Contacts of the helix formed by residues 84 - 113 (chain B) in PDB entry 3N3B
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 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 3.9 26.7 - - - +
16B ASP* 4.8 4.7 - - + -
19B ASP* 2.7 28.6 + - - +
82B ALA* 3.9 7.2 - - - +
83B LEU* 1.3 87.5 - - + +
85B PRO* 1.4 73.0 - - + +
86B HIS* 3.7 8.5 + - - -
87B GLU* 3.2 27.5 + - - +
88B GLU* 3.5 7.2 + - - +
202B LYS* 4.0 4.0 + - - +
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Residues in contact with PRO 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 6.2 2.5 - - + -
71A ASN* 5.7 0.2 + - - -
7B SER* 6.0 4.5 - - - +
9B ILE* 3.4 33.4 - - + +
15B SER* 5.9 2.0 - - - +
83B LEU 4.8 0.9 - - - +
84B THR* 1.4 89.1 - - + +
86B HIS* 1.3 69.7 + - + +
88B GLU* 3.4 22.1 + - - +
89B ALA 3.4 15.4 + - - -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.0 14.3 - - + +
10B ASN 2.7 29.4 + - - -
11B TRP* 3.7 33.7 - + + -
13B LYS 3.7 15.9 - - - -
14B ILE* 3.6 26.4 - - + +
15B SER* 4.5 7.9 + - - -
19B ASP* 3.8 24.2 + - + +
84B THR* 3.1 12.5 - - - -
85B PRO* 1.3 88.5 - - + +
87B GLU* 1.3 63.6 + - - +
89B ALA* 3.3 2.8 + - - +
90B VAL* 3.1 28.6 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 4.2 0.4 + - - -
78B LEU* 4.9 1.0 - - - +
81B ASP 4.5 2.8 - - - +
82B ALA* 3.6 19.8 - - + +
83B LEU* 2.8 26.2 + - - +
84B THR* 3.2 22.2 + - - +
86B HIS* 1.3 74.3 - - - +
88B GLU* 1.3 58.6 + - - +
90B VAL* 3.3 2.5 + - - +
91B LEU* 3.0 41.4 + - + +
151B LYS* 4.6 8.5 + - - -
198B TYR* 3.3 30.6 + - + +
202B LYS* 3.2 39.2 + - - +
206B ASN* 5.4 0.7 + - - -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 4.5 3.7 + - - +
72A VAL* 4.0 34.8 - - + +
79B MET* 4.0 23.3 - - + +
82B ALA* 3.6 20.3 - - + +
84B THR 3.5 5.8 + - - +
85B PRO* 3.4 23.0 + - - +
86B HIS 3.3 0.2 - - - -
87B GLU* 1.3 78.4 - - - +
89B ALA* 1.3 60.4 + - - +
91B LEU* 3.5 10.2 + - - +
92B SER* 3.2 23.7 + - - -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 4.1 14.5 - - - +
96A PHE* 4.9 0.2 - - - -
99A ALA* 4.0 18.3 - - + +
9B ILE* 4.4 5.4 - - + -
11B TRP* 3.7 25.6 - - + -
23B TRP* 3.5 13.7 - - + -
85B PRO 3.4 7.9 + - - +
86B HIS 3.3 9.1 + - - +
87B GLU 3.3 0.4 - - - -
88B GLU* 1.3 75.9 - - - +
90B VAL* 1.3 64.9 + - - +
92B SER* 3.3 16.0 + - - -
93B ASN 3.4 4.9 + - - -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 4.7 0.9 - - + -
19B ASP 3.6 23.6 - - - +
22B VAL* 3.9 19.1 - - + -
23B TRP* 3.8 26.7 - - + +
26B LEU* 4.1 11.9 - - + -
86B HIS 3.1 17.9 + - - +
87B GLU 3.3 5.4 + - - +
89B ALA* 1.3 73.4 - - - +
91B LEU* 1.3 60.7 + - - +
93B ASN* 3.0 7.1 + - + +
94B ILE* 3.0 27.1 + - + +
198B TYR* 3.7 31.2 - - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA* 4.2 9.8 - - + +
78B LEU* 3.7 56.8 - - + +
79B MET* 3.7 24.6 - - + +
82B ALA* 4.6 2.0 - - + -
