Contacts of the helix formed by residues 107 - 130 (chain F) in PDB entry 6BAA
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 TYR 107 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F GLU 5.6 0.7 - - - -
89F ILE* 3.5 20.2 - - + +
92F GLY* 3.7 29.4 - - - -
93F ILE* 3.7 26.0 - - + +
96F ASP* 3.2 28.6 + - + -
102F ARG* 5.2 6.2 + - - -
103F HIS 3.3 26.7 - - - -
104F LEU* 4.1 16.4 - - - +
105F HIS 3.5 0.4 - - - -
106F LEU* 1.3 81.0 - - + +
108F MET* 1.3 89.5 + - + +
109F PRO* 2.9 6.1 - - - -
110F ALA* 3.4 7.7 + - - +
111F GLY 3.3 14.4 + - - -
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Residues in contact with MET 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LEU* 3.0 36.8 + - + +
105F HIS* 5.2 0.2 - - - -
107F TYR* 1.3 97.8 - - + +
109F PRO* 1.3 68.9 - - + +
111F GLY* 3.1 4.9 + - - +
112F MET* 2.9 45.5 + - + +
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Residues in contact with PRO 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F ASP* 4.1 27.4 - - + +
32F ASN* 4.9 9.2 - - + -
33F VAL* 4.4 12.1 - - + +
36F HIS* 3.7 12.7 - - - -
105F HIS* 3.2 27.1 - - + +
106F LEU 4.2 1.6 - - - -
107F TYR* 2.9 14.6 - - - +
108F MET* 1.3 96.0 - - + +
110F ALA* 1.3 63.3 + - + +
112F MET* 3.2 12.1 + - + +
113F ALA* 3.1 16.5 + - - +
153F LYS* 5.8 5.6 - - - +
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Residues in contact with ALA 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LEU* 4.2 11.1 - - + +
88F GLU* 4.7 13.7 - - + +
89F ILE* 3.8 23.9 - - + +
106F LEU 5.9 0.2 - - - +
107F TYR* 3.6 11.9 - - - +
108F MET 3.2 0.4 - - - -
109F PRO* 1.3 83.2 - - + +
111F GLY* 1.3 62.6 + - - +
113F ALA* 2.9 19.7 + - - +
114F PHE* 3.1 11.6 + - - +
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Residues in contact with GLY 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ILE* 3.4 17.8 - - - +
107F TYR 3.3 5.6 + - - -
108F MET* 3.1 11.6 + - - -
110F ALA* 1.3 78.6 - - - +
112F MET* 1.3 62.2 + - - +
114F PHE* 3.1 9.3 + - - +
115F MET* 3.1 25.9 + - - +
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Residues in contact with MET 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B MET* 5.6 1.3 - - - -
33F VAL* 4.1 17.0 - - + +
36F HIS* 3.7 15.9 - - + +
37F VAL* 3.7 28.0 - - + -
40F LEU* 5.1 7.2 - - + +
108F MET* 2.9 52.1 + - + +
109F PRO* 3.7 11.4 - - + +
110F ALA 3.2 0.2 - - - -
111F GLY* 1.3 75.9 - - - +
113F ALA* 1.3 51.8 + - - +
115F MET* 3.3 11.0 + - + +
116F ALA* 2.7 35.5 + - - +
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Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F HIS* 3.2 37.4 - - + +
85F LEU* 3.4 20.8 - - + +
109F PRO 3.1 6.8 + - - +
110F ALA* 2.9 13.8 + - - +
112F MET* 1.3 77.7 - - - +
114F PHE* 1.3 51.2 + - - +
116F ALA* 3.4 1.5 - - - +
117F ALA* 2.6 37.6 + - - +
142F TYR* 5.4 0.3 + - - -
175F LEU* 6.1 0.7 - - + -
179F TYR* 4.5 6.4 + - - +
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Residues in contact with PHE 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F LEU* 3.9 35.9 - - + -
85F LEU* 3.4 16.9 - - + +
86F VAL* 4.5 22.9 - - + -
89F ILE* 5.6 4.7 - - + -
110F ALA 3.1 10.5 + - - +
111F GLY* 3.1 12.5 + - - +
113F ALA* 1.3 77.1 - - - +
115F MET* 1.3 81.9 + - - +
117F ALA* 3.3 4.1 + - - +
118F ILE* 3.2 40.5 + - + +
