Contacts of the helix formed by residues 114 - 144 (chain W) in PDB entry 1BFR
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 TYR 114 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 3.8 8.5 - - - +
105A ILE* 3.6 39.9 - - + -
106A GLY* 3.7 13.2 - - - -
109A ASP* 5.9 1.9 - - + +
117A ARG* 5.3 2.7 - - - -
121A ILE* 3.8 26.7 - - + -
124A LEU* 4.0 12.1 - - + -
109W ASP* 4.0 30.7 + - - -
112W HIS* 2.9 58.6 + + + -
113W ASP* 1.3 71.0 - - - +
115W VAL* 1.3 57.3 + - - +
117W ARG* 3.4 21.4 + - - +
118W ASP* 2.9 33.4 + - - +
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Residues in contact with VAL 115 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 5.2 0.4 - - - +
121A ILE* 4.6 4.5 - - + +
124A LEU* 4.1 11.8 - - + +
125A ARG* 3.6 51.8 + - + +
128A GLU* 3.5 34.1 - - + +
61W ARG* 3.7 16.2 - - - +
113W ASP* 3.4 1.2 + - - -
114W TYR* 1.3 76.4 - - - +
116W SER* 1.3 61.8 + - - +
118W ASP* 3.4 5.6 + - - +
119W MET* 3.1 23.2 + - + +
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Residues in contact with SER 116 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W VAL* 4.0 11.8 - - - +
11W LEU* 4.3 6.7 - - - +
61W ARG* 3.0 26.3 + - - +
65W LEU* 3.8 7.4 - - - +
108W ALA* 4.6 0.4 - - - -
113W ASP* 2.8 38.6 + - - -
115W VAL* 1.3 72.3 - - - +
117W ARG* 1.3 63.8 + - - +
119W MET* 3.4 8.5 - - - +
120W MET* 3.1 36.6 + - - +
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Residues in contact with ARG 117 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 3.2 23.8 - - - +
118A ASP* 5.0 0.4 + - - -
121A ILE* 3.2 16.1 - - - +
109H ASP* 4.9 2.0 + - - -
114H TYR* 5.3 3.0 - - - -
117H ARG* 3.0 37.0 - - - +
105W ILE* 3.6 27.3 - - + +
108W ALA* 4.0 7.9 - - + +
109W ASP* 3.2 40.1 + - - +
113W ASP 3.0 14.3 + - - +
114W TYR* 3.4 16.3 + - - +
115W VAL 3.3 0.2 - - - -
116W SER* 1.3 75.4 - - - +
118W ASP* 1.3 85.8 + - - +
120W MET* 3.1 15.1 + - - +
121W ILE* 3.0 24.3 + - + +
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Residues in contact with ASP 118 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASP* 5.6 3.8 - - - +
121A ILE* 3.3 22.7 - - + +
125A ARG* 3.4 24.7 + - - +
117H ARG* 5.1 0.3 + - - -
118H ASP* 5.5 3.5 - - - +
114W TYR 2.9 19.3 + - - +
115W VAL 3.4 3.3 + - - +
117W ARG* 1.3 101.5 + - - +
119W MET* 1.3 63.6 + - - +
121W ILE* 3.1 11.1 + - - +
122W GLU* 3.1 29.8 + - + +
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Residues in contact with MET 119 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W LEU* 4.3 9.9 - - + -
57W ARG* 3.7 47.5 + - - +
58W TYR* 3.5 38.8 - - + -
61W ARG* 4.0 33.0 - - + -
115W VAL* 3.1 14.7 + - + +
116W SER* 3.4 8.3 - - - +
118W ASP* 1.3 75.1 - - - +
120W MET* 1.3 72.6 + - + +
122W GLU* 3.4 4.1 + - - +
123W ILE* 3.1 26.3 + - + +
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Residues in contact with MET 120 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W VAL* 5.3 2.0 - - + -
10W TYR* 5.7 1.3 - - + -
11W LEU* 3.9 15.0 - - + -
14W LEU* 3.6 26.9 - - - -
58W TYR* 4.4 6.7 - - + -
101W LEU* 3.9 11.2 - - + +
104W ALA* 3.7 24.2 - - + +
105W ILE* 3.6 14.8 - - + +
108W ALA* 3.6 30.1 - - + -
116W SER* 3.1 21.5 + - - +
117W ARG* 3.1 8.5 + - - +
119W MET* 1.3 89.1 - - + +
121W ILE* 1.3 55.6 + - - +
