Contacts of the helix formed by residues 80 - 103 (chain X) in PDB entry 5GJQ
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 LEU 80 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13G TRP* 4.3 13.7 - - + -
19G ILE* 4.6 5.4 - - + -
22G ILE* 5.1 8.1 - - + -
150G SER* 5.3 13.2 - - - +
152G ASN* 6.1 4.3 - - + +
29X ALA* 4.8 5.0 + - + -
79X GLY* 1.3 71.2 - - - -
81X LEU* 1.3 68.0 + - - +
82X ALA* 4.4 12.3 - - + +
83X ASP* 3.2 16.7 + - - +
84X ALA* 3.2 17.0 + - - +
129X ARG* 3.7 30.7 - - - +
132X GLY* 2.7 19.6 + - - +
133X CYS* 4.1 0.2 - - - +
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Residues in contact with LEU 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G ASN* 3.3 36.3 - - - +
63X ASN* 3.4 22.0 - - + +
64X LYS 4.6 7.4 - - - +
65X ARG* 4.2 31.9 - - + +
67X PHE* 5.1 1.3 - - + -
77X VAL* 4.5 13.7 - - + -
79X GLY 3.0 7.8 + - - +
80X LEU* 1.3 76.8 - - - +
82X ALA* 1.3 63.5 + - - +
84X ALA* 2.9 8.6 + - + +
85X ARG* 2.9 50.5 + - + +
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Residues in contact with ALA 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G GLN* 3.8 21.4 - - + +
120G THR* 5.8 1.3 - - - +
150G SER 3.6 24.0 - - - +
151G ALA* 4.1 16.6 - - + +
152G ASN* 4.5 3.3 - - + +
80X LEU* 3.4 9.0 - - + +
81X LEU* 1.3 76.9 - - - +
83X ASP* 1.3 66.3 + - - +
85X ARG* 3.1 13.4 + - - +
86X SER* 3.0 23.7 + - - -
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Residues in contact with ASP 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G GLN* 3.2 20.8 + - - +
120G THR* 4.8 0.5 + - - -
80X LEU* 3.2 20.2 + - - +
81X LEU 3.2 0.4 - - - -
82X ALA* 1.3 76.1 - - - +
84X ALA* 1.3 63.2 + - - +
86X SER* 2.5 24.1 + - - -
87X LEU* 2.9 12.6 + - - +
129X ARG* 2.3 36.6 + - - -
131X PHE* 3.8 13.4 - - + -
132X GLY* 2.9 20.5 + - - +
133X CYS* 3.9 15.3 - - - -
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Residues in contact with ALA 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X PHE* 4.6 3.2 - - + -
75X MET* 4.0 4.5 - - - +
77X VAL* 3.6 39.7 - - + -
78X ALA 5.3 0.9 - - - +
79X GLY 5.8 0.2 - - - +
80X LEU 3.2 8.7 + - - +
81X LEU* 2.9 16.0 + - + +
83X ASP* 1.3 79.7 - - - +
85X ARG* 1.3 57.0 + - - +
87X LEU* 3.3 4.2 + - - +
88X ALA* 2.9 28.6 + - - +
133X CYS* 3.7 16.3 - - + -
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Residues in contact with ARG 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G GLY* 6.2 2.5 - - - -
151G ALA 4.4 2.4 + - - -
152G ASN* 3.2 23.6 + - - +
153G TYR* 3.1 72.0 + - - +
63X ASN* 4.0 14.6 - - - +
64X LYS 5.2 1.8 + - - +
67X PHE* 3.9 24.4 - - + -
81X LEU* 2.9 43.1 + - + +
82X ALA* 3.1 11.7 + - - +
84X ALA* 1.3 71.7 - - - +
86X SER* 1.3 68.2 + - - +
88X ALA* 3.0 9.8 + - - +
89X ASP* 3.0 28.1 + - - +
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Residues in contact with SER 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G SER* 6.3 3.1 - - - +
117G GLN* 3.8 23.0 + - - -
82X ALA 3.0 10.4 + - - -
83X ASP* 2.5 28.2 + - - -
85X ARG* 1.3 75.5 - - - +
87X LEU* 1.3 59.4 + - - +
89X ASP* 3.0 13.2 + - - +
90X ILE* 2.9 38.6 + - - +
131X PHE* 3.6 15.4 - - - -
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X MET* 4.2 10.4 - - + +
83X ASP 2.9 12.2 + - - +
84X ALA* 3.7 5.4 - - - +