87B GLU* 3.0 40.5 + - + +
88B GLU* 3.7 6.7 - - - +
89B ALA 3.4 0.2 - - - -
90B VAL* 1.3 75.2 - - - +
92B SER* 1.3 57.6 + - - +
94B ILE* 3.7 22.7 - - + +
95B SER* 2.9 30.5 + - - -
198B TYR* 5.1 5.4 - - + -
199B ILE* 5.1 3.8 - - + -
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 2.8 30.4 + - - -
92A SER 4.2 2.6 - - - +
95A SER* 3.7 9.1 + - - -
96A PHE* 3.5 26.5 - - - +
99A ALA* 4.9 1.1 - - - -
79B MET* 4.0 14.6 - - - +
88B GLU 3.2 13.8 + - - -
89B ALA 3.3 12.1 - - - -
91B LEU* 1.3 76.3 - - - +
93B ASN* 1.3 61.1 + - - +
95B SER* 3.9 2.8 - - - -
96B PHE* 3.2 16.3 + - - +
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 3.3 43.6 - - + -
23B TRP* 4.7 5.2 - - + -
26B LEU* 3.4 39.2 + - + +
27B THR* 3.7 13.6 - - - +
30B PHE* 6.2 1.2 - - - -
89B ALA 3.4 5.8 + - - +
90B VAL* 3.0 13.0 + - + +
92B SER* 1.3 77.8 - - - +
94B ILE* 1.3 60.4 + - - +
96B PHE* 3.3 3.5 + - - +
97B MET* 2.9 45.5 + - - +
195B HIS* 5.0 0.2 + - - -
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.8 13.0 - - + -
75B ALA* 4.1 14.1 - - + -
90B VAL* 3.0 30.2 + - + +
91B LEU* 3.7 25.6 - - + +
92B SER 3.5 0.2 - - - -
93B ASN* 1.3 77.1 - - - +
95B SER* 1.3 56.9 + - - +
97B MET* 3.2 3.1 + - - +
98B GLU* 2.9 42.6 + - - +
195B HIS* 3.6 44.3 - - + +
198B TYR* 4.3 13.2 - - + -
199B ILE* 4.9 15.7 - - + -
321B MN 4.6 0.7 - - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET* 5.8 1.6 - - - +
92A SER* 3.9 7.9 + - - -
71B ASN* 2.9 43.4 + - - +
75B ALA* 3.8 17.5 - - - +
76B PRO* 4.1 6.5 - - - +
79B MET* 4.3 11.4 - - - +
91B LEU 2.9 18.1 + - - -
92B SER* 3.9 4.7 - - - -
93B ASN 3.3 0.2 - - - -
94B ILE* 1.3 75.4 - - - +
96B PHE* 1.3 61.8 + - - +
98B GLU* 3.3 14.6 + - - +
99B ALA 3.4 2.4 + - - -
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.9 9.4 - + - -
27A THR* 3.9 15.0 - - + -
30A PHE* 5.5 0.2 - + - -
92A SER* 3.5 26.8 - - - +
93A ASN* 3.3 45.3 - - + -
96A PHE* 3.6 29.2 - + + -
30B PHE* 3.7 30.7 - + - -
32B LEU* 5.2 0.2 - - + -
92B SER 3.2 11.7 + - - +
93B ASN* 3.3 2.9 + - - +
95B SER* 1.3 77.6 - - - +
97B MET* 1.3 77.0 + - + +
99B ALA* 3.0 16.8 + - - +
100B VAL* 3.1 30.4 + - + +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 5.3 6.3 - - + +
29B ASN 5.1 0.2 - - - +
30B PHE* 4.3 15.0 - - - -
31B TRP* 3.5 36.6 - - + +
93B ASN* 2.9 37.5 + - - +
94B ILE 3.2 4.5 + - - +
96B PHE* 1.3 97.0 - - + +
98B GLU* 1.3 59.2 + - - +
100B VAL* 3.3 15.1 + - + +
101B HIS* 3.0 40.9 + - - +
191B ASP* 3.4 25.8 - - - +
195B HIS* 4.6 10.1 - - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 3.0 10.8 - - - +
70B GLN* 3.7 20.6 - - + +
71B ASN* 3.7 18.4 - - - +
75B ALA* 5.0 1.0 - - + +
94B ILE* 2.9 34.6 + - + +
95B SER* 3.5 9.0 - - - +
96B PHE 3.2 0.2 - - - -
97B MET* 1.3 75.8 - - - +
99B ALA* 1.3 58.4 + - - +
101B HIS* 3.4 4.4 + - - +
102B ALA* 3.1 26.9 + - - +
