Contacts of the helix formed by residues 100 - 124 (chain B) in PDB entry 3V3Q
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 SER 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU 4.2 0.2 + - - -
99B LEU* 1.3 73.5 - - - +
101B PRO* 1.3 68.6 - - - +
102B ALA 3.6 0.6 + - - -
103B ASP* 2.9 28.0 + - - +
104B GLN* 2.9 25.5 + - - +
188B GLN* 2.6 34.4 + - - -
189B GLU* 3.8 19.7 + - - -
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Residues in contact with PRO 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU 4.0 2.9 - - - +
100B SER* 1.3 86.7 - - - +
102B ALA* 1.3 57.8 + - - +
104B GLN* 3.4 15.7 + - + +
105B ASP* 3.0 37.1 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B SER* 3.2 1.8 + - - -
101B PRO* 1.3 78.2 - - - +
103B ASP* 1.3 59.9 + - - +
105B ASP* 3.5 5.9 + - - +
106B LEU* 3.0 30.3 + - - +
188B GLN* 3.6 29.8 - - + +
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.3 8.9 - - + +
100B SER* 2.9 30.3 + - - +
102B ALA* 1.3 76.3 - - - +
104B GLN* 1.3 59.4 + - - +
106B LEU* 3.5 2.6 + - - +
107B LEU* 3.0 38.7 + - - +
186B GLY 4.2 2.1 - - - +
187B LEU* 3.6 22.9 - - + +
188B GLN* 2.8 28.8 + - - +
189B GLU* 2.9 34.8 + - - +
193B VAL* 4.4 6.1 - - + +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 3.0 25.5 - - - +
96B PHE* 3.4 47.0 + - + +
97B ALA* 3.4 17.3 + - - +
99B LEU* 2.7 26.9 + - + +
100B SER 2.9 14.0 + - - +
101B PRO* 3.6 14.8 - - + +
102B ALA 3.3 0.2 - - - -
103B ASP* 1.3 75.3 - - - +
105B ASP* 1.3 68.3 + - - +
107B LEU* 4.8 0.4 - - - -
108B LEU* 3.1 26.3 + - + +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 5.6 6.9 + - - -
101B PRO* 3.0 21.9 + - - +
102B ALA* 4.0 6.1 - - - +
104B GLN* 1.3 82.8 - - - +
106B LEU* 1.4 56.5 + - - +
108B LEU* 3.8 10.4 - - - +
109B GLU* 3.0 47.6 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA 3.0 18.9 + - - +
103B ASP* 3.9 4.7 - - - +
105B ASP* 1.4 72.4 - - - +
107B LEU* 1.3 60.6 + - - +
109B GLU* 4.7 9.9 - - + +
110B SER* 2.7 52.6 + - - +
184B ARG* 3.9 14.8 - - + -
185B HIS 3.2 27.8 - - - +
186B GLY* 3.7 22.2 - - - +
187B LEU* 3.9 11.0 - - + +
263B ASP 6.1 1.8 - - - +
264B THR* 6.5 0.2 - - + -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 4.0 10.1 - - + -
99B LEU* 3.6 30.3 - - + -
103B ASP 3.0 26.3 + - - +
104B GLN 4.0 2.7 - - - +
106B LEU* 1.3 75.6 - - - +
108B LEU* 1.3 58.8 + - - +
110B SER* 3.9 4.0 - - - -
111B ALA* 3.0 34.5 + - - +
180B LEU* 3.5 29.6 - - + +
181B ILE* 4.4 3.6 - - + -
182B THR 3.3 28.9 - - - +
184B ARG* 3.9 13.3 + - + -
187B LEU* 4.1 11.7 - - + -
193B VAL* 4.0 16.2 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 3.8 25.1 - - + +
87B ARG* 4.1 33.7 - - + +
90B ALA* 3.8 18.2 - - + -
96B PHE* 4.0 16.6 - - + -
104B GLN* 3.1 20.2 + - + +
105B ASP* 3.8 11.4 - - - +
107B LEU* 1.3 79.1 - - - +
109B GLU* 1.3 58.8 + - + +
111B ALA* 3.3 1.7 + - - +
112B PHE* 2.9 33.1 + - - +
115B LEU* 5.2 0.3 - - - +
180B LEU* 3.7 20.8 - - + +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASP* 3.0 32.3 + - - +
106B LEU* 4.0 10.2 - - + +
108B LEU* 1.3 79.2 - - + +
110B SER* 1.3 61.2 + - - +
