Contacts of the helix formed by residues 92 - 119 (chain J) in PDB entry 1MFR
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 THR 92 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J PHE* 3.6 19.6 - - - -
44J LEU* 3.8 8.0 - - - +
47J VAL* 4.1 17.5 - - + +
91J ASN* 1.3 73.8 - - - +
93J LEU* 1.3 57.8 + - - +
95J ALA* 3.9 1.0 - - - +
96J MET* 3.0 39.1 + - + +
151J LEU* 4.1 7.6 - - + -
156J LEU* 4.0 7.2 - - - -
163J GLU* 2.8 30.5 + - - +
166J PHE* 3.8 34.1 - - + -
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Residues in contact with LEU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ASN* 2.9 10.7 + - - +
92J THR* 1.3 75.4 - - - +
94J GLU* 1.3 61.4 + - - +
96J MET* 3.3 1.6 + - - +
97J GLN* 2.9 52.1 + - + +
148J ILE* 3.9 29.6 - - + +
151J LEU* 3.9 23.6 - - + -
152J LYS* 4.3 16.4 - - + -
156J LEU* 3.4 17.6 - - + +
157J PRO* 3.7 35.0 - - + -
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Residues in contact with GLU 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ARG* 3.0 40.0 + - - +
89J TRP 3.4 11.9 - - - +
90J GLY* 3.7 8.8 - - - -
91J ASN* 3.1 28.1 + - - +
92J THR 3.4 0.2 - - - -
93J LEU* 1.3 78.7 - - - +
95J ALA* 1.3 58.2 + - - +
97J GLN* 3.5 14.5 + - - +
98J ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J MET* 3.8 9.8 - - - +
37J PHE* 3.7 27.1 - - + -
51J PHE* 4.1 10.5 - - + -
89J TRP* 3.7 17.0 + - + -
91J ASN 3.0 18.4 + - - +
92J THR 3.9 2.2 - - - +
94J GLU* 1.3 76.0 - - - +
96J MET* 1.3 60.5 + - - +
98J ALA* 3.4 7.7 + - - +
99J ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J VAL* 4.6 4.0 - - + -
50J PHE* 4.0 16.2 - - + -
51J PHE* 3.7 31.0 - - + -
92J THR* 3.0 27.6 + - + +
93J LEU 3.3 3.8 + - - +
95J ALA* 1.3 74.2 - - - +
97J GLN* 1.3 61.9 + - - +
99J ALA* 3.5 1.7 - - - +
100J LEU* 2.8 23.4 + - - +
144J ILE* 3.4 20.8 - - + +
147J PHE* 3.9 32.5 - - + -
148J ILE* 3.7 17.9 - - + +
151J LEU* 3.8 16.8 - - + -
166J PHE* 4.3 16.8 - - + -
171J VAL* 5.3 1.6 - - + -
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Residues in contact with GLN 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J LEU* 2.9 41.8 + - + +
94J GLU* 3.8 14.7 - - + +
96J MET* 1.3 73.8 - - - +
98J ALA* 1.3 65.4 + - - +
100J LEU* 3.3 3.3 + - - +
101J GLN* 3.1 25.8 + - - +
148J ILE* 4.0 21.7 - - + +
152J LYS* 4.1 21.7 + - - -
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Residues in contact with ALA 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J MET* 4.0 4.0 - - + -
85J GLU* 5.4 4.0 - - - +
86J ARG* 5.6 2.2 - - - +
89J TRP* 3.8 33.0 - - + -
94J GLU 3.0 14.7 + - - +
95J ALA 3.5 8.1 - - - +
97J GLN* 1.3 76.9 - - - +
99J ALA* 1.3 57.4 + - - +
101J GLN* 3.4 7.2 + - - +
102J LEU* 3.0 27.7 + - - +
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Residues in contact with ALA 99 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 3.9 27.6 - - + +
33J MET* 4.5 5.6 - - + -
51J PHE* 4.2 8.3 - - + -
95J ALA 2.9 17.7 + - - +
96J MET* 3.5 9.9 - - - +
97J GLN 3.2 0.2 - - - -
98J ALA* 1.3 75.5 - - - +
100J LEU* 1.3 59.3 + - - +
102J LEU* 3.2 6.2 + - - +
103J GLU* 2.9 35.0 + - - +
144J ILE* 4.1 12.8 - - + -
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Residues in contact with LEU 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J MET 2.8 20.6 + - - +
97J GLN* 3.3 6.0 + - - +
99J ALA* 1.3 72.8 - - - +
101J GLN* 1.3 59.0 + - + +
103J GLU* 3.4 3.5 + - - +
104J LYS* 3.0 42.8 + - + +
141J ILE* 3.9 41.3 - - + +
144J ILE* 3.9 12.3 - - + +
145J GLY* 4.5 3.1 - - - +
148J ILE* 3.7 22.4 - - + -
3N GLN* 3.8 37.7 - - + +
4N VAL* 5.0 0.4 - - + -
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Residues in contact with GLN 101 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J GLN 3.1 12.2 + - - +
