Contacts of the helix formed by residues 75 - 105 (chain C) in PDB entry 1L0N
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 75 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL 3.1 1.6 + - - -
74C ASN* 1.3 86.2 - - + +
76C GLY* 1.3 63.6 + - - +
77C TRP* 3.2 16.7 + - - +
78C ILE* 3.4 16.0 - - + +
79C ILE* 3.3 25.7 + - + +
200D HIS* 4.2 13.5 - + - -
204D MET* 3.9 14.8 - - + -
57E GLN* 3.4 68.0 - - + +
60E SER* 4.4 11.9 - - - -
61E SER* 5.0 0.9 - - - -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 3.3 31.9 - - - +
73C VAL* 2.9 15.6 + - - -
74C ASN 2.8 5.4 + - - -
75C TYR* 1.3 78.4 - - - +
77C TRP* 1.3 51.8 + - - +
79C ILE* 3.2 10.1 + - - +
80C ARG* 2.7 36.4 + - - +
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Residues in contact with TRP 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE 3.8 3.8 + - - -
70C CYS* 3.9 32.1 - - - +
73C VAL 5.3 1.3 - - - -
75C TYR* 4.4 17.1 - + - +
76C GLY* 1.3 77.3 - - - +
78C ILE* 1.3 106.9 + - + +
80C ARG* 3.2 2.1 + - - +
81C TYR* 2.8 45.0 + + + -
243C VAL 5.4 1.3 - - - -
244C LEU* 4.2 6.3 - - + -
197D GLU* 3.6 44.6 - - + +
200D HIS* 3.9 24.6 + - + +
201D ARG* 3.6 41.3 - - + -
204D MET* 4.0 10.8 - - + -
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 3.4 19.3 - - + +
77C TRP* 1.3 112.2 - - + +
79C ILE* 1.3 56.0 + - + +
81C TYR* 3.2 3.4 + - - +
82C MET* 2.7 64.9 + - + +
240C MET* 5.6 0.2 - - - -
243C VAL* 4.3 5.4 - - + -
244C LEU* 4.1 16.6 - - + -
204D MET* 3.7 15.9 - - + -
57E GLN* 2.9 30.3 - - - +
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.6 25.7 - - - +
50C PHE* 4.1 15.9 - - + -
51C LEU* 3.6 20.6 - - + +
69C ILE* 6.0 0.2 - - + -
73C VAL* 6.0 0.9 - - + -
75C TYR* 3.3 17.2 + - + +
76C GLY* 3.2 10.0 + - - +
78C ILE* 1.3 80.6 - - + +
80C ARG* 1.3 63.7 + - - +
82C MET* 3.3 8.2 + - - +
83C HIS* 3.1 20.4 + - - +
57E GLN* 6.2 1.1 - - + +
58E PHE* 4.0 41.1 - - + +
61E SER* 4.2 22.9 - - - +
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Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.9 10.7 - - + +
66C VAL* 3.5 30.7 - - + +
69C ILE* 4.3 8.3 - - + -
70C CYS* 3.9 26.3 - - - -
76C GLY 2.7 19.2 + - - +
77C TRP 3.2 4.2 + - - +
79C ILE* 1.3 73.1 - - - +
81C TYR* 1.3 83.5 + - - +
83C HIS* 3.2 6.6 + - - +
84C ALA* 3.0 24.7 + - - +
134C PRO* 4.3 8.9 - - - +
255C ASN* 5.6 2.8 - - - +
256C TYR* 4.6 21.1 + - - -
382C HEM 2.6 52.4 + - - +
118D ARG* 5.0 0.6 - - - +
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Residues in contact with TYR 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C CYS* 4.3 11.7 - - - +
77C TRP* 2.8 42.6 + + + +
80C ARG* 1.3 97.7 - - - +
82C MET* 1.3 55.5 + - - +
84C ALA* 4.1 6.5 - - + -
85C ASN* 2.7 42.9 + - - +
243C VAL* 3.8 24.9 - - + +
247C PRO* 3.9 31.9 - - + -
248C ASP* 4.8 2.2 - - - -
256C TYR* 4.5 5.4 - - - -
118D ARG* 2.5 37.5 + - - -
195D GLU* 5.4 0.2 - - - -
197D GLU* 3.0 26.3 + - + -
201D ARG* 5.7 0.2 - - - -
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Residues in contact with MET 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 4.1 11.2 - - + +
