Contacts of the helix formed by residues 100 - 121 (chain A) in PDB entry 5JTM
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 ALA 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 3.1 25.5 + - + +
97A CYS 3.6 0.6 + - - -
99A GLY* 1.4 79.5 - - - +
101A TYR* 1.4 60.6 + - - +
102A CYS 3.5 0.9 - - - -
103A PRO* 3.5 9.3 - - - +
104A ASN* 3.1 28.3 + - - +
133A PHE* 4.4 6.2 - - - +
134A ASP* 3.6 15.7 - - - -
137A PHE* 3.5 28.0 - - + -
14E LEU* 5.0 0.4 - - + -
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A MET* 3.2 30.5 - - - +
11A PHE* 3.4 43.4 - + + +
86A ILE* 5.1 0.4 - - + -
96A HIS* 3.3 14.5 + + + +
97A CYS* 3.1 37.5 + - + -
100A ALA* 1.4 76.8 - - - +
102A CYS* 1.3 93.4 + - - +
104A ASN* 3.2 15.6 + - + +
105A ILE* 3.1 31.0 + - + +
134A ASP* 4.2 13.7 - - + +
1C MET* 4.8 19.0 - - + +
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Residues in contact with CYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 4.2 12.3 - - - -
58A VAL* 4.1 15.9 - - + -
84A PHE* 4.3 9.9 - - + -
86A ILE* 4.4 15.0 - - - -
97A CYS 2.9 23.3 + - - +
98A LEU* 3.5 18.8 - - - +
101A TYR* 1.3 94.4 - - - +
103A PRO* 1.4 69.4 - - + +
105A ILE* 3.2 25.1 + - - +
106A LEU* 3.3 13.7 + - - +
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Residues in contact with PRO 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 5.3 0.2 - - - -
60A LEU* 4.1 22.2 - - + +
98A LEU 3.3 17.3 - - - +
99A GLY 3.6 18.2 - - - +
100A ALA* 3.5 17.5 - - - +
102A CYS* 1.4 86.4 - - + +
104A ASN* 1.4 52.2 + - - +
106A LEU* 3.1 9.2 + - + +
107A PHE* 2.8 37.5 + - - +
133A PHE* 4.5 15.9 - - + -
11E LEU* 4.7 3.6 - - + -
15E PHE* 3.7 21.1 - - + -
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ALA 3.1 15.0 + - - -
101A TYR* 3.2 14.8 + - + +
103A PRO* 1.4 77.5 - - - +
105A ILE* 1.3 59.4 + - + +
107A PHE* 4.3 7.4 - - - +
108A PRO* 3.2 23.8 - - - +
131A VAL 3.5 10.2 - - - +
132A ASN* 4.7 4.1 + - - +
133A PHE* 3.2 26.3 - - - -
134A ASP* 2.9 38.4 + - - +
104C ASN* 5.4 1.7 + - - +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.8 28.3 - - + -
13A ILE* 3.3 26.9 - - + -
16A ILE* 3.7 15.7 - - + -
84A PHE* 3.8 8.7 - - + -
101A TYR* 3.1 18.4 + - + +
102A CYS* 3.3 13.5 - - - +
103A PRO 3.1 0.6 - - - -
104A ASN* 1.3 78.9 - - + +
106A LEU* 1.3 59.7 + - - +
108A PRO* 3.3 8.1 - - - +
109A TYR* 3.1 27.6 - - + -
130C PRO* 5.6 1.3 - - + -
132C ASN* 3.8 25.1 - - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.0 11.7 - - + -
58A VAL* 3.3 33.2 - - + +
60A LEU* 4.2 14.8 - - + +
80A GLN* 3.4 33.0 - - + +
81A GLY 3.5 24.7 - - - +
82A GLY* 3.8 1.3 - - - -
84A PHE* 3.7 28.7 - - + -
102A CYS 3.8 5.8 - - - +
103A PRO* 3.1 9.9 + - + +
105A ILE* 1.3 78.4 - - - +
107A PHE* 1.3 59.0 + - - +
108A PRO 3.6 0.2 - - - -
109A TYR* 3.2 9.3 + - - +
110A ALA* 2.9 26.1 + - - +
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Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 6.5 1.6 - - + -