86X SER* 1.3 81.8 + - - +
88X ALA* 1.3 57.0 + - - +
90X ILE* 3.3 14.6 + - + +
91X ALA* 2.9 29.5 + - - +
115X VAL* 4.7 7.3 - - + +
118X TYR* 4.3 6.1 - - + -
119X VAL* 3.7 24.0 - - + -
131X PHE* 3.7 36.6 - - + -
133X CYS* 3.4 28.5 - - - +
135X PHE* 3.7 24.2 - - + -
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Residues in contact with ALA 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X PHE* 4.1 24.7 - - + -
69X VAL* 4.3 1.6 - - + +
75X MET* 3.9 22.6 - - - +
84X ALA 2.9 14.0 + - - +
85X ARG* 3.0 12.8 + - - +
87X LEU* 1.3 75.5 - - - +
89X ASP* 1.3 62.4 + - - +
91X ALA* 3.3 3.2 + - - +
92X ARG* 2.9 39.3 + - - +
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Residues in contact with ASP 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G SER* 3.4 24.5 + - - -
85X ARG* 3.0 19.3 + - - +
86X SER* 3.0 12.1 + - - +
88X ALA* 1.3 76.2 - - - +
90X ILE* 1.3 64.3 + - + +
92X ARG* 3.3 29.4 + - - +
93X GLU* 3.0 24.6 + - - +
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Residues in contact with ILE 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X SER* 2.9 37.1 + - - +
87X LEU* 3.5 14.8 - - + +
88X ALA 3.2 0.2 - - - -
89X ASP* 1.3 77.4 - - + +
91X ALA* 1.3 58.9 + - - +
93X GLU* 3.2 6.5 + - - +
94X GLU* 2.9 34.0 + - + +
115X VAL* 4.8 12.3 - - + -
118X TYR* 3.4 65.3 - - + +
131X PHE* 4.9 2.0 - - + -
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Residues in contact with ALA 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X VAL* 3.7 27.5 - - + +
75X MET* 5.1 3.8 - - + -
87X LEU 2.9 17.8 + - - +
88X ALA* 3.7 4.9 - - - +
90X ILE* 1.3 76.6 - - - +
92X ARG* 1.3 62.2 - - - +
94X GLU* 3.1 3.5 + - - +
95X ALA* 2.9 24.9 + - - +
111X LEU* 3.7 5.8 - - + +
115X VAL* 3.9 28.5 - - + -
135X PHE* 6.0 0.4 - - + -
137X LEU* 5.4 3.6 - - + -
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Residues in contact with ARG 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X PHE* 5.0 16.5 - - - -
68X ASN 3.0 19.4 + - - +
69X VAL* 3.3 28.5 - - - +
88X ALA* 2.9 24.9 + - - +
89X ASP* 3.4 27.0 + - - +
91X ALA* 1.3 75.9 - - - +
93X GLU* 1.3 58.6 + - - +
95X ALA* 3.3 4.0 + - - +
96X SER* 2.9 28.9 + - - -
73g ASP* 5.1 7.3 + - - +
76g LEU* 3.3 33.0 + - + +
77g LEU* 3.2 35.5 - - - +
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Residues in contact with GLU 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X ASP 3.0 16.4 + - - +
90X ILE* 3.7 5.8 - - - +
92X ARG* 1.3 73.4 - - - +
94X GLU* 1.3 60.8 + - - +
96X SER* 4.2 5.2 - - - -
97X ASN* 2.9 59.8 + - - +
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Residues in contact with GLU 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X ILE* 2.9 18.8 + - + +
91X ALA* 3.1 10.3 + - - +
93X GLU* 1.3 78.0 - - - +
95X ALA* 1.3 56.3 + - - +
97X ASN* 3.9 7.8 - - - +
98X PHE* 2.9 31.9 + - - +
106X ILE* 4.6 4.6 - - + +
110X HIS* 5.8 0.5 - - - -
111X LEU* 3.9 13.5 - - + -
114X ARG* 2.8 65.7 + - + +
115X VAL* 4.8 3.8 - - + -
118X TYR* 6.1 1.2 - - - +
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Residues in contact with ALA 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X VAL* 4.4 3.8 - - + +
70X ASP* 3.4 35.8 - - + +
91X ALA 2.9 12.8 + - - +
92X ARG 3.5 8.5 - - - +
94X GLU* 1.3 75.3 - - - +