158B GLU* 2.9 4.7 - - - +
192B GLU* 3.8 0.4 - - - -
195B HIS* 3.1 7.5 + - - -
320B MN 2.1 34.9 + - - -
321B MN 2.0 31.2 + - - -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 4.7 3.6 + - - -
23A TRP* 4.2 9.5 - - + -
89A ALA* 4.1 24.5 - - + +
92A SER* 4.7 0.2 - - - -
71B ASN* 3.7 30.2 - - - +
95B SER 3.4 2.0 + - - +
96B PHE* 3.0 13.2 + - - +
98B GLU* 1.3 78.2 - - - +
100B VAL* 1.3 58.3 - - - +
102B ALA* 3.6 5.9 + - - +
103B ARG* 3.0 28.6 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 4.0 10.1 - - + -
31B TRP* 3.7 30.7 - - + +
32B LEU* 4.5 6.3 - - + -
33B PRO* 4.1 18.1 - - + +
96B PHE* 3.1 42.5 + - + +
97B MET* 3.5 27.1 - - + +
98B GLU 3.3 0.4 - - - -
99B ALA* 1.3 75.2 - - - +
101B HIS* 1.3 59.7 + - - +
103B ARG* 3.3 6.8 + - - +
104B SER* 3.0 28.1 + - - -
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 3.5 23.9 - + - -
67B ASP* 3.4 19.5 - - - +
97B MET* 3.0 28.2 + - + +
98B GLU* 3.4 4.9 + - - +
99B ALA 3.4 0.2 - - - -
100B VAL* 1.3 77.3 - - + +
102B ALA* 1.3 60.4 + - - +
104B SER* 2.6 25.9 + - - -
105B TYR* 3.2 14.5 - - - +
188B ILE* 3.7 21.8 - - + +
191B ASP* 2.9 37.4 + - + +
192B GLU* 3.2 18.4 - - - -
195B HIS* 4.3 4.7 - + - -
320B MN 2.5 23.8 + - - -
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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
----------------------------------------------------------
9A ILE* 3.8 25.3 - - + +
64B THR* 4.1 10.9 - - + +
67B ASP* 4.0 11.6 - - + +
68B THR* 3.9 14.4 - - - +
98B GLU 3.1 14.0 + - - +
99B ALA* 3.9 6.7 - - - +
100B VAL 3.3 0.2 - - - -
101B HIS* 1.3 79.3 - - - +
103B ARG* 1.3 61.1 + - - +
105B TYR* 3.5 27.1 + - - +
106B SER* 3.9 5.9 + - - -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.5 54.7 + - + +
12A ASN* 5.4 2.4 + - - -
20A LEU* 3.9 22.2 - - - +
23A TRP* 3.8 33.9 - - + +
24A ASN* 5.2 2.2 + - - +
33B PRO* 3.9 18.2 - - - -
34B GLU* 3.9 17.9 + - - -
99B ALA 3.0 18.7 + - - +
100B VAL* 3.6 5.8 - - - +
101B HIS 3.3 0.2 - - - -
102B ALA* 1.3 74.9 - - - +
104B SER* 1.3 64.1 + - - +
106B SER* 3.3 5.4 + - - -
107B SER* 3.0 28.5 + - - +
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TRP* 4.2 7.9 - - - -
33B PRO* 3.9 24.9 - - - -
100B VAL 3.0 13.5 + - - -
101B HIS* 2.6 21.1 + - - -
103B ARG* 1.3 74.4 - - - +
105B TYR* 1.3 61.1 + - - +
107B SER* 3.3 4.2 + - - -
108B ILE* 3.1 30.3 + - - +
184B LEU* 3.7 18.4 - - - +
188B ILE* 3.6 18.0 - - - +
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.7 38.4 - + + +
63B LEU* 3.6 34.1 - - + +
64B THR* 3.3 30.7 - - - +
67B ASP* 2.8 26.8 + - - -
101B HIS 3.2 20.9 - - - -
102B ALA* 3.7 12.3 - - - +
103B ARG 3.2 0.4 - - - -
104B SER* 1.3 78.4 - - - +
106B SER* 1.3 59.5 + - - +
108B ILE* 3.2 13.2 + - + +
109B PHE* 3.0 36.6 + - + -
162B PHE* 3.9 4.5 - - - -
166B PHE* 4.3 5.2 - - - -