47C THR* 4.2 22.2 - - + -
78C ILE* 2.7 49.9 + - + +
79C ILE 3.7 3.6 - - - +
81C TYR* 1.3 69.8 - - - +
83C HIS* 1.3 57.8 + - - +
86C GLY* 2.8 32.4 + - - -
239C LEU* 4.0 10.7 - - + +
240C MET* 3.6 38.6 - - + -
243C VAL* 4.0 9.6 - - + -
54E VAL* 5.4 11.9 - - + -
57E GLN* 5.4 4.5 - - - +
58E PHE* 4.6 18.4 - - + -
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Residues in contact with HIS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLN* 2.9 53.4 + - - +
47C THR* 3.1 23.5 + - - +
48C GLY* 3.4 9.6 + - - -
51C LEU* 3.8 13.9 - - + -
79C ILE 3.1 12.5 + - - +
80C ARG 3.2 9.4 + - - +
82C MET* 1.3 72.7 - - - +
84C ALA* 1.3 67.3 + - - +
86C GLY 3.0 4.7 + - - -
87C ALA* 3.1 2.3 + - - +
382C HEM 2.0 85.3 + + + +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ARG* 3.0 10.5 + - - +
81C TYR* 3.6 14.8 - - + +
83C HIS* 1.3 81.9 - - - +
85C ASN* 1.3 66.8 + - - +
87C ALA* 3.2 17.0 + - - +
88C SER* 3.7 5.0 + - - -
247C PRO 5.5 2.9 - - - +
382C HEM 3.5 34.8 + - + +
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Residues in contact with ASN 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C TYR* 2.7 29.0 + - - +
84C ALA* 1.3 71.4 - - - +
86C GLY* 1.3 57.6 + - - +
87C ALA 3.1 2.2 - - - -
88C SER* 3.1 7.9 + - - +
89C MET* 2.8 30.3 + - - +
239C LEU* 3.7 7.4 - - + -
242C LEU* 3.3 30.6 - - + +
243C VAL* 3.5 37.0 - - + +
246C ALA 5.0 0.7 - - - +
247C PRO* 3.6 25.8 + - - +
250C LEU* 4.8 10.2 + - - +
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Residues in contact with GLY 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C CYS* 4.6 2.9 - - - -
43C LEU* 4.3 12.6 - - - -
44C GLN* 3.0 11.2 - - - +
82C MET 2.8 25.0 + - - -
83C HIS 3.0 1.3 + - - -
85C ASN* 1.3 73.4 - - - +
87C ALA* 1.3 56.9 + - - +
89C MET* 3.6 5.6 - - - +
90C PHE* 2.7 31.2 + - - +
239C LEU* 3.6 10.5 - - - +
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLN* 2.7 15.5 + - - +
83C HIS 3.1 2.5 + - - +
84C ALA 3.3 12.6 - - - +
86C GLY* 1.3 78.4 - - - +
88C SER* 1.3 60.9 + - - +
90C PHE* 3.5 1.9 + - - +
91C PHE* 3.1 31.5 + - - -
127C ALA* 5.5 0.4 - - + -
273C TYR* 4.3 9.4 - - + +
382C HEM 3.5 44.6 - - + -
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA 3.7 3.5 + - - -
85C ASN* 3.1 11.8 + - - -
87C ALA* 1.3 75.9 - - - +
89C MET* 1.3 61.9 + - - +
91C PHE* 2.9 16.0 + - - -
92C ILE* 2.9 20.7 + - - +
242C LEU* 5.1 1.6 - - - -
250C LEU* 3.6 24.6 - - - +
271C GLU* 5.0 1.9 + - - -
272C TRP* 2.6 38.8 + - - -
273C TYR* 3.8 8.4 - - - -
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C CYS* 4.0 11.7 - - - -
85C ASN* 2.8 20.1 + - + +
86C GLY* 3.7 8.1 - - - +
88C SER* 1.3 77.0 - - - +
90C PHE* 1.3 60.4 + - - +
92C ILE* 3.3 14.9 + - + +
93C CYS* 3.1 33.1 + - - -
235C LEU* 3.7 28.5 - - + +
238C ALA* 3.7 32.3 - - + +
239C LEU* 3.7 27.4 - - + -
242C LEU* 5.0 12.8 - - + -
250C LEU* 6.5 0.4 - - - -
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Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.7 9.9 - - + +
40C CYS* 3.4 32.3 - - + -
41C LEU* 3.6 39.0 - - + -
44C GLN* 4.7 2.2 - - + -
