Contacts of the helix formed by residues 113 - 145 (chain A) in PDB entry 3IS7
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 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.5 20.9 - - + +
61A ARG* 3.0 14.2 + - - -
65A LEU* 4.0 9.0 - - - +
108A CYS* 2.9 24.9 + - + +
111A VAL* 3.3 14.9 - - + +
112A HIS* 1.3 70.4 - - - +
114A TYR* 1.3 59.7 + - - +
115A VAL* 3.6 1.6 + - - +
116A SER* 2.4 42.0 + - - -
117A ARG 3.2 13.5 + - - -
102H ARG* 4.0 6.8 + - - +
128H GLU* 4.9 0.2 - - - +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 3.7 35.5 + - - -
112A HIS* 3.2 45.6 + - + -
113A ASP* 1.3 74.7 + - - +
115A VAL* 1.3 60.7 + - - +
117A ARG* 3.4 9.6 - - - +
118A ASP* 3.0 27.9 + - - +
102H ARG* 3.9 13.9 - - + +
105H ILE* 3.4 44.9 - - + +
106H VAL* 3.0 30.8 + - - +
117H ARG* 3.8 17.3 + - - +
121H LYS* 4.4 16.9 - - + +
124H LEU* 4.0 17.3 - - + -
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 3.5 32.1 - - - +
113A ASP* 3.3 1.0 + - - -
114A TYR* 1.3 75.4 - - - +
116A SER* 1.3 63.6 + - - +
118A ASP* 3.3 7.1 + - + +
119A LEU* 3.2 23.2 + - + +
121H LYS* 5.0 4.5 - - + +
124H LEU* 3.9 13.9 - - + +
125H GLU* 3.8 42.0 - - + +
128H GLU* 3.6 25.8 + - + +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.1 5.5 - - - +
11A LEU* 4.3 9.8 - - - +
61A ARG* 3.0 24.3 + - - +
65A LEU* 4.0 5.7 - - - +
108A CYS* 3.7 13.7 - - - -
113A ASP* 2.4 38.2 + - - -
115A VAL* 1.3 76.8 - - - +
117A ARG* 1.3 63.2 + - - +
119A LEU* 3.4 7.1 - - - +
120A LEU* 2.9 29.0 + - - +
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.7 26.8 - - + +
108A CYS* 3.9 14.3 - - + +
109A GLU* 2.7 42.4 + - - +
113A ASP 3.2 11.3 + - - +
114A TYR* 3.4 14.4 - - + +
116A SER* 1.3 80.2 - - - +
118A ASP* 1.3 59.0 + - - +
120A LEU* 3.2 6.8 + - - +
121A LYS* 2.9 33.8 + - + +
117H ARG* 4.0 14.5 - - - +
109W GLU* 2.6 41.0 + - - -
114W TYR* 3.8 19.2 + - - +
117W ARG* 4.2 13.5 - - - +
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR 3.0 17.9 + - - +
115A VAL* 3.8 7.4 - - + +
116A SER 3.3 0.2 - - - -
117A ARG* 1.3 74.3 - - - +
119A LEU* 1.3 66.3 + - - +
121A LYS* 3.3 17.1 + - - +
122A ASP* 3.0 35.8 + - - +
121H LYS* 3.7 26.9 - - + +
122H ASP* 5.2 1.9 - - - +
125H GLU* 4.4 12.2 - - - +
118W ASP* 5.6 1.2 - - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.4 2.0 - - + -
57A LYS* 4.0 24.5 - - + +
58A LEU* 3.8 33.7 - - + +
61A ARG* 3.9 36.3 - - + -
115A VAL* 3.2 10.8 + - + +
116A SER* 3.4 9.0 - - - +
118A ASP* 1.3 79.7 - - - +
120A LEU* 1.3 66.6 + - + +
122A ASP* 3.2 8.0 + - - +
123A ILE* 3.0 36.3 + - + +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.0 25.4 - - + -
14A ILE* 4.3 6.3 - - + -
58A LEU* 4.2 15.3 - - + -
101A LEU* 4.1 24.9 - - + +
104A ALA* 3.8 28.9 - - + -
105A ILE* 3.7 19.1 - - + -
108A CYS* 3.8 22.0 - - - -
116A SER 2.9 21.2 + - - +
117A ARG 3.2 1.1 + - - +
119A LEU* 1.3 78.7 - - + +
