Contacts of the helix formed by residues 104 - 130 (chain B) in PDB entry 5YWB
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 LEU 104 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 1.3 69.6 - - - +
105B HIS* 1.3 59.5 + - - +
106B LEU 2.9 11.5 + - - -
107B TYR* 3.1 34.7 + - + +
108B MET* 3.1 35.1 + - + +
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP* 5.7 10.1 - - + -
26B CYS* 5.1 14.6 - - + +
29B ASP* 3.2 24.2 - - + +
30B ALA* 6.2 1.6 - - + +
33B VAL* 5.5 0.7 - - - +
103B HIS 3.4 0.6 - - - -
104B LEU* 1.3 76.3 - - - +
106B LEU* 1.3 63.5 + - + +
107B TYR 3.5 0.2 - - - -
108B MET* 4.2 11.1 - - - +
109B PRO* 3.9 6.4 - - - +
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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
----------------------------------------------------------
25B GLY 5.1 2.0 - - - -
26B CYS* 3.6 37.2 - - - +
29B ASP* 4.8 6.6 - - + +
92B GLY* 5.7 1.0 - - - -
95B SER* 5.0 13.9 - - - +
103B HIS* 3.6 46.2 - - + +
104B LEU 2.9 1.4 + - - -
105B HIS* 1.3 84.4 - - + +
107B TYR* 1.3 59.6 + - + +
108B MET 3.6 0.2 - - - -
109B PRO* 4.1 8.4 - - - +
168B ARG* 4.6 15.6 + - - -
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU 5.4 2.5 - - - +
89B ILE* 5.6 11.6 - - + +
92B GLY* 3.5 39.5 - - - -
93B ILE* 5.4 12.6 - - + -
96B ASP* 4.9 9.6 - - + -
103B HIS 3.3 27.6 - - - -
104B LEU* 3.1 38.4 + - + +
106B LEU* 1.3 77.7 - - + +
108B MET* 1.3 77.2 + - - +
109B PRO* 3.3 2.8 - - - -
110B ALA* 3.6 13.5 + - + +
111B GLY* 3.9 6.1 + - - -
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.1 15.3 - - + -
104B LEU* 3.1 32.1 + - + +
105B HIS* 4.2 7.2 - - - -
107B TYR* 1.3 91.6 - - - +
109B PRO* 1.3 70.9 - - + +
111B GLY* 3.1 7.7 + - - +
112B MET* 3.0 45.4 + - + +
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 3.7 31.4 - - + +
32B ASN* 4.4 17.9 - - + +
33B VAL* 3.8 11.4 - - + -
36B HIS* 3.9 8.1 + - + +
88B GLU* 4.9 3.4 - - - +
105B HIS 3.9 10.8 - - - +
106B LEU 4.1 6.5 - - - +
107B TYR* 3.5 3.8 - - - -
108B MET* 1.3 93.2 - - + +
110B ALA* 1.3 57.3 + - - +
112B MET* 3.3 3.2 + - + +
113B ALA* 2.9 30.7 + - - +
150B LYS* 5.4 6.3 - - - +
153B LYS* 5.0 7.0 - - - -
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.0 9.4 - - + +
88B GLU* 3.6 42.3 + - + +
89B ILE* 3.8 23.3 - - + +
107B TYR* 3.6 9.9 + - - +
108B MET 3.2 1.0 - - - -
109B PRO* 1.3 77.6 - - - +
111B GLY* 1.3 58.6 + - - +
113B ALA* 3.3 1.9 + - - +
114B PHE* 2.9 30.8 + - - +
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 4.7 9.0 - - - +
107B TYR 3.9 4.0 + - - -
108B MET* 3.1 12.1 + - - -
110B ALA* 1.3 78.1 - - - +
112B MET* 1.3 65.8 + - - +
114B PHE* 3.7 15.7 - - - +
115B MET* 3.8 14.4 + - - +
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Residues in contact with MET 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.1 21.1 - - + +
36B HIS* 3.6 24.1 - - + +
37B VAL* 3.9 28.0 - - + +
40B LEU* 3.7 28.9 - - + +
41B PHE* 6.5 0.2 - - + -
108B MET* 3.0 38.5 + - + +
109B PRO* 3.8 1.3 - - + +
111B GLY* 1.3 81.7 - - - +