86C GLY 2.7 21.5 + - - +
87C ALA 3.5 7.0 - - - +
88C SER 3.1 0.2 - - - -
89C MET* 1.3 72.7 - - - +
91C PHE* 1.3 59.6 + + + +
93C CYS* 4.7 1.6 - - - -
94C LEU* 3.0 37.5 + - + +
123C VAL* 3.5 42.0 - - + -
189C ILE* 5.3 1.8 - - + -
381C HEM 4.1 22.0 - - + -
382C HEM 4.2 17.7 - - + -
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Residues in contact with PHE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ALA 3.1 23.3 + - - +
88C SER 2.9 8.6 + - - +
90C PHE* 1.3 79.8 - - + +
92C ILE* 1.3 60.0 + - - +
94C LEU* 3.4 19.3 - - + +
95C TYR* 2.8 54.0 + + + -
120C LEU* 4.8 0.4 - - + -
123C VAL* 3.8 24.2 - - + -
124C MET* 3.7 36.6 - - + -
127C ALA* 3.6 23.6 - - + -
272C TRP* 4.1 4.5 - - + -
273C TYR* 3.6 49.8 - + + -
382C HEM 5.0 1.6 - - + -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 5.7 2.2 - - + -
88C SER* 2.9 20.1 + - - +
89C MET* 3.8 17.3 - - + +
91C PHE* 1.3 71.5 - - - +
93C CYS* 1.3 59.7 + - - +
95C TYR* 3.1 6.2 + - + +
96C MET* 2.7 57.5 + - + +
250C LEU* 5.9 3.6 - - + -
272C TRP* 3.6 25.4 - - + -
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Residues in contact with CYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 4.0 30.4 - - + +
36C LEU* 4.2 8.7 - - + -
37C LEU* 3.6 23.3 - - + +
40C CYS* 4.4 3.8 - - - -
89C MET* 3.1 25.6 + - - +
90C PHE* 4.1 0.7 - - - +
92C ILE* 1.3 78.8 - - - +
94C LEU* 1.3 63.7 + - - +
96C MET* 3.0 4.0 + - - +
97C HIS* 2.9 24.9 + - - +
235C LEU* 3.6 28.9 - - - -
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.5 19.9 - - + +
90C PHE* 3.0 29.8 + - + +
91C PHE* 3.4 30.3 - - + +
93C CYS* 1.3 75.8 - - - +
95C TYR* 1.3 65.2 - - + +
97C HIS* 3.3 4.3 + - - +
98C VAL* 3.0 28.2 + - + +
120C LEU* 3.6 30.5 - - + -
123C VAL* 3.8 17.5 - - + -
381C HEM 4.1 33.9 - - + -
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 2.8 43.7 + + - +
92C ILE* 3.8 4.9 - - + +
94C LEU* 1.3 80.9 - - + +
96C MET* 1.3 64.4 + - - +
98C VAL* 3.6 8.7 + - + +
99C GLY* 3.1 18.9 + - - -
120C LEU* 4.6 19.3 - - + -
124C MET* 4.9 6.5 - - - -
272C TRP* 4.3 15.9 - + - -
273C TYR* 2.7 41.4 + - + -
276C PHE* 3.7 21.4 - + - -
298C ILE* 6.3 0.4 - - + -
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Residues in contact with MET 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP* 3.5 32.8 - - + -
33C PHE* 3.4 42.4 - - + -
92C ILE* 2.7 42.1 + - + +
93C CYS 3.4 7.4 - - - +
95C TYR* 1.3 72.3 - - - +
97C HIS* 1.3 53.6 + - - +
99C GLY* 3.1 3.4 + - - -
100C ARG* 2.6 38.2 + - - +
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Residues in contact with HIS 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP 5.2 0.8 + - - -
33C PHE* 3.9 8.4 + - + +
34C GLY* 3.5 21.7 + - - -
37C LEU* 3.5 12.1 - - + -
93C CYS 2.9 18.6 + - - +
94C LEU* 3.4 4.7 - - - +
96C MET* 1.3 69.9 - - - +
98C VAL* 1.3 65.8 + - + +
100C ARG* 3.2 35.6 + - - +
101C GLY* 3.2 18.2 + - - -
113C TRP* 5.5 0.3 - - - -
381C HEM 2.3 92.8 + + + +
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Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU 3.0 17.9 + - - +
95C TYR* 4.1 9.0 - - + +
