEU* 3.5 22.7 - - - +
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Residues in contact with LEU 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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120A ILE* 2.9 20.1 + - + +
121A THR* 3.4 12.1 - - + +
123A SER* 1.4 73.3 - - - +
125A VAL* 1.3 59.6 + - - +
127A LEU* 3.4 9.0 + - + +
128A LEU* 3.1 33.7 + - + +
179A LEU* 3.6 49.9 - - + +
182A SER* 4.5 8.1 - - - -
183A SER* 3.7 28.9 - - - +
186A LEU* 5.0 3.1 - - + -
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Residues in contact with VAL 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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105A SER* 3.3 32.8 - - - +
106A GLY 5.7 0.2 - - - +
121A THR* 2.9 20.2 + - + +
122A GLN* 3.4 9.6 - - - +
124A LEU* 1.3 72.6 - - - +
126A PHE* 1.4 58.3 + - - +
128A LEU* 3.4 11.2 + - + +
129A LEU* 3.0 40.5 + - + +
104B LEU* 3.7 33.2 - - + +
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Residues in contact with PHE 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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98A ILE* 3.5 46.0 - - + -
101A LEU* 3.7 23.7 - - + +
102A TRP* 3.5 29.6 - + + -
105A SER* 3.4 20.4 - - - +
122A GLN 3.0 20.2 + - - +
123A SER 3.5 2.7 - - - +
125A VAL* 1.4 76.0 - - - +
127A LEU* 1.3 59.9 + - + +
129A LEU* 3.6 4.4 + - - +
130A ALA* 2.9 39.7 + - + +
385A LEU* 3.7 18.2 - - + -
386A ILE* 3.7 13.5 - - + -
389A LEU* 4.0 14.8 - - + -
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Residues in contact with LEU 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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123A SER 2.9 14.8 + - - +
124A LEU* 3.4 13.7 - - + +
126A PHE* 1.3 79.7 - - + +
128A LEU* 1.4 56.9 + - + +
130A ALA* 3.4 4.8 + - + +
131A THR* 3.0 39.7 + - + +
178A LEU* 3.8 32.8 - - + +
179A LEU* 5.3 3.1 - - + +
182A SER* 3.4 34.1 - - - +
186A LEU* 6.2 0.2 - - + -
385A LEU* 3.8 30.5 - - + -
389A LEU* 6.0 3.6 - - + -
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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 LEU* 3.1 22.9 + - + +
125A VAL* 3.4 16.8 + - + +
127A LEU* 1.4 76.6 - - - +
129A LEU* 1.4 55.6 + - - +
131A THR* 3.3 6.8 + - - -
132A LEU* 3.2 26.5 + - - +
175A GLN* 3.5 16.5 - - + +
178A LEU* 5.9 0.2 - - - -
179A LEU* 3.6 37.9 - - + +
100B TYR* 3.2 28.2 + - + +
104B LEU* 3.8 24.4 - - + +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.1 14.4 - - + -
104A LEU 5.2 0.9 - - - +
105A SER* 4.1 22.9 - - - -
125A VAL* 3.0 27.7 + - + +
126A PHE* 3.9 3.4 - - - +
128A LEU* 1.4 74.7 - - - +
130A ALA* 1.4 66.4 + - - +
132A LEU* 3.1 7.1 + - + +
133A PHE* 3.0 36.0 + - + -
101B LEU* 3.8 29.2 - - + -
104B LEU* 3.8 25.8 - - + +
129B LEU* 3.9 32.5 - - + -
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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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101A LEU* 4.2 17.4 - - + +
126A PHE* 2.9 30.2 + - + +
127A LEU* 3.4 8.0 + - + +
129A LEU* 1.4 76.6 - - - +
131A THR* 1.4 58.7 + - + +
133A PHE* 3.4 6.0 + - - +
134A SER* 2.9 32.1 + - - +
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Residues in contact with THR 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 3.0 24.4 + - + +
128A LEU 3.3 1.4 + - - -
130A ALA* 1.4 73.6 - - + +
132A LEU* 1.4 61.5 + - - +
134A SER* 3.6 9.4 - - - +
135A ALA* 2.9 31.2 + - - +
171A PHE* 3.6 5.1 - - - -
174A THR* 5.7 3.6 - - + -
175A GLN* 3.1 31.6 + - - +
178A LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU 3.2 19.3 + - - +
129A LEU* 3.1 6.8 + - + +
131A THR* 1.4 77.6 + - - +
133A PHE* 1.3 69.9 + - + +
135A ALA* 3.5 1.4 + - - +
136A LEU* 3.1 54.2 + - + +
171A PHE* 3.9 13.7 - - + -
95B PHE* 5.1 6.1 - - + -
97B GLY* 4.9 7.6 - - - +
100B TYR* 3.5 37.0 - - + -
101B LEU* 4.2 28.0 - - + +
104B LEU* 3.8 14.4 - - + -
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Residues in contact with PHE 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.7 30.5 - - + -
129A LEU* 3.0 39.4 + - + +