96X SER* 1.3 64.6 + - - +
98X PHE* 3.3 3.5 + - - +
99X ARG* 3.0 23.4 + - - +
106X ILE* 3.8 25.2 + - + +
111X LEU* 4.2 4.1 - - + +
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Residues in contact with SER 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X ARG 2.9 16.9 + - - -
93X GLU* 3.6 8.5 - - - -
95X ALA* 1.3 75.9 - - - +
97X ASN* 1.3 70.7 + - - +
99X ARG* 3.1 7.3 + - - +
100X SER* 3.0 25.5 + - - -
69g GLN* 2.7 43.6 + - - +
73g ASP* 4.2 9.6 + - - -
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Residues in contact with ASN 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X GLU* 2.9 47.0 + - - +
94X GLU* 3.9 7.4 - - - +
96X SER* 1.3 78.1 + - - +
98X PHE* 1.3 66.9 + - - +
100X SER* 3.3 7.1 + - - +
101X ASN* 3.0 39.8 + - - +
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Residues in contact with PHE 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X GLU* 2.9 20.7 + - - +
95X ALA 3.5 5.2 - - - +
96X SER 3.2 0.2 - - - -
97X ASN* 1.3 76.1 - - - +
99X ARG* 1.3 56.6 + - - +
102X PHE* 2.9 52.3 + + + +
104X TYR* 3.6 32.8 - + - -
106X ILE* 3.5 27.8 - - + -
107X PRO* 3.6 25.6 - - + -
110X HIS* 3.4 36.1 - + - -
66a HIS* 3.3 28.5 - + - -
70a LEU* 5.0 0.2 - - + -
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Residues in contact with ARG 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X ASP* 3.0 41.1 + - - -
71X ARG* 3.8 25.5 - - - +
95X ALA 3.0 8.6 + - - +
96X SER* 3.1 15.2 + - - +
98X PHE* 1.3 76.9 - - - +
100X SER* 1.3 61.4 + - - +
103X GLY* 2.8 41.1 + - - +
104X TYR 3.7 15.0 + - - +
105X ASN* 4.1 18.6 + - - +
65g GLN* 5.3 1.2 + - + -
68g GLY 6.0 0.2 - - - -
69g GLN* 2.0 49.4 + - + +
72g ILE* 3.6 22.0 - - - +
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Residues in contact with SER 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96X SER* 3.0 16.9 + - - -
97X ASN* 3.9 7.9 + - - -
99X ARG* 1.3 79.2 - - - +
101X ASN* 1.3 66.4 + - - +
103X GLY* 4.8 0.9 + - - -
84a LYS* 4.6 0.3 + - - -
85a GLU* 3.2 21.3 - - - +
65g GLN* 3.4 33.1 + - - +
69g GLN* 3.8 16.6 - - - +
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Residues in contact with ASN 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97X ASN* 3.0 31.3 + - - +
100X SER* 1.3 85.3 - - - +
102X PHE* 1.3 76.6 + - + +
81a SER* 4.4 4.6 - - - +
82a LEU* 3.3 22.7 - - + +
85a GLU* 4.1 22.9 - - + +
89a ARG* 5.8 1.0 + - - -
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Residues in contact with PHE 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PHE* 2.9 45.5 + + + +
101X ASN* 1.3 92.4 - - + +
103X GLY* 1.3 59.0 + - - +
104X TYR* 3.4 27.7 + - + -
110X HIS* 5.9 1.1 - + - -
62a GLN* 5.2 7.0 - - + -
66a HIS* 4.2 24.7 - + + -
77a HIS* 4.2 1.6 + - - -
78a THR* 3.8 25.7 - - + -
81a SER* 3.5 20.7 + - - -
82a LEU* 3.6 33.0 - - + -
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Residues in contact with GLY 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X ARG* 2.8 26.9 + - - +
100X SER 5.3 0.4 - - - -
101X ASN 3.8 0.4 - - - -
102X PHE* 1.3 77.7 - - - +
104X TYR* 1.3 60.9 + - - +
105X ASN* 5.2 0.9 - - - +
77a HIS* 4.3 13.8 - - - -
81a SER* 4.1 10.1 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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