62A VAL* 5.1 15.0 - - + -
103A PRO 2.8 20.7 + - - +
104A ASN* 4.3 6.5 - - - -
106A LEU* 1.3 76.1 - - - +
108A PRO* 1.4 63.7 - - + +
110A ALA* 4.3 4.9 - - + -
111A ARG* 2.9 67.8 + - + +
128A LEU* 3.8 33.2 - - + -
129A ALA 4.0 1.3 - - - -
130A PRO* 3.9 13.5 - - + -
131A VAL* 4.0 14.1 - - + -
133A PHE* 5.0 9.2 - + + -
8E LEU* 3.6 27.8 - - + -
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Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASN 3.2 21.5 - - - +
105A ILE 3.3 11.0 - - - +
107A PHE* 1.4 91.3 - - + +
109A TYR* 1.3 59.3 + - + +
111A ARG* 3.4 24.8 - - - +
112A GLU* 3.1 29.1 + - - +
104C ASN* 3.8 38.4 - - - +
105C ILE* 4.5 7.9 - - + +
108C PRO* 3.4 12.1 - - + +
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Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.9 30.5 - - + -
80A GLN* 3.3 24.9 + - - +
105A ILE* 3.1 30.3 - - + -
106A LEU* 3.2 6.6 + - - +
108A PRO* 1.3 79.2 - - + +
110A ALA* 1.3 60.8 + - - +
112A GLU* 3.4 4.2 + - - +
113A CYS* 3.0 26.9 + - - +
104C ASN* 5.8 3.1 - - - -
107C PHE* 3.2 34.0 - + - -
108C PRO* 3.9 20.9 - - + -
111C ARG* 3.4 34.6 - - - -
130C PRO* 3.5 21.3 - - + +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 5.0 0.4 - - + +
62A VAL* 4.1 26.2 - - + -
78A VAL* 4.2 9.3 - - + +
80A GLN* 3.5 24.8 - - + +
106A LEU 2.9 16.6 + - - +
107A PHE* 3.9 8.7 - - + +
109A TYR* 1.3 72.1 - - - +
111A ARG* 1.4 65.2 + - - +
113A CYS* 3.7 1.4 + - - +
114A ILE* 3.2 31.9 + - - +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PHE* 2.9 52.9 + - + +
108A PRO* 3.4 24.7 - - - +
110A ALA* 1.4 76.7 - - - +
112A GLU* 1.3 52.5 + - - +
114A ILE* 3.2 9.6 + - - +
115A THR* 2.8 37.6 + - - +
127A ASN* 4.4 5.2 - - - +
128A LEU* 2.9 41.5 + - + +
130A PRO* 3.3 19.8 - - - +
13C ILE* 3.8 12.8 - - - +
105C ILE* 3.1 39.6 - - - +
109C TYR* 3.3 24.5 - - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PRO 3.1 14.4 + - - +
109A TYR* 3.8 4.4 - - - +
111A ARG* 1.3 80.6 - - - +
113A CYS* 1.3 53.5 + - - +
115A THR* 3.3 1.4 + - - -
116A SER* 2.8 34.3 + - - -
120B ARG* 2.9 40.9 + - - -
108C PRO* 3.4 32.5 - - + +
109C TYR* 3.6 52.8 - - + +
112C GLU* 4.2 7.0 - - - +
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 3.8 9.0 - - + -
21A ILE* 3.7 29.8 - - - -
78A VAL* 3.5 34.5 - - + -
80A GLN* 4.5 0.2 - - - +
109A TYR 3.0 17.5 + - - +
110A ALA 4.2 0.2 - - - +
111A ARG 3.4 0.2 - - - -
112A GLU* 1.3 76.4 - - - +
114A ILE* 1.3 60.1 + - - +
116A SER* 3.9 2.1 - - - -
117A MET* 3.3 27.7 + - - +
117B MET* 5.0 1.1 - - - +
120B ARG* 3.4 29.1 - - - +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 3.9 32.1 - - + +
64A VAL* 3.7 36.1 - - + -
76A CYS* 3.6 28.1 - - + +
78A VAL* 3.8 16.8 - - + -
110A ALA 3.2 16.1 + - - +
111A ARG* 3.2 11.2 + - - +
112A GLU 3.2 0.4 - - - -
113A CYS* 1.3 75.2 - - - +
115A THR* 1.4 65.9 + - - +
117A MET* 3.1 12.6 + - - +
118A VAL* 3.1 29.5 + - + +
126A LEU* 4.8 5.2 - - + +
