Contacts of the helix formed by residues 75 - 107 (chain D) in PDB entry 4O46
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 ASN 75 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 4.1 3.8 + - - +
73D ASP* 3.3 16.0 + - - +
74D GLY* 1.3 73.0 - - - +
76D GLU* 1.3 66.2 + - - +
77D LYS* 3.7 7.6 + - - +
78D LYS* 3.3 38.3 + - + +
79D ILE* 3.0 28.0 + - + +
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Residues in contact with GLU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D GLY 3.8 4.8 + - - -
75D ASN* 1.3 74.1 + - - +
77D LYS* 1.4 63.9 + - + +
79D ILE* 3.6 5.1 + - - +
80D GLU* 3.4 21.1 + - - +
37E LEU 3.7 5.7 - - - +
38E SER* 3.2 21.9 - - - -
39E ASN* 2.8 56.1 + - - +
42E ARG* 4.2 3.6 + - - -
119E SER* 5.3 1.0 + - - -
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Residues in contact with LYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 4.2 18.8 - - - +
6B GLN* 3.8 26.8 + - + +
75D ASN* 3.5 6.5 + - - +
76D GLU* 1.4 79.2 - - + +
78D LYS* 1.3 64.1 + - - +
80D GLU* 3.7 4.8 + - - +
81D MET* 3.4 21.1 + - - +
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 6.3 0.4 - - - -
9B GLN* 5.5 7.9 - - + -
13B LEU* 6.1 2.0 - - - -
66D ILE* 5.2 7.5 - - - +
70D THR* 4.7 18.8 - - - -
73D ASP* 5.4 5.1 + - - +
75D ASN* 3.3 35.2 + - + +
77D LYS* 1.3 74.6 - - - +
79D ILE* 1.4 60.0 + - - +
81D MET* 3.2 19.0 + - + +
82D VAL* 3.0 44.8 + - + +
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Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 5.1 5.3 - - + +
70D THR* 3.7 33.0 - - - +
71D SER* 4.0 13.5 - - - +
74D GLY* 5.8 0.9 - - - -
75D ASN 3.0 22.1 + - - +
76D GLU* 3.8 6.1 - - - +
78D LYS* 1.4 74.5 - - - +
80D GLU* 1.3 57.5 + - - +
82D VAL* 3.4 7.5 + - - +
83D ARG* 2.9 51.0 + - - +
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 5.9 2.0 - - - +
76D GLU 3.4 13.2 + - - +
77D LYS* 4.0 6.7 - - - +
78D LYS 3.3 0.6 - - - -
79D ILE* 1.3 77.2 - - - +
81D MET* 1.3 58.0 + - - +
83D ARG* 3.5 4.8 + - - +
84D ALA* 2.9 38.4 + - + +
113E SER* 2.6 26.7 + - - -
115E THR* 2.8 29.7 + - - +
116E GLN* 3.2 34.9 + - + +
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 3.5 38.3 - - + +
9B GLN* 3.4 34.8 - - + +
10B LYS* 4.0 28.0 - - + +
13B LEU* 3.6 28.0 - - + -
77D LYS 3.4 4.8 + - - +
78D LYS* 3.2 22.4 + - + +
80D GLU* 1.3 76.9 - - - +
82D VAL* 1.3 59.6 + - + +
84D ALA* 3.6 5.5 + - - +
85D TYR* 3.1 27.5 + - - +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.7 28.9 - - + -
63D ILE* 3.4 25.5 - - + +
66D ILE* 4.2 12.6 - - + -
67D GLU* 3.7 35.2 - - + +
70D THR* 4.9 4.7 - - - -
78D LYS* 3.0 37.0 + - + +
79D ILE* 3.8 7.0 - - - +
80D GLU 3.4 0.2 - - - -
81D MET* 1.3 72.7 - - + +
83D ARG* 1.3 59.9 + - - +
85D TYR* 3.3 1.7 + - - +
86D ARG* 3.0 24.1 + - - +
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Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 3.3 27.7 + - + +