98J ALA* 3.7 9.4 - - - +
100J LEU* 1.3 76.1 - - + +
102J LEU* 1.3 61.9 + - - +
104J LYS* 3.2 10.1 + - - +
105J THR* 2.9 34.1 + - - +
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Residues in contact with LEU 102 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LEU* 5.4 1.6 - - + -
25J TYR* 4.1 27.6 - - + -
26J ALA* 3.9 26.0 - - + +
29J THR* 3.7 28.5 - - + -
30J TYR* 3.9 32.1 - - + +
33J MET* 5.2 0.4 - - + -
98J ALA 3.0 18.7 + - - +
99J ALA* 3.2 5.4 + - - +
101J GLN* 1.3 76.9 - - - +
103J GLU* 1.3 59.2 + - + +
105J THR* 3.4 10.8 + - + -
106J VAL* 3.1 35.7 + - + +
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Residues in contact with GLU 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J ALA* 6.5 0.7 - - - -
30J TYR* 2.8 28.3 + - - +
54J HIS* 3.6 14.6 + - - -
58J GLU* 3.4 12.6 - - - +
99J ALA 2.9 14.5 + - - +
100J LEU* 3.8 5.2 - - - +
102J LEU* 1.3 77.4 - - - +
104J LYS* 1.3 59.3 + - - +
106J VAL* 3.3 5.9 + - - +
107J ASN* 2.8 25.6 + - - +
137J GLN* 3.0 28.9 + - - +
140J ASP* 4.4 7.0 - - + -
141J ILE* 3.9 14.8 - - + -
144J ILE* 3.9 14.1 - - + -
177J MG 2.9 27.9 - - - -
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Residues in contact with LYS 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J LEU* 3.0 29.1 + - + +
101J GLN* 3.7 9.2 - - - +
103J GLU* 1.3 75.3 - - - +
105J THR* 1.3 56.6 + - - +
107J ASN* 4.1 0.4 - - - -
108J GLN* 2.9 25.1 + - - +
141J ILE* 4.2 11.2 - - + -
2N SER 5.0 0.4 + - - -
3N GLN* 3.0 29.5 + - - +
4N VAL 4.5 5.4 - - - +
5N ARG 3.5 16.8 + - - -
6N GLN* 3.1 44.7 + - + +
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Residues in contact with THR 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LEU* 4.6 19.5 - - + -
25J TYR* 6.5 0.4 - - + -
101J GLN* 2.9 21.7 + - - +
102J LEU* 3.5 13.0 - - + +
104J LYS* 1.3 76.6 - - - +
106J VAL* 1.3 63.0 + - - +
108J GLN* 3.4 6.1 + - - +
109J ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J MET* 4.6 2.0 - - - +
22J LEU* 3.9 28.9 - - + +
23J GLU* 4.0 10.3 - - - +
26J ALA* 4.2 24.7 - - + -
58J GLU* 4.9 0.4 - - - +
102J LEU* 3.1 19.9 + - + +
103J GLU* 3.7 10.1 - - - +
105J THR* 1.3 71.9 - - - +
107J ASN* 1.3 65.5 + - - +
109J ALA* 3.2 3.1 + - - +
110J LEU* 3.0 31.9 + - + +
137J GLN* 3.9 11.4 - - - +
176J MG 3.8 22.2 - - - -
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Residues in contact with ASN 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J GLU 2.8 21.4 + - - +
104J LYS 3.6 0.7 - - - +
106J VAL* 1.3 73.8 - - - +
108J GLN* 1.3 58.6 + - - +
110J LEU* 3.1 9.9 + - - +
111J LEU* 2.9 42.4 + - - +
134J LEU* 4.8 8.5 - - - +
137J GLN* 3.6 22.5 - - - +
138J VAL* 5.0 9.8 - - - +
141J ILE* 3.9 17.0 - - + +
6N GLN* 3.1 40.5 + - - +
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Residues in contact with GLN 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J LYS 2.9 18.4 + - - +
105J THR* 3.6 6.7 - - - +
107J ASN* 1.3 78.7 - - - +
109J ALA* 1.3 57.5 + - - +
111J LEU* 3.4 15.9 + - - +
112J ASP* 2.9 64.5 + - - +
6N GLN* 3.6 20.2 + - - +
7N ASN* 5.8 2.6 - - - +
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Residues in contact with ALA 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J MET* 3.1 20.5 - - + +
22J LEU* 3.7 22.7 - - + -
105J THR 3.1 14.3 + - - +
106J VAL 3.4 8.7 - - - +
108J GLN* 1.3 77.1 - - - +
110J LEU* 1.3 57.4 + - - +
112J ASP* 3.4 9.7 + - - +
113J LEU* 2.9 21.7 + - - +
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Residues in contact with LEU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J MET* 3.7 24.7 - - + -
23J GLU* 4.9 1.6 - - - +
65J PHE* 4.0 21.3 - - + -
106J VAL* 3.0 24.0 + - + +
107J ASN* 3.4 6.7 - - - +
109J ALA* 1.3 75.4 - - - +
111J LEU* 1.3 60.9 + - - +