97C HIS* 1.3 77.2 - - - +
99C GLY* 1.3 66.3 + - - +
101C GLY* 3.1 4.0 + - - -
102C LEU* 3.0 25.0 + - + +
113C TRP* 4.2 10.8 - - + -
120C LEU* 4.8 8.5 - - + -
301C LEU* 4.1 33.4 - - + -
381C HEM 3.6 42.4 - - + -
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Residues in contact with GLY 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR 3.1 12.9 + - - -
96C MET 3.4 3.4 - - - -
98C VAL* 1.3 82.9 - - - +
100C ARG* 1.3 62.8 + - - +
102C LEU* 3.0 10.2 + - - +
103C TYR* 2.9 24.5 + - - +
325C PHE* 3.9 15.7 - - - -
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP* 3.3 49.4 + - + +
31C TRP* 3.3 40.0 - - + +
96C MET 2.6 21.2 + - - +
97C HIS* 3.2 42.5 + - - +
98C VAL 3.2 0.2 - - - -
99C GLY* 1.3 72.6 - - - +
101C GLY* 1.3 69.0 + - - +
103C TYR* 3.4 2.2 + - - -
104C TYR* 2.9 50.4 + - + +
106C SER* 4.3 1.3 - - - -
381C HEM 2.9 50.5 + - - +
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C HIS 3.2 5.6 + - - -
98C VAL 3.1 6.8 + - - -
100C ARG* 1.3 82.7 - - - +
102C LEU* 1.3 66.1 + - - +
105C GLY 3.0 18.9 + - - -
106C SER* 3.0 29.7 + - - -
107C TYR* 3.4 7.2 - - - -
113C TRP* 4.4 10.5 - - - -
381C HEM 5.4 1.1 - - - -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 3.0 15.4 + - + +
99C GLY* 3.0 12.2 + - - +
101C GLY* 1.3 79.5 - - - +
103C TYR* 1.3 63.7 + - - +
105C GLY 3.5 1.2 + - - -
107C TYR* 3.4 19.1 + - + +
113C TRP* 4.5 7.8 - - + -
301C LEU* 5.1 8.3 - - + -
304C ILE* 3.8 44.2 - - + -
315C MET* 3.8 9.6 - - + +
318C ARG* 5.9 0.2 + - - -
325C PHE* 4.6 10.5 - - + -
328C LEU* 4.2 24.2 - - + -
362C ILE* 5.9 0.7 - - + -
366C MET* 4.7 20.6 - - + -
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Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY 2.9 15.1 + - - +
100C ARG* 3.8 4.5 - - - +
102C LEU* 1.3 79.1 - - - +
104C TYR* 1.3 101.1 + + + +
105C GLY 3.6 0.3 + - - -
313C ARG 4.8 0.2 - - - +
314C SER 4.0 0.3 - - - -
315C MET* 3.2 60.4 + - + +
316C MET* 4.1 9.3 + - - -
318C ARG* 5.2 0.3 + - - -
322C GLN* 3.3 34.2 + - + +
325C PHE* 3.6 44.5 - + + -
326C TRP* 4.4 13.7 - + - -
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Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 5.0 0.9 + - - -
30C TRP* 4.4 20.0 - + - -
31C TRP* 3.8 27.1 - + + -
100C ARG* 2.9 37.3 + - + +
103C TYR* 1.3 107.4 - + + +
105C GLY* 1.3 55.7 + - - +
106C SER* 3.2 10.3 - - - +
206C ASN* 2.9 28.0 - - - +
207C ASN 4.6 0.4 - - - +
208C PRO* 3.3 41.1 - - + +
313C ARG* 3.6 12.4 - - - +
314C SER* 3.2 28.4 - - - -
316C MET* 4.9 3.4 - - + -
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Residues in contact with GLY 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C GLY 3.0 4.6 + - - -
102C LEU 3.5 2.8 + - - -
103C TYR 3.4 4.0 + - - -
104C TYR* 1.3 78.0 - - - +
106C SER* 1.3 65.7 + - - +
107C TYR* 2.9 26.2 + - - -
108C THR* 2.9 26.2 + - - +
308C HIS* 4.9 0.4 - - - -
313C ARG* 3.1 23.7 + - - -
318C ARG* 5.8 0.2 - - - +
----------------------------------------------------------
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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