121A LYS* 1.3 56.6 + - - +
123A ILE* 3.2 7.2 + - + +
124A LEU* 2.8 28.1 + - - +
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 4.0 8.5 - - + +
117A ARG* 2.9 24.3 + - + +
118A ASP* 3.6 15.0 - - - +
120A LEU* 1.3 74.5 - - - +
122A ASP* 1.3 71.4 + - - +
124A LEU* 3.3 7.7 + - + +
125A GLU* 2.9 33.5 + - + +
114W TYR* 4.5 25.1 - - + +
115W VAL* 4.8 3.2 - - + +
118W ASP* 3.9 35.2 - - + +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 5.0 1.5 + - - -
118A ASP* 3.0 27.6 + - - +
119A LEU* 3.5 11.2 - - - +
121A LYS* 1.3 81.5 - - - +
123A ILE* 1.3 65.1 + - + +
125A GLU* 3.4 11.6 + - - +
126A SER* 3.4 20.1 + - - -
118W ASP* 5.4 1.4 - - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.8 1.1 - - + -
18A GLU* 3.5 21.5 - - - +
54A HIS* 3.8 34.3 - - + +
57A LYS* 5.7 3.1 - - + -
58A LEU* 3.8 37.5 - - + -
101A LEU* 4.3 11.9 - - + -
119A LEU* 3.0 31.3 + - + +
120A LEU* 3.2 12.3 + - + +
122A ASP* 1.3 76.4 - - + +
124A LEU* 1.3 58.4 + - - +
126A SER* 3.2 4.7 + - - -
127A GLU* 2.9 42.5 + - + +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 3.6 24.2 - - - +
101A LEU* 4.1 24.9 - - + -
102A ARG* 3.9 28.7 - - + +
105A ILE* 3.9 22.7 - - + -
120A LEU 2.8 16.5 + - - +
121A LYS* 3.5 5.6 - - - +
123A ILE* 1.3 74.1 - - - +
125A GLU* 1.3 67.8 + - - +
127A GLU* 3.2 1.6 + - - +
128A GLU* 2.9 34.9 + - + +
114W TYR* 4.0 20.2 - - + -
115W VAL* 3.9 13.2 - - + -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 2.9 19.9 + - + +
122A ASP* 3.8 11.1 - - - +
123A ILE 3.3 0.2 - - - -
124A LEU* 1.3 78.8 - - - +
126A SER* 1.3 58.3 + - - +
128A GLU* 3.4 3.4 + - - +
129A GLU* 3.0 46.7 + - + +
115W VAL* 3.8 29.8 - - + +
118W ASP* 4.1 15.4 - - - +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 5.2 5.0 + - - +
54A HIS* 3.0 31.3 - - - -
122A ASP 3.4 9.9 + - - -
123A ILE 3.2 7.7 + - - -
125A GLU* 1.3 78.8 - - - +
127A GLU* 1.3 58.9 + - - +
129A GLU* 3.4 18.4 + - - +
130A HIS* 3.0 25.5 + - - +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.2 19.0 - - - +
51A GLU* 2.7 31.9 - - - +
54A HIS* 3.6 7.1 + - - -
94A GLU* 2.5 39.1 - - - +
97A ALA* 5.0 7.4 - - + -
98A THR* 4.1 14.8 - - - +
101A LEU* 4.0 18.4 - - + -
123A ILE* 2.9 22.5 + - + +
124A LEU* 3.2 4.7 + - - +
126A SER* 1.3 76.1 + - - +
128A GLU* 1.3 58.6 + - - +
130A HIS* 2.9 7.3 + - - +
131A ILE* 2.8 33.8 + - - +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 4.5 3.8 - - - +
102A ARG* 2.8 38.7 + - - +
124A LEU* 2.9 27.6 + - + +
125A GLU* 3.8 5.2 - - - +
127A GLU* 1.3 68.9 - - - +
129A GLU* 1.3 65.2 + - - +
131A ILE* 3.3 13.7 + - + +
132A ASP* 2.9 22.9 + - - +
61W ARG* 2.8 44.9 + - - +
64W PHE* 3.7 20.7 - - + -
113W ASP* 4.6 0.2 - - - +
115W VAL* 3.4 22.2 - - + +
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.0 36.6 + - + +
126A SER* 3.6 21.4 + - - +
127A GLU 3.2 0.2 - - - -