71D SER* 5.3 10.1 - - - -
79D ILE* 2.9 34.0 + - - +
80D GLU* 3.7 5.9 + - - +
82D VAL* 1.3 76.3 - - - +
84D ALA* 1.4 55.4 + - - +
86D ARG* 3.3 29.7 + - - +
87D GLU* 3.1 21.8 + - - +
115E THR* 3.4 49.7 + - + +
116E GLN* 5.0 2.4 - - - +
117E TYR* 4.7 4.4 - - - +
118E GLU* 2.9 39.3 + - - -
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D GLU* 2.9 27.7 + - - +
81D MET* 3.8 7.0 - - - +
82D VAL 3.3 0.2 - - - -
83D ARG* 1.4 71.2 - - - +
85D TYR* 1.3 60.3 + - - +
87D GLU* 3.2 10.1 + - - +
88D LYS* 2.9 26.9 + - - +
115E THR* 4.1 5.8 - - - +
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Residues in contact with TYR 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 3.8 24.5 - - + -
13B LEU* 4.2 13.7 - - + -
14B ALA* 3.4 23.1 - - + +
17B ALA* 4.2 2.5 - - + -
19B ARG* 3.2 25.5 + - - +
22B ASP* 2.7 38.5 + - + +
63D ILE* 3.6 29.6 - - + -
81D MET 3.1 18.3 + - - +
82D VAL 3.3 5.4 + - - +
84D ALA* 1.3 73.1 - - - +
86D ARG* 1.4 64.1 + - - +
88D LYS* 3.2 24.0 + - + +
89D ILE* 3.1 44.0 + - + +
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Residues in contact with ARG 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TRP* 3.4 33.3 - - + +
63D ILE* 3.7 21.9 - - + +
64D SER* 3.4 21.5 + - - +
67D GLU* 2.8 38.5 + - + +
82D VAL* 3.0 14.1 + - + +
83D ARG* 3.4 32.2 + - - +
85D TYR* 1.4 74.3 - - - +
87D GLU* 1.4 81.4 + - - +
89D ILE* 3.5 6.0 + - - +
90D GLU* 2.9 40.5 + - - +
115E THR* 4.7 3.4 - - - +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG 3.1 10.6 + - - +
84D ALA* 3.3 12.3 - - - +
86D ARG* 1.4 87.6 + - - +
88D LYS* 1.3 57.9 + - - +
90D GLU* 3.0 27.6 - - - +
91D LYS* 3.0 51.5 + - + +
114E GLU* 4.1 18.0 - - + +
115E THR* 3.4 23.5 + - + +
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 4.1 4.9 - - - +
22B ASP* 3.2 32.9 + - - +
84D ALA 2.9 13.5 + - - +
85D TYR* 3.4 31.2 - - + +
87D GLU* 1.3 77.2 - - - +
89D ILE* 1.4 61.1 + - - +
91D LYS* 3.5 8.3 + - - +
92D GLU* 3.2 39.1 + - + +
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Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 3.6 33.0 - - - +
56D ARG* 3.4 34.9 - - + +
59D SER* 4.2 7.4 - - - -
60D TRP* 3.8 15.9 - - + +
63D ILE* 3.8 29.8 - - + -
85D TYR* 3.1 36.5 + - + +
86D ARG* 3.8 4.3 - - - +
88D LYS* 1.4 71.4 - - + +
90D GLU* 1.4 60.8 + - - +
92D GLU* 3.1 9.6 + - - +
93D LEU* 2.9 27.6 + - + +
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TRP* 2.9 38.1 + - + +
86D ARG* 2.9 29.6 + - - +
87D GLU* 3.0 30.4 - - + +
89D ILE* 1.4 74.6 - - - +
91D LYS* 1.4 52.9 + - + +
93D LEU* 3.2 9.0 + - - +
94D GLU* 2.9 47.7 + - - +
137D VAL* 3.8 31.7 - - + +
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Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 5.5 1.7 - - - +
87D GLU* 3.0 36.0 + - + +
88D LYS* 3.7 7.6 - - - +
90D GLU* 1.4 74.1 - - + +
92D GLU* 1.3 56.9 + - + +
94D GLU* 3.5 14.1 + - - +