123W ILE* 3.2 6.9 + - - +
124W LEU* 2.8 29.6 + - - +
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Residues in contact with ILE 121 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 3.9 27.1 - - + +
115H VAL* 4.7 5.1 - - + +
117H ARG* 3.3 29.8 - - - +
118H ASP* 3.3 27.4 - - + +
105W ILE* 3.7 31.2 - - + -
117W ARG* 3.0 27.1 + - - +
118W ASP* 3.1 10.7 + - - +
120W MET* 1.3 69.6 - - - +
122W GLU* 1.3 57.7 + - + +
124W LEU* 3.2 2.5 + - - +
125W ARG* 2.9 36.1 + - - +
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Residues in contact with GLU 122 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 4.8 12.0 + - - -
57W ARG* 3.0 36.3 + - - +
118W ASP* 3.1 17.3 + - + +
119W MET 3.4 7.0 - - - +
121W ILE* 1.3 73.0 - - - +
123W ILE* 1.3 64.6 + - - +
125W ARG* 3.3 27.2 + - - +
126W ASP* 3.2 26.1 + - - +
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Residues in contact with ILE 123 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W GLU* 4.0 7.2 - - - +
54W HIS* 3.6 47.3 - - + +
57W ARG* 4.1 18.2 - - + +
58W TYR* 3.6 46.0 - - + +
101W LEU* 4.7 4.5 - - + -
119W MET* 3.1 28.3 + - + +
120W MET* 3.2 6.0 + - - +
122W GLU* 1.3 74.6 - - - +
124W LEU* 1.3 62.3 + - - +
126W ASP* 3.1 4.9 + - - +
127W GLU* 3.0 24.2 + - + +
202W MN 4.1 1.8 - - - +
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Residues in contact with LEU 124 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 4.1 20.2 - - + -
115H VAL* 4.0 13.0 - - + -
98W ALA* 4.1 24.5 - - + +
101W LEU* 3.9 26.4 - - + +
102W ARG* 3.8 32.1 - - + +
105W ILE* 3.8 23.3 - - + -
120W MET 2.8 20.4 + - - +
121W ILE* 3.2 5.1 + - - +
123W ILE* 1.3 70.5 - - - +
125W ARG* 1.3 59.1 + - - +
127W GLU* 3.2 3.2 + - + +
128W GLU* 2.9 32.7 + - + +
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Residues in contact with ARG 125 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H VAL* 3.9 29.2 + - + +
118H ASP* 3.6 35.8 + - - +
122H GLU* 4.7 10.8 + - - -
121W ILE* 2.9 21.6 + - - +
122W GLU* 3.5 32.7 - - - +
123W ILE 3.3 0.2 - - - -
124W LEU* 1.3 76.3 - - - +
126W ASP* 1.3 64.3 - - - +
128W GLU* 3.4 3.5 + - - +
129W GLY* 3.2 17.3 + - - -
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Residues in contact with ASP 126 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W ASP* 5.1 7.0 - - - +
54W HIS* 2.8 33.5 + - + -
57W ARG* 5.8 1.4 + - - -
122W GLU 3.2 14.0 + - - +
123W ILE* 3.1 7.7 + - - +
125W ARG* 1.3 78.3 - - - +
127W GLU* 1.3 63.8 + - - +
129W GLY* 3.2 4.4 + - - +
130W HIS* 3.1 31.8 + - - +
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Residues in contact with GLU 127 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W GLU* 4.7 0.7 - - - +
51W GLU* 2.9 7.6 - - - +
54W HIS* 3.1 13.7 - - - -
94W GLU* 2.8 22.4 - - - +
97W GLY* 5.8 2.4 - - - -
98W ALA* 5.2 6.1 - - + +
101W LEU* 4.1 20.0 - - + -
123W ILE 3.0 14.2 + - - +
124W LEU* 3.6 9.6 - - + +
126W ASP* 1.3 71.2 - - - +
128W GLU* 1.3 66.1 + - - +
130W HIS* 3.0 3.5 + - - -
131W ILE* 2.9 32.4 + - + +
201W MN 2.2 29.4 + - - -
202W MN 2.5 30.4 + - - +
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Residues in contact with GLU 128 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 3.7 19.3 - - + +
61H ARG* 2.9 39.3 + - - +
