Contacts of the helix formed by residues 59 - 86 (chain P) in PDB entry 4GUN
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 ASP 59 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P ALA* 2.9 17.1 + - - +
57P LYS* 3.2 16.1 - - + +
58P ARG* 1.4 72.4 - - - +
60P LEU* 1.3 50.2 + - - +
61P LYS* 3.9 10.2 + - - +
62P SER* 3.1 30.6 + - - -
63P VAL* 2.9 35.8 + - - +
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Residues in contact with LEU 60 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O ILE* 3.8 22.4 - - + -
44O TYR* 3.4 37.7 - - + +
74O GLY* 3.7 27.1 - - - +
77O HIS* 3.6 29.4 - - + -
78O THR* 3.7 15.3 - - - +
58P ARG* 3.2 25.2 + - + +
59P ASP* 1.3 71.1 - - - +
61P LYS* 1.4 58.5 + - - +
63P VAL* 3.8 5.8 - - + +
64P VAL* 2.9 35.1 + - + +
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Residues in contact with LYS 61 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O THR* 4.9 12.2 + - + +
141O LYS* 5.1 2.8 - - - +
157O THR* 5.4 3.1 - - + -
158O ILE 3.4 26.7 - - - +
159O SER* 3.5 26.8 - - - +
160O ALA 3.3 20.6 + - - -
161O PRO* 3.8 14.7 + - + +
163O LEU 2.6 26.5 + - - -
164O VAL* 4.7 4.6 - - - +
165O PRO* 4.8 4.8 - - - +
59P ASP* 3.3 9.9 + - - +
60P LEU* 1.4 74.9 - - - +
62P SER* 1.3 60.1 + - - +
64P VAL* 3.9 2.1 - - - +
65P GLU* 3.3 17.2 + - - +
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Residues in contact with SER 62 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159O SER 5.5 0.2 - - - -
54P ALA* 3.6 7.7 - - - +
59P ASP* 3.1 30.8 + - - -
61P LYS* 1.3 77.1 - - - +
63P VAL* 1.4 59.0 + - - +
64P VAL 3.3 0.4 - - - -
65P GLU* 3.1 8.3 + - - +
66P ILE* 2.9 52.5 + - - +
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Residues in contact with VAL 63 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O TYR* 3.8 18.2 - - + +
70O ILE* 3.7 28.5 - - + -
51P LEU* 4.0 11.9 - - + +
54P ALA* 3.6 30.7 - - + +
55P VAL* 3.7 22.2 - - + +
59P ASP 2.9 25.5 + - - +
60P LEU* 3.8 8.5 - - + +
62P SER* 1.4 75.1 - - - +
64P VAL* 1.4 63.0 + - + +
66P ILE* 3.4 2.0 + - - +
67P GLN* 3.2 24.0 + - - +
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Residues in contact with VAL 64 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O ILE* 4.3 5.6 - - - +
71O LYS* 3.9 22.0 - - + +
74O GLY* 4.0 10.5 - - - -
75O GLY* 3.8 27.6 - - - +
78O THR* 5.4 0.7 - - - +
155O GLN 6.0 0.4 - - - +
156O ASP* 6.1 0.9 - - - -
157O THR* 3.7 28.9 - - + +
159O SER* 3.8 10.4 + - - +
60P LEU* 2.9 20.2 + - + +
61P LYS 3.9 2.9 - - - +
63P VAL* 1.4 76.9 - - + +
65P GLU* 1.4 57.6 + - - +
67P GLN* 2.7 36.9 + - - +
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Residues in contact with GLU 65 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159O SER* 2.7 45.6 + - - +
160O ALA* 3.7 5.5 + - - +
161O PRO* 3.7 21.5 - - + +
61P LYS 3.3 12.9 + - - +
62P SER* 3.1 12.4 + - - +
64P VAL* 1.4 77.7 - - - +
66P ILE* 1.4 63.1 + - + +
68P GLN* 3.5 20.3 + - - +