95D ALA* 3.0 29.9 + - - +
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 2.9 43.1 + - - -
56D ARG* 3.2 30.3 + - + +
88D LYS* 3.2 28.2 + - + +
89D ILE* 3.1 9.5 + - - +
91D LYS* 1.3 74.9 - - - +
93D LEU* 1.4 60.8 + - - +
95D ALA* 3.3 8.2 + - - +
96D VAL* 3.2 28.4 + - + +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D VAL* 4.0 12.3 - - + +
56D ARG* 3.8 17.2 - - + +
57D ARG* 3.7 39.5 - - + +
60D TRP* 4.7 4.9 - - + -
89D ILE* 2.9 12.0 + - + +
90D GLU* 3.3 10.1 - - - +
92D GLU* 1.4 75.5 - - - +
94D GLU* 1.3 63.4 + - - +
96D VAL* 3.1 9.3 + - - +
97D CYS* 3.1 39.6 + - - -
133D TYR* 3.8 24.9 - - + +
134D LEU* 4.8 1.6 - - - +
137D VAL* 4.3 27.4 - - + -
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Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.4 45.1 + - - +
90D GLU* 2.9 32.6 + - - +
91D LYS* 3.8 15.5 + - - +
93D LEU* 1.3 70.8 - - + +
95D ALA* 1.3 56.4 + - - +
97D CYS* 3.4 3.1 + - - +
98D GLN* 3.0 29.7 + - - +
134D LEU* 3.7 22.6 - - + +
137D VAL* 3.8 23.2 - - + +
138D ALA* 5.3 4.3 + - - +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 5.3 0.4 + - - -
2C VAL* 5.2 15.5 - - + -
91D LYS 3.0 14.3 + - - +
92D GLU* 3.5 12.3 - - - +
93D LEU 3.3 0.2 - - - -
94D GLU* 1.3 73.7 - - - +
96D VAL* 1.4 60.2 + - + +
98D GLN* 3.5 7.3 + - - +
99D ASP* 3.0 28.6 + - - +
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D TYR* 4.0 19.7 - - + +
52D VAL* 3.8 33.0 - - + -
53D VAL* 3.9 23.8 - - + +
56D ARG* 4.7 12.1 - - - +
92D GLU 3.2 16.1 + - - +
93D LEU* 3.1 8.8 + - - +
95D ALA* 1.4 74.9 - - + +
97D CYS* 1.4 59.3 + - - +
99D ASP* 3.2 8.6 + - - +
100D VAL* 3.1 31.2 + - + +
130D TYR* 5.1 0.2 - - + -
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Residues in contact with CYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D VAL* 3.9 20.2 - - - -
93D LEU* 3.1 22.9 + - - -
94D GLU 3.7 7.4 - - - +
96D VAL* 1.4 72.0 - - - +
98D GLN* 1.4 58.5 + - - +
100D VAL* 3.4 1.4 + - - +
101D LEU* 2.9 37.3 + - - +
130D TYR* 3.6 37.0 - - + +
133D TYR* 4.0 9.6 - - - -
134D LEU* 3.7 25.8 - - + -
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Residues in contact with GLN 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 5.6 2.9 - - - -
2C VAL* 4.0 30.5 - - + +
29C ASN* 5.3 6.1 - - - +
33C LEU* 4.3 12.6 - - + -
94D GLU 3.0 16.7 + - - +
95D ALA* 3.7 8.1 - - - +
97D CYS* 1.4 73.5 - - - +
99D ASP* 1.3 58.1 + - - +
101D LEU* 3.4 7.6 + - - +
102D SER* 3.0 44.5 + - - +
134D LEU* 5.4 0.8 - - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 4.5 3.8 - - - +
28D LYS* 3.2 33.4 + - - +
49D TYR* 2.7 31.1 + - + -
95D ALA 3.0 14.6 + - - +
96D VAL* 3.3 12.5 - - - +
98D GLN* 1.3 78.0 - - - +
100D VAL* 1.4 61.2 + - - +
102D SER* 3.6 4.9 + - - -
103D LEU* 3.3 22.2 + - - +
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU* 6.0 1.6 - - + -
49D TYR* 3.3 34.3 - - + -
96D VAL* 3.1 17.0 + - + +
97D CYS 3.7 4.5 - - - +