113B ALA* 1.3 62.1 + - - +
114B PHE 3.1 1.7 + - - -
115B MET* 3.3 7.3 + - + +
116B ALA* 2.9 26.5 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS* 3.4 31.0 - - + +
85B LEU* 3.5 27.1 - - + +
88B GLU* 5.3 0.4 - - - +
109B PRO 2.9 16.0 + - - +
112B MET* 1.3 76.5 - - - +
114B PHE* 1.3 56.2 + - - +
116B ALA* 3.6 1.5 - - - +
117B ALA* 2.8 32.2 + - - +
142B TYR* 4.9 0.5 + - - -
150B LYS* 6.2 2.2 - - - +
175B LEU* 6.0 0.9 - - + -
179B TYR* 4.1 9.6 - - - +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 3.4 31.6 - - + -
85B LEU* 3.5 21.9 - - + +
86B VAL* 5.6 6.3 - - + -
89B ILE* 5.3 12.3 - - + -
110B ALA 2.9 17.0 + - - +
111B GLY* 3.7 9.6 - - - +
112B MET 3.1 0.2 - - - -
113B ALA* 1.3 77.9 - - - +
115B MET* 1.3 75.6 + - + +
117B ALA* 3.3 2.3 + - - +
118B ILE* 3.0 57.2 + - + +
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Residues in contact with MET 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.3 30.4 - - + +
44B PHE* 6.3 3.4 - - + -
111B GLY 3.8 12.1 + - - +
112B MET* 3.3 6.9 + - - +
114B PHE* 1.3 96.3 - - + +
116B ALA* 1.3 57.7 + - - +
118B ILE* 3.7 15.7 - - + +
119B THR* 2.8 31.6 + - - +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS* 3.6 20.6 - - + +
39B LEU* 3.9 8.8 - - + +
40B LEU* 4.0 9.6 - - - +
112B MET 2.9 17.2 + - - +
113B ALA 3.6 2.5 - - - +
114B PHE 3.2 0.2 - - - -
115B MET* 1.3 77.2 - - - +
117B ALA* 1.3 56.6 + - - +
119B THR* 3.3 5.0 + - - +
120B SER* 2.8 28.1 + - - -
142B TYR* 3.2 32.5 - - + +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 4.4 13.7 - - + +
81B LEU* 4.7 21.5 - - + -
82B LEU* 5.8 2.0 - - + +
85B LEU* 4.6 11.0 - - + -
113B ALA 2.8 17.6 + - - +
114B PHE 3.8 3.1 - - - +
116B ALA* 1.3 73.2 - - - +
118B ILE* 1.3 62.8 + - + +
120B SER* 3.2 8.8 + - - -
121B VAL* 2.9 31.3 + - - +
142B TYR* 4.9 1.0 + - - -
143B TRP* 5.8 3.4 - - + -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 5.5 6.1 - - + -
114B PHE* 3.0 53.6 + - + +
115B MET* 3.8 17.7 - - + +
117B ALA* 1.3 76.2 - - + +
119B THR* 1.3 58.7 + - - +
121B VAL* 3.2 11.6 + - + +
122B VAL* 2.9 34.1 + - + +
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.9 21.3 - - + -
40B LEU* 3.6 12.3 - - + +
43B THR* 3.2 43.3 + - + +
44B PHE* 5.6 1.0 - - - -
115B MET* 2.8 18.0 + - - +
116B ALA 3.7 5.8 - - - +
118B ILE* 1.3 75.0 - - - +
120B SER* 1.3 62.7 + - - +
122B VAL* 3.2 10.1 + - - +
123B TYR* 2.8 31.4 + - + +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.8 2.9 - - - -
74B ARG* 5.3 5.5 + - - -
78B THR* 5.4 3.2 + - - -
116B ALA 2.8 15.0 + - - -
117B ALA* 3.2 12.8 + - - -
119B THR* 1.3 75.4 - - - +
121B VAL* 1.3 59.7 + - - +
123B TYR* 3.3 2.1 + - - +
124B TYR* 2.9 29.5 + - - +
139B LEU* 3.9 28.6 - - - +
142B TYR* 5.6 0.4 - - - -
143B TRP* 3.8 26.4 - - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 3.7 40.6 - - + -
78B THR* 3.6 33.7 - - + +
117B ALA 2.9 10.0 + - - +
118B ILE* 3.4 15.0 - - + +
120B SER* 1.3 77.6 - - - +
122B VAL* 1.3 62.3 + - + +
124B TYR* 3.2 6.4 + - - +