64H PHE* 3.8 11.3 - - + -
115H VAL* 3.5 17.9 - - + +
102W ARG* 2.7 35.0 + - - +
124W LEU* 2.9 26.8 + - + +
125W ARG* 3.4 5.4 + - - +
127W GLU* 1.3 70.7 - - - +
129W GLY* 1.3 57.5 + - - +
131W ILE* 3.3 15.8 + - + +
132W ASP* 2.9 28.8 + - - +
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Residues in contact with GLY 129 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125W ARG 3.2 12.3 + - - -
126W ASP* 3.2 5.1 + - - -
127W GLU 3.2 1.0 - - - -
128W GLU* 1.3 72.6 - - - +
130W HIS* 1.3 67.0 + - - +
132W ASP* 3.3 8.4 + - - +
133W TRP* 3.2 20.3 + - - +
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Residues in contact with HIS 130 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W TYR* 3.5 14.6 + - - +
47W GLU* 3.5 35.1 - - + +
50W ASP* 2.8 34.3 + - + -
51W GLU* 3.4 13.6 + - - -
54W HIS* 4.9 1.1 - + - -
94W GLU* 3.2 13.0 - - - +
126W ASP* 3.1 18.0 + - - +
127W GLU* 3.0 6.4 + - - +
129W GLY* 1.3 75.3 - - - +
131W ILE* 1.3 64.2 + - - +
133W TRP* 3.2 3.7 + - - +
134W LEU* 3.0 28.1 + - - +
201W MN 2.1 32.7 + - - -
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Residues in contact with ILE 131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 4.2 22.0 - - + -
64H PHE* 4.6 1.1 - - + -
91W LEU* 3.8 21.1 - - + -
94W GLU* 3.6 24.0 + - + +
95W LEU* 3.7 25.4 - - + -
98W ALA* 4.3 18.4 - - + -
127W GLU* 2.9 21.2 + - + +
128W GLU* 3.5 17.5 - - + +
130W HIS* 1.3 75.6 - - - +
132W ASP* 1.3 63.3 + - - +
134W LEU* 3.3 2.8 + - - +
135W GLU* 3.0 44.0 + - - +
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Residues in contact with ASP 132 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ASN* 4.2 12.4 - - - +
64H PHE* 3.7 29.9 - - + +
128W GLU 2.9 14.3 + - - +
129W GLY* 3.6 10.8 - - - +
130W HIS 3.3 0.2 - - - -
131W ILE* 1.3 75.6 - - - +
133W TRP* 1.3 62.9 + - - +
135W GLU* 3.5 5.8 + - - +
136W THR* 3.1 37.7 + - - -
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Residues in contact with TRP 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39W ARG* 4.0 10.1 - - - +
40W LEU* 4.1 21.1 - - + -
43W VAL* 3.5 43.7 - - + +
44W GLU* 3.6 28.7 - - + -
47W GLU* 3.8 17.9 - - - +
87W LEU* 4.8 5.4 - - + -
129W GLY 3.2 10.4 + - - +
130W HIS 3.2 5.8 + - - +
132W ASP* 1.3 78.0 - - - +
134W LEU* 1.3 92.7 + - + +
136W THR* 3.2 5.3 + - - -
137W GLU* 3.0 62.3 + - + +
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Residues in contact with LEU 134 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W TYR* 3.8 21.5 - - - +
44W GLU* 4.1 6.1 - - - +
47W GLU* 4.6 1.3 - - - +
87W LEU* 3.8 30.3 - - + +
90W ASP* 3.9 13.7 - - + -
91W LEU* 3.8 34.3 - - + +
94W GLU* 4.1 6.5 - - + -
130W HIS 3.0 21.8 + - - +
131W ILE* 3.9 3.8 - - - +
133W TRP* 1.3 101.7 - - + +
135W GLU* 1.3 62.4 + - - +
137W GLU* 3.3 3.5 + - - +
138W LEU* 3.0 29.5 + - + +
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Residues in contact with GLU 135 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 3.0 41.2 + - - +
64H PHE* 4.0 12.5 - - - -
66H GLU* 4.3 4.1 - - - +
91W LEU* 4.1 24.2 - - + +
95W LEU* 5.5 2.1 - - - +
131W ILE* 3.0 30.6 + - - +
132W ASP* 3.8 5.6 - - - +
134W LEU* 1.3 77.2 - - - +
136W THR* 1.3 63.3 + - - +
138W LEU* 3.3 4.0 + - - +
139W ASP* 3.0 29.9 + - - +