99D ASP* 1.4 71.8 - - - +
101D LEU* 1.3 60.0 + - - +
103D LEU* 3.0 16.4 + - + +
104D LEU* 2.9 37.2 + - + +
108D LEU* 6.4 0.2 - - + -
126D MET* 3.7 29.8 - - + -
130D TYR* 3.8 30.3 - - + -
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D CYS 2.9 27.5 + - - +
98D GLN* 4.0 5.8 - - - +
100D VAL* 1.3 71.5 - - - +
102D SER* 1.3 56.6 + - - +
104D LEU* 3.5 6.5 + - + +
105D ASP* 2.9 39.6 + - - +
127D LYS* 3.7 35.0 - - + +
130D TYR* 4.1 15.3 - - + -
131D TYR* 3.7 48.2 - - + +
134D LEU* 3.9 19.5 - - + -
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 3.1 32.9 + - - +
33C LEU* 5.1 0.9 - - - -
107C TYR* 4.0 6.1 - - - -
98D GLN* 3.0 28.2 + - - +
99D ASP* 3.9 5.2 - - - -
101D LEU* 1.3 72.1 - - - +
103D LEU* 1.4 57.0 + - - +
105D ASP* 4.7 2.0 - - - -
106D ASN* 2.8 47.7 + - - +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 5.6 0.9 - - - +
107C TYR* 5.1 1.1 - - - +
28D LYS* 3.7 37.0 - - + +
31D THR* 3.8 24.7 - - + -
32D GLU* 4.3 11.2 - - + +
45D LEU* 4.4 9.9 - - + -
49D TYR* 3.8 35.7 - - + +
99D ASP 3.3 14.1 + - - +
100D VAL* 3.0 10.9 + - + +
102D SER* 1.4 76.3 - - - +
104D LEU* 1.3 57.1 + - - +
107D TYR* 3.0 37.4 + - + +
108D LEU* 3.0 18.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D VAL* 2.9 34.8 + - + +
101D LEU* 3.6 15.7 - - + +
103D LEU* 1.3 77.7 - - - +
105D ASP* 1.3 61.3 + - - +
108D LEU* 3.5 13.3 + - + -
109D ILE* 2.8 44.1 + - + +
123D TYR* 3.6 46.9 - - + +
126D MET* 3.9 16.2 - - + +
127D LYS* 3.7 30.7 - - + +
----------------------------------------------------------
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Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 2.9 24.6 + - - +
102D SER* 4.2 2.2 - - - +
104D LEU* 1.3 78.4 - - - +
106D ASN* 1.3 69.3 + - - +
109D ILE* 4.1 6.4 - - - +
110D LYS* 3.8 15.4 + - - +
127D LYS* 2.8 44.6 + - - +
131D TYR* 4.6 7.4 + - - -
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Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU 4.1 2.2 + - - -
34C ASN* 3.1 31.0 + - - +
106C ASN* 4.7 12.3 - - - +
107C TYR* 2.9 45.4 + - + +
34D ASN* 4.7 2.9 - - - +
102D SER* 2.8 42.2 + - - +
105D ASP* 1.3 80.2 - - - +
107D TYR* 1.4 66.2 + - + +
110D LYS* 4.1 13.0 - - - +
----------------------------------------------------------
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 5.8 0.2 - - - -
102C SER* 3.7 14.0 + - - -
103C LEU* 5.1 1.2 - - - +
106C ASN* 2.9 45.0 + - + +
107C TYR* 3.7 29.8 - + - -
31D THR* 3.4 28.3 - - + +
32D GLU* 3.7 34.9 + - + +
34D ASN* 3.3 20.9 - - - +
103D LEU* 3.0 28.9 + - + +
105D ASP 3.6 1.0 - - - -
106D ASN* 1.4 84.5 - - + +
108D LEU* 1.3 64.0 + - + +
109D ILE 3.8 0.7 - - - -
110D LYS* 4.2 2.7 - - - -
111D ASN* 2.9 36.3 + - - +
----------------------------------------------------------
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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