69P ASN* 4.3 8.3 + - - +
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Residues in contact with ILE 66 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P ALA* 3.4 33.7 - - + +
50P ALA* 3.4 36.1 - - + +
51P LEU* 3.9 8.7 - - + +
54P ALA* 3.8 8.5 - - + -
62P SER* 2.9 38.5 + - - +
63P VAL* 3.4 4.5 + - - +
65P GLU* 1.4 73.8 - - + +
67P GLN* 1.4 64.9 + - - +
68P GLN 3.1 2.9 - - - -
69P ASN* 2.9 24.1 + - + +
70P ILE* 3.2 18.6 + - + +
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Residues in contact with GLN 67 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67O GLN* 3.2 41.9 - - + +
68O GLN* 4.7 1.7 + - - -
70O ILE* 5.0 7.2 - - + -
71O LYS* 3.5 49.8 - - + +
51P LEU* 5.3 1.1 - - + -
63P VAL 3.2 11.4 + - - +
64P VAL* 2.7 33.5 + - - +
66P ILE* 1.4 75.7 - - - +
68P GLN* 1.4 84.7 + - - +
70P ILE* 3.3 6.2 + - - +
71P LYS* 2.9 34.0 + - - +
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Residues in contact with GLN 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M GLN* 2.9 27.9 - - - +
71O LYS* 5.8 2.6 - - - +
65P GLU 3.6 13.0 - - - +
66P ILE 3.1 0.6 + - - -
67P GLN* 1.4 94.6 + - - +
69P ASN* 1.3 59.9 + - - +
71P LYS* 3.4 39.9 + - - +
72P PHE* 3.0 28.4 + - - +
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Residues in contact with ASN 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M GLN* 2.9 24.0 + - - +
47P ALA* 4.0 16.9 - - + +
65P GLU* 4.6 10.8 + - - +
66P ILE* 2.9 17.5 + - - +
68P GLN* 1.3 76.2 - - - +
70P ILE* 1.3 60.1 + - - +
73P HIS* 3.0 48.7 + - + +
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Residues in contact with ILE 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63O VAL* 3.6 25.8 - - + -
64O VAL* 4.3 2.9 - - + +
67O GLN* 3.4 35.9 - - + +
44P TYR* 3.9 13.0 - - + -
47P ALA* 3.8 17.3 - - + -
48P ILE* 3.9 11.7 - - + -
51P LEU* 3.5 26.7 - - + -
66P ILE* 3.2 30.7 + - + +
67P GLN* 3.6 7.0 - - - +
69P ASN* 1.3 73.1 - - - +
71P LYS* 1.3 56.9 + - - +
74P GLY* 2.8 31.7 + - - -
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Residues in contact with LYS 71 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O VAL* 4.2 23.4 - - + +
67O GLN* 4.2 11.6 - - + +
68O GLN* 5.7 7.5 - - - +
67P GLN* 2.9 21.6 + - - +
68P GLN* 3.4 42.6 + - - +
70P ILE* 1.3 76.4 - - - +
72P PHE* 1.3 57.7 + - - +
75P GLY* 3.0 26.5 + - - -
155P GLN 4.1 4.2 - - - +
156P ASP* 3.2 34.0 + - - +
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Residues in contact with PHE 72 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M GLN* 3.5 58.3 - - + +
131M GLY 4.1 1.3 - - - -
40P TYR* 3.6 24.5 - + - -
68P GLN* 3.0 19.8 + - - +
69P ASN 4.2 1.3 - - - +
71P LYS* 1.3 74.8 - - - +
73P HIS* 1.3 81.4 + + - +
76P GLY* 2.8 25.5 + - - -
154P ASN* 4.4 4.7 - - + -
155P GLN* 3.2 40.2 - - + +
172P TRP* 3.7 24.0 - + - -
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Residues in contact with HIS 73 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M GLN* 4.7 4.0 + - - -
