Contacts of the helix formed by residues 81 - 104 (chain F) 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 81 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E PHE* 4.4 13.5 - - + -
14E GLY 5.8 0.9 - - - +
16E LEU* 4.3 22.0 - - + -
150E SER* 6.6 0.2 - - - -
30F ALA* 5.0 11.0 - - + +
79F SER 4.2 0.6 + - - -
80F GLY* 1.3 74.7 - - - +
82F ILE* 1.3 65.5 + - - +
83F ALA* 3.2 4.9 - - + +
84F ASP* 3.0 39.0 + - - +
85F ALA* 3.2 8.5 + - - +
138F GLY* 2.9 31.1 + - - +
139F VAL* 4.2 2.2 - - - +
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Residues in contact with ILE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E THR* 5.2 9.8 - - + +
65F GLU 4.5 7.6 - - - +
66F LYS* 4.6 22.9 - - + +
78F MET* 4.0 52.5 - - + +
79F SER* 4.3 1.6 - - - -
80F GLY 3.3 24.8 + - - +
81F LEU* 1.3 75.1 - - - +
83F ALA* 1.3 55.6 + - - +
85F ALA* 2.8 20.5 + - + -
86F LYS* 3.0 15.1 + - + +
139F VAL* 5.2 0.2 - - + -
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Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E GLN* 3.3 27.5 - - + +
150E SER* 3.2 29.8 - - - +
151E GLY 4.0 19.7 - - - -
152E THR* 4.2 10.1 - - + +
81F LEU* 4.8 2.9 - - + -
82F ILE* 1.3 78.8 - - - +
84F ASP* 1.3 64.8 + - - +
86F LYS* 3.6 16.4 + - - +
87F THR* 3.9 2.1 + - - -
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Residues in contact with ASP 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 5.3 1.0 - - - +
116E GLN* 3.7 16.3 + - - +
119E THR* 5.0 1.4 + - - -
120E GLN* 4.4 0.2 + - - -
150E SER 5.3 0.3 - - - +
81F LEU* 3.0 27.9 + - - +
83F ALA* 1.3 83.3 - - - +
85F ALA* 1.3 64.8 + - - +
86F LYS 3.5 0.2 + - - -
87F THR* 3.6 7.0 + - - -
88F LEU* 3.8 2.1 - - - +
135F ARG* 2.2 36.0 + - - -
137F PHE* 3.4 36.2 - - + -
138F GLY 3.4 22.6 + - - +
139F VAL* 4.6 4.3 - - + -
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Residues in contact with ALA 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F MET* 3.4 31.6 - - + -
81F LEU 3.2 2.0 + - - -
82F ILE* 2.8 16.7 + - - +
84F ASP* 1.3 77.6 - - - +
86F LYS* 1.3 64.4 + - - +
88F LEU* 3.1 7.1 + - - +
89F ILE* 2.9 29.0 + - + +
139F VAL* 3.8 27.8 - - + +
141F LEU* 4.8 1.8 - - + -
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Residues in contact with LYS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E SER* 6.4 2.2 - - - -
78F MET* 5.3 0.8 - - - -
82F ILE* 3.0 10.5 + - + +
83F ALA* 3.7 13.2 - - - +
84F ASP 3.3 0.4 - - - -
85F ALA* 1.3 76.9 - - - +
87F THR* 1.3 57.1 - - - +
89F ILE* 3.4 6.8 + - - +
90F ASP* 3.0 29.6 + - - +
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Residues in contact with THR 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E GLN* 3.5 23.4 + - - -
120E GLN* 4.4 0.3 + - - -
83F ALA 3.9 3.1 + - - -
84F ASP 3.7 11.8 + - - -
85F ALA 3.2 0.2 - - - -
86F LYS* 1.3 77.8 - - - +
88F LEU* 1.3 58.8 + - + +
90F ASP* 3.3 7.0 + - - +
91F LYS* 3.0 27.2 + - + +
119F LEU* 6.1 2.7 - - + -
133F MET* 4.3 13.7 - - + -
137F PHE* 3.9 20.0 - - + -
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ASP 3.8 3.6 - - - +
85F ALA* 3.1 5.5 + - - +
87F THR* 1.3 73.4 - - + +
89F ILE* 1.3 66.6 + - - +
91F LYS* 3.3 6.5 + - - +
92F ALA* 2.9 24.1 + - - +
116F VAL* 3.9 21.1 - - + +
119F LEU* 4.1 23.1 - - + +
137F PHE* 3.6 44.9 - - + -
139F VAL* 3.6 30.7 - - + -