130A ALA* 3.8 7.0 - - - +
132A LEU* 1.3 82.8 - - + +
134A SER* 1.4 58.4 + - - +
136A LEU* 3.4 4.7 + - + +
137A ALA* 2.9 35.0 + - - +
101B LEU* 4.4 19.3 - - + -
129B LEU* 4.2 20.6 - - + -
132B LEU* 5.0 7.4 - - + -
133B PHE* 3.4 43.7 - + + -
136B LEU* 6.4 2.5 - - + -
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Residues in contact with SER 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA* 2.9 23.1 + - - +
131A THR* 3.6 11.4 - - - +
133A PHE* 1.4 75.4 - - - +
135A ALA* 1.4 60.2 + - - +
137A ALA* 4.2 3.0 - - - +
138A GLY* 3.4 19.2 + - - -
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Residues in contact with ALA 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A THR 2.9 18.1 + - - +
132A LEU 3.8 3.6 - - - +
134A SER* 1.4 77.2 - - - +
136A LEU* 1.3 58.0 + - - +
138A GLY 3.5 1.0 + - - -
139A LEU* 3.1 34.9 + - + +
171A PHE* 3.8 25.8 - - + -
95B PHE* 4.9 11.4 - - + -
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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 LEU* 3.1 43.3 + - + +
133A PHE* 4.0 5.2 - - + +
135A ALA* 1.3 78.7 - - + +
137A ALA* 1.3 56.1 + - - +
139A LEU* 3.6 11.7 + - + +
140A PRO* 3.4 9.5 - - - +
88B GLU* 2.8 28.1 - - - +
91B LEU* 4.9 2.0 - - + +
92B ILE* 3.9 36.1 - - + +
95B PHE* 4.0 29.6 - - + -
97B GLY* 4.7 10.5 - - - -
133B PHE* 4.3 19.5 - - + -
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Residues in contact with ALA 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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84A TYR* 4.5 11.4 - - + +
88A GLU* 5.7 3.1 - - - +
133A PHE* 2.9 18.9 + - + +
134A SER* 4.2 3.4 - - - +
136A LEU* 1.3 76.3 - - - +
138A GLY* 1.3 57.7 + - - +
140A PRO* 3.5 3.5 - - - +
141A TRP* 3.4 14.4 + - - -
84B TYR* 3.1 22.7 + - - +
88B GLU* 3.3 8.7 - - - -
133B PHE* 4.5 11.6 - - + -
137B ALA* 5.6 4.7 - - + -
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Residues in contact with GLY 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 SER 3.4 12.1 + - - -
135A ALA 3.9 2.9 - - - -
136A LEU 3.3 0.2 - - - -
137A ALA* 1.3 78.1 - - - +
139A LEU* 1.3 61.9 + - - +
140A PRO* 3.5 1.6 - - - -
141A TRP* 3.3 14.0 + - - +
142A SER* 3.1 23.2 + - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA* 3.1 19.9 + - + +
136A LEU* 3.7 12.1 - - + +
138A GLY* 1.3 75.5 - - - +
140A PRO* 1.4 63.2 - - + +
142A SER* 3.3 7.3 + - - -
143A LEU* 2.9 29.5 + - - +
163A PHE* 4.5 16.2 - - + -
164A MET* 4.6 5.2 - - - -
167A ALA* 4.0 21.1 - - + -
91B LEU* 3.7 34.1 - - + -
95B PHE* 3.7 32.1 - - + -
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Residues in contact with PRO 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 LEU 3.4 13.5 - - - +
137A ALA 3.5 11.7 - - - +
138A GLY 3.5 0.7 - - - -
139A LEU* 1.4 88.4 - - + +
141A TRP* 1.4 55.4 + - - +
143A LEU* 3.5 4.7 + - + +
144A TYR* 3.0 26.9 + - - +
84B TYR* 3.8 21.8 - - + -
87B THR* 3.9 19.5 - - + +
88B GLU* 3.4 32.1 - - + +
91B LEU* 3.5 16.4 - - + -
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Residues in contact with TRP 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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77A PHE* 3.2 31.3 - + + -
80A TRP* 3.9 23.1 - - + -
81A SER* 3.7 36.8 - - - -
84A TYR* 3.6 43.1 - + + -
137A ALA 3.4 20.2 - - - -
138A GLY* 3.5 10.8 - - - +
139A LEU 3.3 0.4 - - - -
140A PRO* 1.4 74.5 - - - +
142A SER* 1.4 57.3 + - - +
144A TYR* 3.2 5.7 + + + +
145A ASN 3.0 23.0 + - - -
84B TYR* 3.3 23.1 - + - -
141B TRP* 4.2 22.7 - + - -
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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 GLY 3.1 13.9 + - - -
139A LEU* 3.5 15.9 - - - +
141A TRP* 1.4 72.8 - - - +
143A LEU* 1.3 62.3 + - - +
145A ASN* 3.5 6.2 + - - +
146A THR* 3.3 28.6 + - - +
163A PHE* 3.2 20.0 - - - -
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Residues in contact with LEU 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU 2.9 17.3 + - - +
140A PRO* 3.6 5.8 - - + +
142A SER* 1.3 74.4 - - - +
144A TYR* 1.4 58.6 + - - +