128A GLU* 1.3 75.9 - - - +
130A HIS* 1.3 64.1 + - - +
132A ASP* 3.2 11.0 + - - +
133A TYR* 3.1 20.3 + - - +
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Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.5 34.8 - + - -
44A GLU* 4.7 2.6 + - - -
47A GLU* 3.2 46.2 + - + +
51A GLU* 5.9 0.4 - - - -
90A ASP* 4.5 5.1 + - - -
94A GLU* 2.8 24.0 + - - +
126A SER 3.0 12.1 + - - +
127A GLU* 2.9 11.3 + - - +
129A GLU* 1.3 79.5 - - - +
131A ILE* 1.3 62.2 + - - +
133A TYR* 3.2 13.6 + + - -
134A LEU* 3.0 47.0 + - + +
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Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.2 12.1 - - + -
94A GLU* 3.5 27.1 - - + +
95A LEU* 4.1 23.3 - - + -
98A THR* 4.0 24.2 - - + +
102A ARG* 6.2 0.2 - - - +
127A GLU 2.8 14.8 + - - +
128A GLU* 3.5 15.7 - - + +
130A HIS* 1.3 76.1 - - - +
132A ASP* 1.3 56.2 + - - +
134A LEU* 3.3 7.4 + - - +
135A GLU* 3.0 52.7 + - - +
2W LYS* 4.2 9.2 - - + +
64W PHE* 4.3 7.4 - - + -
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU 2.9 13.0 + - - +
129A GLU* 3.3 15.6 - - - +
130A HIS 3.2 0.2 - - - -
131A ILE* 1.3 73.5 - - - +
133A TYR* 1.3 65.8 + - - +
135A GLU* 4.0 3.8 - - - +
136A THR* 2.9 35.6 + - - -
64W PHE* 3.8 30.4 - - + +
34X ASP* 4.4 14.0 - - - +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.6 25.8 + - - +
43A HIS* 3.3 56.4 - + + +
44A GLU* 5.4 2.9 - - - -
47A GLU* 4.9 1.1 - - - +
87A LEU* 4.6 4.0 - - + -
129A GLU 3.1 9.3 + - - +
130A HIS* 3.5 17.3 - + + +
132A ASP* 1.3 81.8 - - - +
134A LEU* 1.3 77.8 + - + +
136A THR* 3.3 4.5 + - - -
137A GLN* 2.9 71.8 + - + +
153A HIS* 5.1 3.0 + - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 5.6 0.4 - - - +
87A LEU* 3.8 33.9 - - + +
90A ASP* 4.0 15.3 - - + +
91A LEU* 3.9 31.4 - - + +
94A GLU* 4.1 5.6 - - + -
130A HIS* 3.0 58.2 + - + +
131A ILE* 3.6 6.3 - - - +
132A ASP 3.3 0.2 - - - -
133A TYR* 1.3 88.8 - - + +
135A GLU* 1.3 65.7 + - - +
137A GLN* 3.2 4.4 + - - +
138A LEU* 3.0 32.9 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.1 22.6 - - + +
95A LEU* 5.7 3.5 - - - +
131A ILE* 3.0 25.4 + - + +
132A ASP* 4.0 3.3 - - - +
134A LEU* 1.3 74.3 - - - +
136A THR* 1.3 58.7 + - - +
138A LEU* 3.6 7.5 + - - +
139A GLY* 3.0 25.3 + - - -
2W LYS* 2.0 39.4 + - - +
64W PHE* 4.7 1.6 - - - -
66W GLU* 4.6 4.4 - - - +
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASP* 2.9 26.4 + - - -
133A TYR* 3.4 6.9 - - - -
135A GLU* 1.3 73.1 - - - +
137A GLN* 1.3 71.0 + - - +
139A GLY* 3.2 2.2 + - - -
140A LEU* 2.8 32.9 + - + +
33X ASN 5.2 1.1 + - - +
34X ASP* 3.1 17.6 + - - -
35X TRP* 3.7 4.7 - - - +
36X GLY* 3.4 36.6 - - - +
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.1 15.3 - - + -
133A TYR* 2.9 70.6 + - + +
134A LEU 3.2 5.6 + - - +
136A THR* 1.3 83.5 - - - +
138A LEU* 1.3 59.3 + - - +
140A LEU* 3.2 12.4 + - - +
141A ILE* 3.0 34.5 + - - +