141F LEU* 3.9 20.6 - - + -
156F MET* 4.5 10.8 - - + -
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F VAL* 3.7 25.1 - - + -
70F ILE* 3.8 12.3 - - + -
76F CYS* 3.8 29.4 - - - -
78F MET* 4.2 9.6 - - + -
85F ALA 2.9 25.6 + - - +
86F LYS* 3.7 6.5 - - - +
88F LEU* 1.3 77.1 - - - +
90F ASP* 1.3 64.7 + - - +
92F ALA* 3.1 5.8 + - - +
93F ARG* 3.0 49.7 + - - +
141F LEU* 4.2 15.7 - - + -
143F PHE* 4.7 3.1 - - + -
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Residues in contact with ASP 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F LYS 3.0 17.9 + - - +
87F THR* 3.7 5.8 - - - +
88F LEU 3.3 0.2 - - - -
89F ILE* 1.3 76.7 - - - +
91F LYS* 1.3 63.6 + - - +
93F ARG* 3.2 13.4 + - - +
94F VAL* 3.0 33.4 + - - +
65e ILE* 5.3 1.2 - - - +
69e ARG* 3.3 44.4 + - - +
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Residues in contact with LYS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F THR* 3.0 14.2 + - + +
88F LEU 3.5 8.1 - - - +
90F ASP* 1.3 78.3 + - - +
92F ALA* 1.3 59.2 + - - +
94F VAL* 3.6 7.2 + - + +
95F GLU* 3.0 62.0 + - + +
115F ALA* 3.8 24.0 + - - +
116F VAL* 5.0 2.2 - - - -
118F ASN* 5.5 2.2 - - - +
119F LEU* 3.5 44.6 - - + +
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Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 3.9 26.2 - - + -
88F LEU 2.9 14.7 + - - +
89F ILE* 3.4 8.7 - - - +
91F LYS* 1.3 76.5 - - - +
93F ARG* 1.3 58.1 + - - +
95F GLU* 3.2 7.4 + - - +
96F THR* 2.9 33.1 + - - +
112F VAL* 4.1 7.3 - - + +
115F ALA* 6.2 0.2 - - - -
116F VAL* 3.7 25.1 - - + +
143F PHE* 4.7 2.0 - - + -
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Residues in contact with ARG 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLU* 5.7 0.4 + - - -
68F VAL* 3.5 28.5 - - - +
69F GLU* 3.0 27.2 + - - +
70F ILE* 3.4 24.5 - - + +
89F ILE* 3.0 34.0 + - - +
90F ASP* 3.2 15.4 + - - +
92F ALA* 1.3 71.7 - - - +
94F VAL* 1.3 65.6 + - + +
96F THR* 2.5 24.9 + - - -
97F GLN* 3.0 14.5 + - + +
65e ILE* 5.5 7.2 - - + -
68e LEU* 3.6 44.1 + - + +
69e ARG* 4.1 13.6 - - - +
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ASP* 3.0 34.3 + - - +
91F LYS* 3.8 7.6 - - + +
93F ARG* 1.3 75.8 - - + +
95F GLU* 1.3 58.4 + - + +
97F GLN* 3.3 1.9 + - - +
98F ASN* 2.8 47.3 + - - +
61e ARG* 3.7 12.3 - - - +
65e ILE* 4.1 26.2 - - + -
69e ARG* 4.9 6.7 - - - +
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Residues in contact with GLU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LYS* 3.0 52.1 + - + +
92F ALA* 3.3 7.4 - - - +
94F VAL* 1.3 76.1 - - + +
96F THR* 1.3 65.1 + - - +
98F ASN* 3.2 9.1 + - - +
99F HIS* 3.0 23.9 + - - +
107F MET* 4.0 19.6 - - + +
112F VAL* 5.8 0.7 - - + -
115F ALA* 4.0 17.7 - - + +
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Residues in contact with THR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 3.9 19.9 + - + -
71F ASP* 4.1 19.1 + - + +
73F HIS* 5.7 0.7 - - + -
74F ILE* 5.2 2.2 - - + -
92F ALA 2.9 16.9 + - - +
93F ARG* 2.5 24.9 + - - -
95F GLU* 1.3 74.1 - - - +
97F GLN* 1.3 68.4 + - - +
99F HIS* 3.3 4.0 + - - +
100F TRP* 2.9 27.5 + - - +
107F MET* 3.8 17.5 + - + +
112F VAL* 3.6 29.6 - - + -
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Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ASP* 3.6 29.3 + - - -