128A LEU* 6.0 0.7 - - + -
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ARG* 2.8 24.7 + - - +
112A GLU 3.6 4.5 - - - -
114A ILE* 1.4 77.3 - - - +
116A SER* 1.3 56.5 - - - +
118A VAL* 3.5 8.7 + - + +
119A SER* 3.0 30.1 + - - -
125A GLN* 3.1 33.7 - - - +
126A LEU 3.0 20.4 + - - +
127A ASN* 3.7 2.6 + - - +
109C TYR* 3.6 31.7 + - + -
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 2.8 18.9 + - - -
113A CYS 3.9 6.3 - - - -
114A ILE 3.2 0.2 - - - -
115A THR* 1.3 76.1 - - - +
117A MET* 1.4 57.9 + - - +
119A SER* 3.3 6.6 + - - -
120A ARG* 2.9 55.1 + - - +
117B MET* 5.2 0.4 - - - +
120B ARG* 2.9 32.6 + - - -
109C TYR* 5.8 0.2 - - - -
112C GLU* 3.5 4.5 + - - -
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.1 27.8 - - + -
22A SER 3.5 19.7 - - - +
23A PHE* 3.3 41.7 - - + -
76A CYS* 3.7 22.9 - - + -
77A GLU 4.0 3.8 - - - +
78A VAL* 4.1 10.3 - - + -
113A CYS 3.3 16.6 - - - +
114A ILE* 3.1 5.0 + - - +
116A SER* 1.4 72.7 - - - +
118A VAL* 1.3 56.2 + - - +
120A ARG* 3.7 9.0 - - - +
121A GLY* 2.8 30.0 + - - -
18B THR* 5.0 0.6 - - - -
21B ILE* 4.0 8.5 - - + -
117B MET* 4.1 18.8 - - + -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.1 7.4 - - - -
74A PHE* 3.6 20.9 - - + -
76A CYS* 3.4 22.0 - - - -
114A ILE* 3.1 18.2 + - + +
115A THR* 3.6 10.3 - - - +
117A MET* 1.3 75.7 - - - +
119A SER* 1.3 56.7 + - - +
121A GLY 3.2 3.6 + - - -
122A THR 3.1 7.6 + - - -
123A PHE* 3.0 42.0 + - + +
124A PRO 3.5 25.1 - - - +
125A GLN* 5.5 0.4 - - - -
126A LEU* 3.9 20.2 - - + +
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 3.0 20.7 + - - -
116A SER* 3.3 7.4 + - - -
118A VAL* 1.3 76.5 - - - +
120A ARG* 1.3 58.9 + - - +
122A THR* 3.1 18.2 + - - -
123A PHE 4.3 9.0 - - - -
125A GLN* 5.9 3.4 - - - -
119D SER* 2.9 47.2 + - - -
120D ARG* 4.1 3.5 + - - +
122D THR* 6.3 0.9 - - - -
125D GLN* 5.8 0.7 + - - -
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A SER* 2.9 40.0 + - - +
117A MET* 3.8 6.5 - - - +
119A SER* 1.3 72.5 - - - +
121A GLY* 1.4 56.4 + - - +
122A THR* 3.1 8.6 + - - -
16B ILE 5.0 0.3 - - - +
17B TYR* 3.7 5.2 - - - -
18B THR* 3.0 36.1 + - + +
80B GLN* 4.8 1.2 - - - +
109B TYR 5.1 1.4 + - - -
112B GLU* 3.0 40.9 + - - +
113B CYS* 3.5 35.6 - - - +
116B SER* 3.0 16.5 + - - -
117B MET* 4.4 7.9 - - - +
112C GLU* 3.0 25.9 + - - -
116D SER* 5.2 1.0 + - - -
119D SER* 5.4 3.1 - - - +
120D ARG* 3.1 9.6 - - - +
125D GLN* 5.5 1.7 + - - -
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.0 7.2 - - - -
32A PHE* 3.8 4.0 - - - -
117A MET 2.8 15.7 + - - -
118A VAL 3.2 4.6 + - - -
120A ARG* 1.4 74.5 - - - +
122A THR* 1.4 69.0 + - - +
123A PHE* 3.1 26.7 + - - -
17B TYR* 4.0 2.6 - - - +
18B THR* 3.3 23.8 - - - +
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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
------------------------------------------------------------
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