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Residues in contact with MET 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F LEU* 4.5 15.7 - - + -
111F GLY 3.1 14.2 + - - +
112F MET* 3.6 11.7 - - + +
114F PHE* 1.3 98.3 - - + +
116F ALA* 1.3 63.1 + - - +
118F ILE* 3.4 13.1 + - + +
119F THR* 3.2 28.4 + - + +
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Residues in contact with ALA 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F HIS* 3.5 26.0 - - + +
39F LEU* 4.0 3.7 - - + +
40F LEU* 3.4 13.9 - - + +
112F MET 2.7 21.0 + - - +
113F ALA* 3.4 5.6 - - - +
115F MET* 1.3 72.0 - - - +
117F ALA* 1.3 53.6 + - - +
119F THR* 2.6 23.9 + - - -
120F SER* 2.6 26.0 + - - -
142F TYR* 4.0 12.6 - - - +
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Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F THR* 5.4 2.7 - - + +
81F LEU* 3.7 19.7 - - + -
82F LEU* 3.4 29.7 - - + +
85F LEU* 4.7 0.2 - - + -
113F ALA 2.6 20.3 + - - +
114F PHE* 3.6 5.6 - - - +
115F MET 3.3 0.2 - - - -
116F ALA* 1.3 73.3 - - - +
118F ILE* 1.3 61.7 + - - +
120F SER* 2.5 25.3 + - - +
121F VAL* 3.1 12.3 + - - +
142F TYR* 5.5 1.3 - - - -
143F TRP* 5.5 2.5 - - + -
179F TYR* 5.6 1.6 - - - +
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Residues in contact with ILE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F LEU* 4.0 21.5 - - + -
114F PHE* 3.2 40.2 + - + +
115F MET* 3.4 15.7 + - + +
116F ALA 3.3 0.2 - - - -
117F ALA* 1.3 76.8 - - - +
119F THR* 1.3 59.9 + - + +
121F VAL* 3.2 11.4 - - + +
122F VAL* 2.9 38.9 + - + +
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Residues in contact with THR 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 4.2 10.0 - - - +
40F LEU* 3.4 24.7 - - + +
43F THR* 5.0 1.8 - - - +
44F PHE* 5.4 10.5 - - + -
47F LEU* 4.9 16.7 - - + +
115F MET* 3.2 14.5 + - + +
116F ALA* 2.6 29.0 + - - -
118F ILE* 1.3 73.0 - - + +
120F SER* 1.3 55.9 + - - +
121F VAL 2.9 5.2 + - - -
122F VAL* 4.4 4.7 - - - +
123F TYR* 2.9 35.6 + - - +
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Residues in contact with SER 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 3.6 23.8 - - - -
78F THR* 5.2 3.9 - - - +
116F ALA 2.6 18.5 + - - -
117F ALA* 2.5 26.0 + - - +
119F THR* 1.3 72.5 + - - +
121F VAL* 1.3 58.4 + - - +
123F TYR* 4.4 6.5 - - - -
124F TYR* 3.9 15.1 + - - +
139F LEU* 4.2 12.7 - - - +
142F TYR* 4.7 0.2 - - - -
143F TRP* 3.6 31.8 - - - -
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ARG* 5.5 2.7 - - + -
75F TRP* 3.6 32.7 - - + -
78F THR* 3.8 31.6 - - + +
82F LEU* 6.1 1.8 - - + -
117F ALA 3.1 12.7 + - - +
118F ILE* 3.2 22.4 - - + +
119F THR 3.0 0.8 - - - -
120F SER* 1.3 79.6 - - - +
122F VAL* 1.3 64.6 + - + +
123F TYR 3.3 1.6 - - - -
124F TYR* 3.3 11.4 + - + +
125F HIS* 2.9 25.8 + - - +
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Residues in contact with VAL 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LEU* 4.9 9.4 - - + -
118F ILE* 2.9 33.3 + - + +
119F THR* 4.1 4.7 - - - +
121F VAL* 1.3 77.7 - - + +
123F TYR* 1.3 60.6 + - - +
125F HIS* 3.0 11.5 + - + +
126F ASN* 2.9 45.7 + - - +
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Residues in contact with TYR 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 5.6 2.2 - - + -
43F THR* 3.7 39.7 - - + +
46F ILE* 4.7 13.6 - - + +
47F LEU* 3.8 26.1 - - + +
119F THR 2.9 18.1 + - - +