149A TYR* 2.7 45.0 + - + +
153A HIS* 3.9 12.3 + - - -
154X MET* 5.3 0.2 - - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 4.2 30.3 + - + +
87A LEU* 3.9 39.7 - - + +
88A GLN* 4.4 13.0 - - + +
91A LEU* 4.2 20.0 - - + -
134A LEU 3.0 31.8 + - - +
135A GLU* 3.7 6.1 - - - +
137A GLN* 1.3 75.7 - - - +
139A GLY* 1.3 63.1 + - - +
141A ILE* 3.3 16.8 + - + +
142A GLN* 3.4 18.5 + - - +
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU 3.0 15.7 + - - -
136A THR* 3.5 4.5 - - - -
138A LEU* 1.3 76.7 - - - +
140A LEU* 1.3 55.8 + - - +
142A GLN* 3.2 9.1 + - - +
143A LYS* 2.9 45.9 + - - +
35X TRP 5.5 0.7 - - - -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 2.8 35.5 + - + +
137A GLN* 3.2 22.4 + - - +
139A GLY* 1.3 69.9 - - - +
141A ILE* 1.3 61.8 + - - +
143A LYS* 4.1 7.9 - - + +
144A VAL* 2.8 40.9 + - + +
149A TYR* 3.9 9.4 - - + -
35X TRP 3.3 20.0 - - - +
36X GLY* 4.1 10.5 - - - +
37X LEU* 4.1 15.3 - - + -
154X MET* 3.9 42.8 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 4.9 1.6 - - + -
84A GLN* 4.1 21.3 - - + +
87A LEU* 4.0 21.5 - - + -
137A GLN 3.0 17.9 + - - +
138A LEU* 3.4 19.1 - - + +
140A LEU* 1.3 74.7 - - - +
142A GLN* 1.3 71.3 + - - +
145A GLY* 2.9 28.1 + - - -
146A LEU* 3.7 31.4 + - + +
149A TYR* 3.5 37.4 - - + -
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 3.8 23.6 - - - +
138A LEU 3.4 12.7 + - - +
139A GLY* 3.2 9.7 + - - +
140A LEU 3.1 0.4 - - - -
141A ILE* 1.3 84.1 - - - +
143A LYS* 1.3 63.5 + - + +
145A GLY* 4.3 2.3 + - - -
147X GLU* 4.9 3.6 - - - +
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLY* 2.9 32.6 + - - +
140A LEU* 3.0 8.9 + - + +
142A GLN* 1.3 80.9 - - + +
144A VAL* 1.3 65.7 + - + +
145A GLY 3.6 0.2 - - - -
35X TRP* 3.8 50.6 + - + +
37X LEU* 4.4 19.3 - - + -
83X THR* 5.9 0.7 - - - +
146X LEU* 5.7 1.4 - - - +
147X GLU* 3.7 15.2 - - - +
150X LEU* 4.0 26.4 - - + +
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Residues in contact with VAL 144 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 2.8 29.4 + - + +
143A LYS* 1.3 79.4 - - + +
145A GLY* 1.3 70.1 + - - +
148A ASN* 3.4 20.4 + - + +
149A TYR* 3.7 22.2 - - + +
147X GLU* 3.4 32.9 - - - +
150X LEU* 3.8 11.7 - - + -
151X GLN* 3.6 29.8 - - + +
154X MET* 4.3 15.9 - - - -
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Residues in contact with GLY 145 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE 2.9 16.4 + - - -
142A GLN 4.3 1.5 - - - -
143A LYS 3.6 1.6 - - - -
144A VAL* 1.3 82.0 - - - +
146A LEU* 1.3 60.3 + - - -
147A GLU 3.4 2.5 - - - -
148A ASN 3.4 1.2 + - - -
149A TYR* 2.9 26.2 + - - +
147X GLU* 4.0 15.1 + - - -
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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
------------------------------------------------------------
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