39P ALA* 3.9 8.7 - - + -
40P TYR* 3.5 33.5 - + - +
43P GLY* 3.5 29.6 - - - -
44P TYR* 3.3 24.1 - - - +
69P ASN* 3.0 39.3 + - + +
72P PHE* 1.3 94.8 - + - +
74P GLY* 1.3 59.3 + - - +
76P GLY 3.4 0.2 + - - -
77P HIS* 3.0 30.1 + - - +
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Residues in contact with GLY 74 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O LEU* 3.7 14.3 - - - +
64O VAL* 3.8 11.9 - - - -
44P TYR* 3.6 19.7 - - - -
70P ILE 2.8 22.0 + - - -
73P HIS* 1.3 72.8 - - - +
75P GLY* 1.3 54.7 + - - +
77P HIS 3.4 0.2 + - - -
78P THR* 3.0 32.2 + - - -
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Residues in contact with GLY 75 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O VAL* 3.7 9.4 - - - +
71P LYS 3.0 14.7 + - - -
74P GLY* 1.3 73.8 - - - +
76P GLY* 1.3 54.4 + - - +
78P THR* 3.2 2.1 + - - -
79P ASN* 2.8 39.1 + - - -
155P GLN 3.2 24.7 - - - -
157P THR* 4.5 9.9 - - - -
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Residues in contact with GLY 76 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P TYR* 3.8 15.3 - - - -
72P PHE 2.8 18.6 + - - -
73P HIS 3.4 2.0 + - - -
75P GLY* 1.3 69.6 - - - +
77P HIS* 1.3 57.6 + - - +
80P HIS* 2.8 37.7 + - - +
155P GLN* 3.3 27.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 77 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O LEU* 3.7 17.3 - - + -
8P ILE* 3.4 44.2 - - + +
9P SER 3.4 25.1 - - - -
11P PRO* 4.3 3.8 - - + -
37P HIS* 3.0 29.3 + - + +
40P TYR* 3.8 5.2 - - + +
41P VAL* 3.8 4.8 - - - +
73P HIS 3.0 14.6 + - - +
74P GLY 3.8 2.7 - - - +
76P GLY* 1.3 75.7 - - - +
78P THR* 1.4 57.0 + - - +
81P SER* 2.8 52.4 + - - -
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Residues in contact with THR 78 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O LEU* 3.8 23.7 + - - +
61O LYS* 4.8 10.9 + - + +
64O VAL* 5.2 0.3 - - - +
74P GLY 3.0 19.4 + - - -
75P GLY* 3.2 5.8 + - - -
77P HIS* 1.4 74.7 - - - +
79P ASN* 1.3 61.3 + - - +
81P SER* 3.4 4.7 + - - -
82P LEU* 3.0 40.1 + - + +
157P THR* 3.8 23.6 - - + +
158P ILE 5.7 2.0 - - - +
----------------------------------------------------------
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Residues in contact with ASN 79 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P GLY 2.8 23.5 + - - +
78P THR* 1.3 71.2 - - - +
80P HIS* 1.3 58.7 + - - +
82P LEU* 3.4 9.0 + - - +
83P PHE* 3.0 28.1 + - - +
134P TRP* 3.4 36.1 - - + +
136P PHE* 3.2 20.8 - - - -
155P GLN* 3.3 23.8 + - - +
156P ASP 3.2 20.4 + - - -
157P THR* 2.7 25.4 + - - -
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Residues in contact with HIS 80 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P HIS* 3.2 19.9 + + - -
36P HIS* 5.0 0.8 - - - +
37P HIS* 3.6 27.1 - + + +
40P TYR* 3.4 25.0 - + - -
76P GLY 2.8 30.5 + - - +
79P ASN* 1.3 76.3 - - - +
81P SER* 1.3 61.4 + - - +
83P PHE* 3.2 6.0 + + - +
84P TRP* 3.1 47.0 + + - +
134P TRP* 3.6 12.6 - + - -