93F ARG* 3.0 16.0 + - + +
94F VAL 3.7 4.7 - - - +
96F THR* 1.3 88.3 + - - +
98F ASN* 1.3 57.1 + - - +
100F TRP* 3.3 29.6 + - - +
101F PHE* 2.8 29.2 + - - +
61e ARG* 4.3 18.2 - - + +
64e ARG* 3.4 35.4 - - + +
65e ILE* 4.0 23.3 - - + +
68e LEU* 4.7 6.6 - - + +
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Residues in contact with ASN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F VAL* 2.8 38.1 + - - +
95F GLU* 3.2 11.3 + - - +
97F GLN* 1.3 72.5 - - - +
99F HIS* 1.3 61.2 + - - +
101F PHE* 3.2 9.5 + - + +
102F THR* 2.9 35.2 + - - +
61e ARG* 2.4 39.7 + - - +
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Residues in contact with HIS 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F GLU* 3.0 9.9 + - - +
96F THR 3.5 1.8 - - - +
97F GLN 3.3 0.2 - - - -
98F ASN* 1.3 78.7 - - - +
100F TRP* 1.3 57.2 + - - +
102F THR* 4.7 0.7 - - - -
103F TYR* 2.9 56.5 + + - +
105F GLU* 3.2 50.7 + - + -
106F THR 3.7 6.7 - - - -
107F MET* 3.3 42.9 - - + +
108F THR* 6.3 0.2 - - + -
75f TYR* 3.8 12.6 - + - -
78f SER* 6.2 0.2 - - - -
79f ASN* 3.8 15.8 + - - -
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Residues in contact with TRP 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ASP* 6.0 1.1 - - - +
96F THR 2.9 17.0 + - - +
97F GLN* 3.7 25.6 - - - +
99F HIS* 1.3 76.8 + - - +
101F PHE* 1.3 79.5 + - + +
104F ASN* 2.8 46.6 + - - -
105F GLU 3.8 16.6 + - - +
106F THR* 5.6 4.3 - - + -
37e ILE 5.5 3.6 - - - -
57e ARG* 3.2 34.4 + - + -
60e ALA* 3.7 24.7 - - + -
61e ARG* 3.8 25.4 - - + -
64e ARG* 6.2 0.2 - - + -
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Residues in contact with PHE 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F GLN 2.8 17.3 + - - +
98F ASN* 3.4 13.2 - - + +
99F HIS 3.2 0.2 - - - -
100F TRP* 1.3 83.5 - - + +
102F THR* 1.3 74.0 + - - +
54e PHE* 4.3 28.3 - + - -
57e ARG* 2.8 61.1 + - + +
58e LEU* 3.3 41.3 - - + -
61e ARG* 4.5 10.8 - - + -
90f ALA* 5.4 0.3 - - - +
94f THR* 4.3 17.7 - - + +
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Residues in contact with THR 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ASN* 2.9 17.4 + - - +
99F HIS* 4.7 0.2 - - - -
101F PHE* 1.3 91.9 - - - +
103F TYR* 1.3 93.9 + - + +
104F ASN 3.7 0.4 - - - -
71f ARG* 3.8 13.0 - - - +
90f ALA* 3.2 29.3 - - - +
91f MET* 3.3 2.1 + - + -
94f THR* 3.9 22.0 - - - +
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Residues in contact with TYR 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F HIS* 2.9 45.4 + + + +
102F THR* 1.3 85.4 - - + +
104F ASN* 1.3 72.8 + - - +
105F GLU* 3.1 19.7 + - + +
71f ARG* 2.3 37.2 + - - -
74f MET* 6.0 0.5 - - - +
75f TYR* 4.1 17.8 + + - +
83f MET* 3.4 23.3 - - + -
86f GLY 4.7 0.2 - - - -
87f ALA* 3.5 23.0 - - + -
90f ALA* 3.9 4.5 - - - -
91f MET* 3.1 39.8 - - + -
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Residues in contact with ASN 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F TRP* 2.8 34.0 + - - -
102F THR 3.7 0.8 - - - -
103F TYR* 1.3 79.4 - - - +
105F GLU* 1.3 58.1 + - - +
57e ARG* 2.9 24.9 + - - +
86f GLY 5.2 3.9 + - - +
87f ALA* 5.7 0.2 - - - -
90f ALA* 4.0 11.0 - - + -
130f TYR* 4.1 14.3 + - - -
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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