112B PHE* 3.5 7.6 + - - +
113B LEU 5.0 0.3 + - - -
256B ILE* 6.5 0.7 - - + -
259B LYS* 3.6 21.0 + - - -
260B ILE* 3.3 46.4 - - + +
263B ASP* 3.3 27.2 - - - +
264B THR* 4.0 8.2 - - + +
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 2.7 37.0 + - - +
107B LEU 4.0 0.7 - - - -
109B GLU* 1.3 76.3 - - - +
111B ALA* 1.3 57.6 + - - +
112B PHE 3.4 0.2 - - - -
113B LEU 5.2 1.1 + - - -
114B GLU* 3.2 8.3 + - - +
184B ARG* 3.2 46.9 + - - +
264B THR* 4.2 18.0 - - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 3.0 19.0 + - - +
108B LEU 4.0 1.6 - - - +
110B SER* 1.3 76.1 - - - +
112B PHE* 1.3 67.2 + - - +
113B LEU 3.4 1.8 - - - -
114B GLU* 3.2 8.9 + - - +
115B LEU* 2.8 42.1 + - + +
179B VAL* 3.9 4.0 - - + +
180B LEU* 3.9 19.7 - - + +
184B ARG* 3.6 13.5 - - - +
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.3 35.4 - - + -
82B SER* 4.1 3.6 - - - -
83B LEU* 4.0 23.1 - - + -
86B ILE* 3.8 29.2 - - + -
108B LEU 2.9 16.2 + - - +
109B GLU 3.5 9.4 + - - +
110B SER 3.4 2.2 - - - -
111B ALA* 1.3 78.1 - - - +
113B LEU* 1.3 87.7 + - + +
115B LEU* 3.7 5.5 - - - +
116B PHE* 2.8 32.8 + - + +
257B ILE* 3.9 21.1 - - + -
260B ILE* 3.9 26.7 - - + -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 4.6 10.8 - - + -
109B GLU 5.0 0.6 + - - -
110B SER 5.2 1.0 + - - +
111B ALA 3.4 0.4 - - - -
112B PHE* 1.3 102.3 - - + +
114B GLU* 1.3 63.2 + - - +
116B PHE* 3.2 4.4 + - + +
117B ILE* 2.9 29.9 + - - +
151B TRP* 4.5 22.0 - - + -
235B CYS* 3.9 28.3 - - + +
238B GLY 4.3 2.2 - - - -
239B LEU* 3.7 42.8 - - + +
242B ILE* 4.4 16.8 - - + -
257B ILE* 6.0 1.1 - - + -
260B ILE* 5.6 8.2 - - + +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B SER 3.2 12.5 + - - +
111B ALA* 3.2 3.8 + - - +
113B LEU* 1.3 79.5 - - - +
115B LEU* 1.3 56.4 + - - +
117B ILE* 3.4 5.9 + - - +
118B LEU* 2.8 32.3 + - - +
179B VAL* 3.5 26.8 - - + +
184B ARG* 3.0 26.5 + - - -
228B LEU* 5.1 0.5 - - - +
231B LEU* 3.9 23.4 - - + +
232B ARG* 3.2 41.4 + - - +
235B CYS* 3.9 22.7 - - + +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 3.4 38.6 - - + -
89B TRP* 3.9 15.0 - - + -
108B LEU* 5.0 1.1 - - + +
111B ALA* 2.8 42.6 + - + +
112B PHE* 3.8 1.1 - - - +
114B GLU* 1.3 71.8 - - - +
116B PHE* 1.3 65.3 + - - +
118B LEU* 4.5 3.6 - - + +
119B ARG* 2.9 37.6 + - - +
176B SER* 3.4 33.9 - - - +
179B VAL* 4.0 13.2 - - + -
180B LEU* 3.9 15.3 - - + +
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU 3.9 20.6 - - - -
79B LEU* 3.6 31.4 - - + -
82B SER* 3.7 25.1 - - - -
86B ILE* 3.9 6.6 - - - +
112B PHE* 2.8 29.1 + + + +
113B LEU* 3.4 6.5 - - + +
115B LEU* 1.3 76.4 - - - +
117B ILE* 1.3 68.1 + - + +
119B ARG* 4.2 2.0 - - - +
120B LEU* 3.0 60.1 + - + +
133B PHE* 4.4 15.0 - + - -
148B PHE* 4.2 20.0 - + - -
151B TRP* 4.5 9.9 - + - -
155B ILE* 5.2 1.1 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU 2.9 28.3 + - - +
114B GLU* 3.8 6.1 - - - +
116B PHE* 1.3 77.1 - - + +
118B LEU* 1.3 67.9 + - - +
120B LEU* 3.8 4.3 - - - +
121B ALA* 2.9 27.7 + - - +
151B TRP* 3.4 38.6 - - + -
155B ILE* 3.9 22.6 - - + +
158B PHE* 4.6 3.8 - - + -