155P GLN* 3.5 13.9 + - - -
170P ASP* 3.3 2.2 + - - -
174P HIS* 3.9 0.4 + - - -
301P MN 2.1 37.5 + - - -
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Residues in contact with SER 81 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P PRO* 3.8 10.8 - - - +
37P HIS* 3.4 13.2 - - - -
77P HIS* 2.8 38.6 + - - -
78P THR* 3.8 4.9 - - - -
80P HIS* 1.3 75.5 - - - +
82P LEU* 1.4 61.6 + - - +
84P TRP* 3.8 9.8 + - - +
85P LYS* 3.3 28.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 82 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P THR* 3.0 34.3 + - + +
79P ASN* 3.5 8.3 - - - +
81P SER* 1.4 73.9 - - - +
83P PHE* 1.4 58.7 + - - +
85P LYS* 3.2 1.5 + - - -
86P ASN* 3.0 19.4 + - - +
136P PHE* 4.1 17.7 - - + -
157P THR* 4.6 2.5 - - - +
165P PRO* 3.8 38.1 - - + +
168P ALA* 3.9 10.5 - - + -
203P ARG* 2.7 50.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 83 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P ILE* 4.8 5.8 - - + -
32P HIS* 3.7 26.9 - + - -
79P ASN 3.0 14.4 + - - +
80P HIS* 3.2 9.6 + + - +
82P LEU* 1.4 71.1 - - - +
84P TRP* 1.3 87.9 + + - +
86P ASN* 3.1 18.6 + - - +
87P LEU* 3.3 37.3 + - + +
134P TRP* 3.9 10.5 - + + -
168P ALA* 3.3 20.6 - - - +
169P ILE* 3.9 0.2 - - - -
170P ASP* 3.5 26.7 - - + -
175P ALA* 5.4 0.2 - - + -
187P TYR* 3.5 21.1 - - - -
191P ILE* 3.6 23.1 - - + -
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Residues in contact with TRP 84 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P PRO* 4.2 5.6 - - + -
13P ILE* 3.7 35.0 - - + +
15P TRP* 3.1 51.3 + + + -
29P ASN* 4.6 5.2 - - - -
32P HIS* 3.4 41.7 - + + -
33P ILE* 3.5 33.0 - - + +
37P HIS* 2.9 27.8 + + - -
80P HIS* 3.1 37.9 + + - -
81P SER* 4.1 7.9 - - - +
83P PHE* 1.3 93.5 - + - +
85P LYS* 1.3 61.5 + - + +
87P LEU* 3.2 8.7 + - + +
----------------------------------------------------------
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Residues in contact with LYS 85 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P PRO* 6.0 5.2 - - - -
12P LYS 5.2 8.6 + - - -
14P ASP* 3.3 28.4 + - - +
81P SER* 3.3 15.2 + - - +
82P LEU* 3.2 2.1 + - - +
83P PHE 3.2 0.8 - - - -
84P TRP* 1.3 80.1 - - + +
86P ASN* 1.4 54.7 + - - +
87P LEU 3.4 1.5 + - - +
196P ASN* 3.4 22.5 + - - -
199P GLU* 3.4 27.1 - - + +
203P ARG* 3.3 19.7 - - - +
----------------------------------------------------------
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Residues in contact with ASN 86 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82P LEU 3.0 14.7 + - - +
83P PHE* 3.1 12.5 + - - +
85P LYS* 1.4 74.5 - - - +
87P LEU* 1.3 54.4 + - - +
167P ILE* 3.7 19.3 - - + -
168P ALA* 2.8 46.9 + - - +
195P ILE* 3.4 21.4 - - - +
196P ASN* 2.8 32.4 + - - +
199P GLU* 4.5 1.8 - - + -
203P ARG* 2.9 26.6 + - - +
----------------------------------------------------------
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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