120F SER* 4.5 4.7 - - - -
122F VAL* 1.3 76.8 - - - +
124F TYR* 1.3 56.1 + - - +
126F ASN* 3.2 3.3 + - + +
127F ILE* 3.0 30.0 + - + +
135F LEU* 2.3 58.6 + - + +
136F LEU* 4.7 2.0 - - + -
138F ALA* 4.2 10.0 - - + +
139F LEU* 3.7 38.1 - - + -
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Residues in contact with TYR 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F PHE* 3.3 33.8 - + + +
69F PRO 5.2 0.5 + - - -
70F GLY 4.7 1.7 + - - -
71F HIS* 3.3 28.3 - - + +
74F ARG* 3.3 50.5 + - + +
75F TRP* 4.6 14.8 - + - -
120F SER 3.9 13.3 + - - +
121F VAL* 3.3 14.4 + - + +
122F VAL 3.2 0.4 - - - -
123F TYR* 1.3 77.9 - - - +
125F HIS* 1.3 61.5 + - - +
127F ILE* 3.2 13.2 - - + +
128F GLU* 2.9 50.6 + - - +
136F LEU* 5.7 8.1 - - + -
139F LEU* 4.5 11.2 - - + -
189F VAL* 5.6 2.9 - - + +
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Residues in contact with HIS 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLN* 6.3 0.9 - - - -
65F TRP* 4.1 18.2 - + - -
75F TRP* 4.0 15.3 - + + -
121F VAL 2.9 13.3 + - - +
122F VAL* 3.0 16.4 + - + +
124F TYR* 1.3 77.8 - - - +
126F ASN* 1.3 60.7 + - - +
128F GLU* 3.4 7.8 + - + +
129F THR* 2.4 50.5 + - + -
223F ASN* 3.1 45.3 + - + +
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Residues in contact with ASN 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 5.9 2.9 - - - +
47F LEU* 3.9 15.7 - - + +
50F GLY* 5.8 7.4 - - - -
54F GLN* 4.0 21.2 - - - +
122F VAL* 2.9 36.2 + - - +
123F TYR* 3.2 6.5 + - + +
124F TYR 3.2 0.2 - - - -
125F HIS* 1.3 82.4 + - - +
127F ILE* 1.3 64.2 + - - +
128F GLU 3.2 0.4 - - - -
129F THR* 3.3 19.9 + - - +
130F SER* 3.3 13.2 + - - +
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Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F PHE* 3.2 27.7 - - + -
123F TYR* 3.0 18.6 + - + +
124F TYR* 3.2 28.3 - - + +
126F ASN* 1.3 79.1 - - - +
128F GLU* 1.3 58.7 + - - +
130F SER 2.8 22.8 - - - +
131F ASN* 3.8 0.7 - - - +
132F PHE* 3.3 33.0 - - + +
135F LEU* 3.7 20.3 - - + +
136F LEU* 3.6 45.1 - - + +
139F LEU* 5.8 0.7 - - + -
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F TRP* 5.3 7.0 - - + -
66F LEU* 3.0 36.9 + - - +
67F HIS* 2.5 44.7 + - + +
68F PHE* 3.5 20.6 - - + +
71F HIS* 3.6 11.5 + - - -
75F TRP* 4.0 15.6 + - - -
124F TYR* 2.9 43.0 + - + +
125F HIS* 3.6 7.5 - - + +
127F ILE* 1.3 75.5 - - - +
129F THR* 1.3 63.8 + - - +
131F ASN* 4.4 5.2 - - - +
223F ASN* 6.1 0.9 - - - -
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Residues in contact with THR 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 4.4 3.2 - - - +
54F GLN* 5.3 8.1 - - - +
61F HIS* 5.6 9.6 - - + +
64F THR* 3.8 23.2 - - - +
65F TRP* 4.5 21.3 - - + -
66F LEU* 4.8 0.7 + - - +
125F HIS* 2.4 43.6 + - + -
126F ASN* 3.4 17.9 + - - +
127F ILE 3.2 0.2 - - - -
128F GLU* 1.3 80.9 - - - +
130F SER* 1.3 62.3 + - - +
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Residues in contact with SER 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 2.7 42.2 + - - +
53B GLY* 4.0 12.9 + - - -
55B PHE* 5.2 5.4 - - - +
56B LEU* 5.8 9.6 - - - +
64F THR* 5.9 0.2 - - - -
126F ASN 3.3 7.2 + - - +
127F ILE* 2.8 17.5 - - - +
129F THR* 1.3 81.3 - - - +
131F ASN* 1.3 63.3 + - - +
132F PHE* 3.2 6.2 + - - +
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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