146A THR* 4.2 1.6 - - - -
147A PHE* 3.0 51.0 + - + +
160A LEU* 6.0 3.6 - - + +
163A PHE* 3.6 32.7 - - + -
164A MET* 5.2 3.4 - - + -
87B THR* 3.7 26.9 - - + -
91B LEU* 3.9 19.1 - - + -
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Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.5 28.5 - + + -
140A PRO 3.0 14.5 + - - +
141A TRP* 3.2 11.6 + + + +
143A LEU* 1.4 75.2 - - - +
145A ASN* 1.3 58.1 + - - +
148A VAL* 2.8 76.7 + - + +
149A ILE* 3.4 19.1 + - + -
80B TRP* 3.7 39.2 - + - -
83B LEU* 5.4 5.6 - - + -
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Residues in contact with ASN 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 5.1 4.9 - - - +
77A PHE* 4.0 20.8 - - + -
141A TRP 3.0 12.2 + - - +
142A SER* 3.8 9.8 + - - +
143A LEU 3.5 0.2 - - - -
144A TYR* 1.3 76.9 - - - +
146A THR* 1.3 67.1 + - - +
149A ILE* 3.2 26.9 + - - +
150A GLU* 2.9 49.7 + - - +
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Residues in contact with THR 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A SER* 3.3 13.3 + - - +
143A LEU 3.6 2.6 + - - -
145A ASN* 1.3 84.9 - - - +
147A PHE* 1.3 83.9 + - - +
150A GLU* 3.4 13.0 - - + +
151A GLU* 3.3 20.8 + - - +
156A ASN* 3.4 23.9 - - - +
158A GLN* 4.0 14.4 - - - +
163A PHE* 3.6 20.2 - - + -
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Residues in contact with PHE 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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143A LEU* 3.0 34.7 + - + +
146A THR* 1.3 96.1 + - - +
148A VAL* 1.3 66.6 + - + +
151A GLU* 3.3 25.2 - - + +
156A ASN* 3.7 13.2 - - - -
158A GLN* 3.5 25.8 - - + -
159A THR* 3.5 25.4 - - - -
160A LEU* 3.6 16.2 - - + -
163A PHE* 3.6 27.8 - + + -
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Residues in contact with VAL 148 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TYR* 2.8 69.1 + - + +
146A THR 3.5 0.4 - - - -
147A PHE* 1.3 81.9 - - + +
149A ILE* 1.4 58.6 + - + +
150A GLU 3.7 0.2 - - - -
152A LYS* 2.9 35.1 + - + +
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Residues in contact with ILE 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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70A TYR* 4.3 3.8 - - + -
73A ASP* 4.3 18.2 - - + +
74A LYS* 4.0 31.9 - - + +
77A PHE* 3.6 27.1 - - + -
144A TYR* 3.4 36.7 + - + -
145A ASN* 3.2 23.7 + - - +
148A VAL* 1.4 75.1 - - + +
150A GLU* 1.3 74.6 + - - +
151A GLU 3.3 0.2 + - - -
152A LYS* 4.7 0.4 - - - -
153A HIS* 3.1 44.6 + - + +
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Residues in contact with GLU 150 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.1 23.7 + - - -
74A LYS* 4.5 5.0 - - - +
145A ASN* 2.9 41.6 + - - +
146A THR* 3.4 17.5 - - + +
149A ILE* 1.3 74.8 - - - +
151A GLU* 1.3 57.7 + - - +
153A HIS 3.9 0.3 - - - -
154A GLY 3.5 1.2 + - - -
155A PHE* 2.7 43.1 + - - +
156A ASN* 3.0 19.1 + - + +
261A SER* 6.1 2.5 - - - -
263A HIS* 2.9 30.1 + - - -
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Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR 3.3 5.7 + - - +
147A PHE* 3.3 36.6 - - + +
148A VAL 3.8 0.4 + - - +
149A ILE 3.2 0.6 - - - -
150A GLU* 1.3 77.0 - - - +
152A LYS* 1.4 65.1 + - - +
154A GLY* 3.2 15.4 + - - -
156A ASN* 2.8 47.4 + - - +
157A GLN 5.5 0.2 - - - -
158A GLN 4.1 4.2 - - - +
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASP* 4.7 6.5 - - - +
148A VAL* 2.9 23.8 + - + +
149A ILE* 3.3 4.0 + - - +
151A GLU* 1.4 76.5 - - - +
153A HIS* 1.3 74.4 + - + +
154A GLY 3.3 2.6 + - - -
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Residues in contact with HIS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS 4.6 4.0 + - - -
69A LEU* 3.8 11.3 - - + +
70A TYR* 3.5 56.8 + + + +
73A ASP* 2.9 34.6 + - - +
149A ILE* 3.1 32.4 + - + +
150A GLU 3.9 0.2 - - - -
151A GLU 3.3 0.2 - - - -
152A LYS* 1.3 87.0 + - + +
154A GLY* 1.3 61.5 + - - +
155A PHE* 3.3 20.0 + - + -
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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