231B LEU* 3.8 15.7 - - + +
234B LEU* 3.9 22.4 - - + -
235B CYS* 3.8 24.5 - - - +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU 2.8 22.7 + - - +
115B LEU* 3.9 4.7 - - + +
117B ILE* 1.3 73.9 - - - +
119B ARG* 1.3 62.1 + - + +
121B ALA* 3.6 3.9 - - - +
122B TYR* 3.1 22.9 + - - +
158B PHE* 3.9 26.0 - - + -
162B LEU* 4.1 7.4 - - + -
172B PHE* 3.5 26.2 - - + -
175B LEU* 4.5 16.4 - - + -
176B SER* 3.8 32.5 - - - +
179B VAL* 3.9 18.8 - - + -
227B LYS* 5.7 1.1 - - + -
228B LEU* 5.5 0.7 - - + -
231B LEU* 3.9 11.4 - - + -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B HIS* 4.5 12.5 + - + +
44B SER* 2.7 48.8 + - - -
85B VAL* 3.5 12.7 - - - +
86B ILE* 3.9 12.2 - - - +
89B TRP* 4.3 18.9 - - - +
115B LEU* 2.9 39.4 + - - +
116B PHE 4.4 0.4 - - - +
118B LEU* 1.3 74.8 - - + +
120B LEU* 1.3 66.2 + - - +
122B TYR* 3.5 1.7 + - - +
123B ARG* 3.0 47.0 + - - +
172B PHE* 4.1 23.6 - - + -
176B SER* 4.9 8.0 + - - -
301B GOL 5.4 1.7 + - - -
302B NA 3.1 26.3 - - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PHE* 3.0 41.2 + - + +
117B ILE* 3.8 3.8 - - - +
118B LEU 3.3 0.2 - - - -
119B ARG* 1.3 77.8 - - - +
121B ALA* 1.3 52.3 + - - +
123B ARG* 3.2 11.4 + - - +
124B SER* 2.6 50.6 + - - +
131B LEU* 4.3 15.7 - - + -
132B ILE 3.3 26.9 - - - +
133B PHE* 3.6 37.5 - - + -
148B PHE* 5.1 0.7 - - + -
152B ILE* 5.1 3.6 - - + -
155B ILE* 4.4 20.2 - - + -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE 2.9 19.4 + - - +
118B LEU 3.6 4.0 - - - +
119B ARG 3.2 0.2 - - - -
120B LEU* 1.3 78.5 - - - +
122B TYR* 1.3 61.8 + - - +
124B SER* 3.6 4.1 + - - -
155B ILE* 4.4 8.9 - - + +
158B PHE* 3.7 24.9 - - + -
159B SER* 2.8 45.0 + - - +
162B LEU* 4.3 5.1 - - + +
163B HIS* 3.4 8.1 + - - -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B HIS* 4.2 15.9 - + - -
118B LEU 3.1 8.8 + - - +
119B ARG 3.9 2.5 - - - +
121B ALA* 1.3 79.3 - - - +
123B ARG* 1.3 60.7 + - - +
124B SER 3.9 0.2 - - - +
162B LEU* 3.8 18.3 - - + +
163B HIS* 3.5 27.5 - + - -
167B VAL* 2.5 38.2 + - + -
168B ASP* 3.4 14.9 - - - -
169B VAL* 3.6 9.6 + - + +
172B PHE* 3.5 62.4 - + + -
301B GOL 4.4 11.2 - - - -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER 5.0 0.4 + - - -
46B PRO* 3.8 11.4 - - + +
119B ARG* 3.0 43.4 + - - +
120B LEU* 3.6 17.2 - - - +
122B TYR* 1.3 79.0 - - - +
124B SER* 1.3 62.7 + - - +
125B LYS* 4.2 6.6 - - - -
132B ILE* 3.0 55.4 + - + +
133B PHE* 3.3 14.2 - - - +
134B CYS* 3.2 27.7 - - - +
301B GOL 3.2 31.3 + - - +
302B NA 3.2 24.2 - - - -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 2.6 31.8 + - - +
121B ALA* 3.6 5.8 + - - -
122B TYR 3.4 1.2 - - - -
123B ARG* 1.3 77.7 - - - +
125B LYS* 1.3 70.6 + - - +
126B PRO* 3.5 3.6 - - - -
130B LYS 3.1 14.1 - - - -
131B LEU* 3.5 14.3 - - - +
132B ILE* 3.3 20.6 + - - +
156B LEU* 5.3 2.9 - - - -
159B SER* 4.5 6.1 - - - -
163B HIS* 3.0 23.6 + - - -
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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
------------------------------------------------------------
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