125B HIS* 2.9 29.2 + - + +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 5.1 3.4 - - - +
47B LEU* 4.6 16.4 - - + -
118B ILE* 2.9 29.4 + - + +
119B THR* 3.2 13.4 + - - +
121B VAL* 1.3 79.1 - - + +
123B TYR* 1.3 63.2 + - - +
125B HIS* 3.3 8.9 + - + +
126B ASN* 2.9 36.7 + - - +
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.5 11.0 - - + -
42B ILE* 3.4 24.4 + - + +
43B THR* 3.3 38.8 - - - -
46B ILE* 3.3 28.8 - - + +
119B THR* 2.8 18.7 + - + +
120B SER* 3.5 9.6 - - - +
122B VAL* 1.3 78.3 - - - +
124B TYR* 1.3 57.8 + - - +
126B ASN* 3.1 9.3 + - + +
127B ILE* 2.9 37.1 + - + +
135B LEU* 4.1 49.1 - - + -
138B ALA* 4.7 8.1 - - + +
139B LEU* 4.3 21.5 - - + -
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.4 38.3 - + - +
69B PRO 4.7 1.9 + - - -
71B HIS* 3.1 46.6 + + + -
74B ARG* 3.3 53.3 + - - -
75B TRP* 4.2 11.2 - - + +
120B SER 2.9 16.9 + - - +
121B VAL* 3.2 6.5 + - - +
123B TYR* 1.3 76.9 - - - +
125B HIS* 1.3 57.9 + - - +
127B ILE* 4.3 8.1 - - + +
128B GLU* 2.9 30.5 + - + +
136B LEU* 4.5 16.8 - - + -
139B LEU* 4.5 12.6 - - + -
189B VAL* 4.7 3.3 - - + +
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Residues in contact with HIS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 4.5 27.4 - + - -
75B TRP* 5.4 10.0 - + + -
121B VAL* 2.9 17.6 + - + +
122B VAL* 3.7 9.5 + - - +
124B TYR* 1.3 77.9 - - - +
126B ASN* 1.3 68.7 + - - +
128B GLU* 3.3 5.9 + - + +
129B THR* 3.0 36.0 + - + +
223B ASN* 4.9 13.2 + - + -
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.4 14.3 + - + +
47B LEU* 4.2 24.2 + - - +
50B GLY* 5.2 9.3 - - - -
122B VAL* 2.9 29.2 + - - +
123B TYR* 3.1 9.4 + - + +
125B HIS* 1.3 88.3 + - - +
127B ILE* 1.3 59.3 + - + +
129B THR* 3.1 23.9 - - + +
130B SER* 3.2 16.6 + - - +
135B LEU* 4.8 9.6 - - + +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.4 0.2 - - - +
68B PHE* 3.7 29.0 - - + -
123B TYR* 2.9 29.4 + - + +
124B TYR* 3.9 12.1 - - + +
126B ASN* 1.3 75.9 - - - +
128B GLU* 1.3 65.4 + - - +
129B THR 3.1 1.8 - - - -
130B SER 2.9 24.1 - - - +
131B ASN* 3.5 4.2 + - - +
132B PHE 4.5 9.2 - - - +
135B LEU* 3.5 47.3 - - + +
136B LEU* 3.6 31.0 - - + -
139B LEU* 4.8 4.7 - - + -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 4.2 19.9 - - + -
66B LEU* 3.5 41.2 + - - +
67B HIS* 5.5 3.4 - - + +
68B PHE* 4.3 5.3 - - + -
71B HIS* 4.6 20.0 - - + +
124B TYR* 2.9 19.3 + - + +
125B HIS* 3.8 7.2 - - + +
127B ILE* 1.3 76.9 - - - +
129B THR* 1.3 62.7 + - - +
130B SER* 4.6 0.2 - - - -
223B ASN* 6.0 2.5 - - + -
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.6 17.7 + - - +
65B TRP* 5.0 14.2 - - - -
66B LEU* 5.0 2.4 - - - +
125B HIS* 3.0 26.7 + - + +
126B ASN* 3.1 28.3 - - + +
128B GLU* 1.3 80.2 - - - +
130B SER* 1.3 63.6 + - - +
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.0 1.3 - - - -
126B ASN 3.2 16.1 + - - +
127B ILE* 2.9 14.4 + - - +
129B THR* 1.3 86.3 - - - +
131B ASN* 1.3 66.8 + - - +
132B PHE* 3.5 23.3 - - - -
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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