185B ILE* 4.3 2.5 - - + -
188B ILE* 3.9 26.8 - - + +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE 4.0 5.9 + - - -
10A ASN* 4.0 10.4 + - - -
11A TRP* 3.2 41.3 + - - +
12A ASN* 3.2 15.6 + - - +
64B THR* 5.5 0.3 - - - +
102B ALA 3.9 3.6 + - - -
103B ARG* 3.3 13.3 + - - -
105B TYR* 1.3 75.2 - - - +
107B SER* 1.3 60.1 + - - +
109B PHE* 3.3 9.5 + - - -
110B SER* 2.9 28.1 + - - -
122B TYR* 4.1 6.1 + - - -
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO* 3.4 29.0 - - - +
34B GLU* 4.7 2.6 + - - -
38B LEU* 3.9 11.5 - - - +
103B ARG* 3.0 29.8 + - - +
104B SER 3.3 10.3 - - - -
105B TYR 3.2 0.4 - - - -
106B SER* 1.3 74.9 - - - +
108B ILE* 1.3 59.2 + - - +
110B SER* 4.1 4.7 - - - -
111B THR* 2.7 33.7 + - - -
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.2 19.3 - - + -
45B TRP* 6.1 0.7 - - + -
56B THR* 5.8 2.2 - - + -
60B PHE* 4.3 32.8 - - + -
104B SER 3.1 15.7 + - - +
105B TYR* 3.2 20.4 + - + +
107B SER* 1.3 73.9 - - - +
109B PHE* 1.3 68.2 + - + +
111B THR* 3.3 2.6 + - - -
112B LEU* 3.0 47.2 + - + +
113B CYS* 4.3 4.4 - - - -
181B THR* 3.9 25.1 - - + -
184B LEU* 4.1 16.6 - - + -
185B ILE* 4.8 0.4 - - + -
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 5.9 0.2 - - - -
12A ASN* 4.0 9.4 - - - +
57B MET* 4.0 21.8 - - + -
60B PHE* 3.6 33.9 - + + -
61B THR* 3.6 21.3 - - + -
64B THR* 4.3 6.7 - - - -
105B TYR* 3.0 28.3 + - + -
106B SER* 3.3 11.9 + - - +
108B ILE* 1.3 78.6 - - + +
110B SER* 1.3 58.1 + - - +
113B CYS* 3.1 46.4 + - - +
118B VAL* 3.8 32.9 - - + +
122B TYR* 3.6 26.7 - + - -
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN* 3.5 23.6 + - - +
106B SER 2.9 20.9 + - - -
107B SER* 4.1 6.3 - - - -
109B PHE* 1.3 73.6 - - - +
111B THR* 1.3 62.1 + - - +
113B CYS 4.8 3.2 - - - +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.7 15.5 - - - +
39B SER* 3.4 43.5 - - - +
42B ILE* 3.9 17.1 - - + +
107B SER 2.7 22.1 + - - -
108B ILE 3.3 3.5 + - - -
109B PHE 3.2 0.6 - - - -
110B SER* 1.3 81.8 + - - +
112B LEU* 1.3 64.8 + - + +
113B CYS 5.2 0.4 - - - -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.8 16.2 - - + +
41B ASP* 3.6 9.0 - - + +
42B ILE* 3.6 40.5 - - + +
45B TRP* 3.2 51.2 + - + -
108B ILE* 3.0 34.4 + - + +
111B THR* 1.3 81.2 - - - +
113B CYS* 1.3 65.9 + - - +
114B GLN* 5.8 0.5 - - - +
178B LEU* 4.3 9.2 - - + -
181B THR* 4.0 17.7 - - + +
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Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 3.7 34.3 - - + +
57B MET* 3.8 21.8 - - - -
108B ILE* 4.3 4.5 - - - -
109B PHE* 3.1 37.0 + - - +
110B SER* 4.8 4.2 - - - +
111B THR 5.2 0.2 - - - -
112B LEU* 1.3 85.9 - - - +
114B GLN* 1.3 65.8 + - - +
115B THR* 4.1 0.9 + - - -
118B VAL* 3.6 17.0 - - + -
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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