113J LEU* 3.4 3.0 + - - +
114J HIS* 2.9 26.3 + - - +
129J LEU* 4.2 13.9 - - + +
133J TYR* 3.9 32.1 - - + -
134J LEU* 3.9 15.0 - - + +
137J GLN* 3.7 31.0 - - + +
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Residues in contact with LEU 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J ASN* 2.9 44.1 + - - +
108J GLN* 3.7 20.6 - - - +
110J LEU* 1.3 74.8 - - - +
112J ASP* 1.3 60.7 + - - +
114J HIS* 3.2 7.3 + - - +
115J LYS* 3.0 27.0 + - - +
134J LEU* 4.6 15.7 - - + -
6N GLN* 4.5 4.0 - - + -
7N ASN* 3.8 32.1 - - + +
123N PRO* 3.7 34.5 - - + +
124N HIS* 5.3 4.5 - - + +
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Residues in contact with ASP 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J GLN* 2.9 49.1 + - - +
109J ALA* 3.4 10.2 - - - +
111J LEU* 1.3 75.6 - - - +
113J LEU* 1.3 60.4 + - - +
115J LYS* 3.3 8.2 + - - +
116J LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J CYS* 4.3 8.3 - - - +
15J ALA* 3.5 31.0 - - + +
16J VAL* 4.3 17.3 - - + -
19J MET* 3.7 34.5 - - + -
65J PHE* 4.5 2.2 - - + -
109J ALA 2.9 17.0 + - - +
110J LEU* 3.7 5.4 - - + +
112J ASP* 1.3 75.6 - - - +
114J HIS* 1.3 58.9 + - - +
116J LEU* 3.4 10.2 + - + +
117J ALA* 3.0 26.2 + - - +
125J LEU* 4.4 10.5 - - + -
129J LEU* 3.9 26.0 - - + -
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Residues in contact with HIS 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J LEU 2.9 15.1 + - - +
111J LEU* 3.3 13.0 - - - +
113J LEU* 1.3 75.0 - - - +
115J LYS* 1.3 60.9 + - - +
117J ALA* 3.3 3.9 + - - +
118J THR* 2.9 42.3 + - - -
126J CYS* 3.6 32.2 + - - +
129J LEU* 3.8 17.4 - - + +
130J GLU* 2.9 25.4 + - - -
134J LEU* 4.2 7.4 - - + -
121N VAL* 6.1 1.2 - - - +
123N PRO* 3.5 37.1 - - + +
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Residues in contact with LYS 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J LEU 3.0 13.0 + - - +
112J ASP* 3.5 11.2 - - - +
114J HIS* 1.3 74.4 + - - +
116J LEU* 1.3 59.9 + - - +
118J THR* 3.2 9.6 + - + +
119J ASP* 2.9 30.0 + - - +
121N VAL* 4.3 24.5 - - + -
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Residues in contact with LEU 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ASP* 3.6 39.5 - - + +
12J CYS* 4.0 11.4 - - - -
15J ALA* 3.7 20.0 - - + -
18J ARG* 5.4 2.2 - - - +
112J ASP 3.0 14.0 + - - +
113J LEU* 3.6 11.0 - - + +
114J HIS 3.3 0.2 - - - -
115J LYS* 1.3 76.9 - - - +
117J ALA* 1.3 57.5 + - - +
119J ASP* 3.3 5.4 + - + +
120J LYS* 2.9 49.8 + - + +
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Residues in contact with ALA 117 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J CYS* 4.3 10.9 - - - -
113J LEU 3.0 14.9 + - - +
114J HIS* 3.5 10.3 - - - +
116J LEU* 1.3 73.6 - - - +
118J THR* 1.3 64.9 + - - +
120J LYS 3.5 0.9 + - - -
121J VAL 3.1 3.6 + - - -
122J ASP* 2.9 34.3 + - + +
125J LEU* 3.9 28.3 - - + -
126J CYS* 3.6 17.9 - - - +
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Residues in contact with THR 118 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J HIS* 2.9 31.5 + - - -
115J LYS* 3.5 9.6 - - + +
117J ALA* 1.3 75.7 - - - +
119J ASP* 1.3 63.9 + - - +
121J VAL* 3.1 18.3 + - - +
122J ASP 5.1 0.2 - - - +
126J CYS* 3.5 15.3 - - - -
121N VAL* 6.4 1.6 - - + -
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Residues in contact with ASP 119 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J LYS 2.9 17.4 + - - +
116J LEU* 3.6 8.7 - - + +
118J THR* 1.3 78.8 - - - +
120J LYS* 1.3 72.4 + - + +
121J VAL* 3.4 8.8 + - - +
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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
------------------------------------------------------------
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