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Residues in contact with THR 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LYS 5.5 0.2 - - - +
34G ASN 3.5 13.6 + - - +
35G TRP* 3.6 8.3 - - - +
36G GLY* 3.5 37.0 - - - +
132W ASP* 3.1 24.9 + - - -
133W TRP* 3.7 4.9 - - - -
135W GLU* 1.3 75.1 - - - +
137W GLU* 1.3 65.6 + - - +
139W ASP* 3.2 7.9 + - + +
140W LEU* 2.9 28.4 + - + +
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Residues in contact with GLU 137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39W ARG* 3.1 38.7 + - - -
87W LEU* 4.2 10.8 - - + -
133W TRP* 3.0 46.6 + - + +
134W LEU* 3.7 6.3 - - - +
136W THR* 1.3 75.2 - - - +
138W LEU* 1.3 64.7 + - - +
140W LEU* 3.1 17.9 + - - +
141W ILE* 2.9 29.1 + - - +
149W TYR* 2.6 37.8 + - - +
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Residues in contact with LEU 138 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84W GLU* 3.9 20.2 - - + +
87W LEU* 3.8 28.0 - - + +
88W ARG* 3.9 49.4 - - + +
91W LEU* 3.7 30.5 - - + -
134W LEU 3.0 18.7 + - - +
135W GLU* 3.8 3.8 - - - +
137W GLU* 1.3 75.5 - - - +
139W ASP* 1.3 63.7 + - - +
141W ILE* 3.6 10.1 + - + +
142W GLN* 2.8 29.7 + - - -
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Residues in contact with ASP 139 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TRP* 5.7 3.3 - - - +
135W GLU* 3.0 21.7 + - - +
136W THR* 3.6 10.1 - - + +
138W LEU* 1.3 76.1 - - - +
140W LEU* 1.3 61.3 + - + +
142W GLN* 3.1 11.5 + - - +
143W LYS* 2.9 53.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TRP 3.4 21.3 - - - +
36G GLY* 4.3 6.7 - - - +
37G LEU* 4.0 19.1 - - + -
150G LEU* 5.9 0.7 - - + -
154G ILE* 4.3 13.5 - - + -
136W THR* 2.9 39.9 + - + +
137W GLU* 3.5 18.8 - - - +
139W ASP* 1.3 72.0 - - + +
141W ILE* 1.3 63.0 + - - +
143W LYS* 3.2 14.0 + - + +
144W MET* 2.9 55.2 + - + +
149W TYR* 4.5 8.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83W VAL* 4.6 4.3 - - + -
84W GLU* 4.2 29.4 - - + +
87W LEU* 4.1 19.3 - - + -
137W GLU 2.9 19.3 + - - +
138W LEU* 3.6 19.5 - - + +
140W LEU* 1.3 74.4 - - - +
142W GLN* 1.3 65.0 + - - +
145W GLY* 3.0 23.6 + - - -
146W LEU* 3.8 29.7 + - + +
149W TYR* 3.7 40.3 - - + -
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Residues in contact with GLN 142 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G GLN* 4.7 2.9 + - - -
84W GLU* 3.2 29.5 + - - +
88W ARG* 3.4 15.1 + - - +
138W LEU* 2.8 26.0 + - - +
139W ASP* 3.1 12.0 + - - +
141W ILE* 1.3 80.5 - - - +
143W LYS* 1.3 65.2 + - + +
145W GLY* 3.7 5.5 + - - -
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Residues in contact with LYS 143 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TRP* 3.6 48.4 + - - +
37G LEU* 5.6 3.3 - - + +
146G LEU* 6.0 0.9 - - - +
147G GLN* 3.7 16.5 + - - +
150G LEU* 3.7 30.3 - - + +
139W ASP* 2.9 43.8 + - - +
140W LEU* 3.2 13.4 + - + +
142W GLN* 1.3 75.0 - - + +
144W MET* 1.3 59.9 + - - +
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Residues in contact with MET 144 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G GLN* 3.5 40.5 + - - +
150G LEU* 4.1 6.1 - - + -
151G GLN* 3.7 40.2 - - - +
154G ILE* 3.9 20.9 - - + -
140W LEU* 2.9 50.2 + - + +
143W LYS* 1.3 74.3 - - - +
145W GLY* 1.3 68.9 + - - +
148W ASN* 3.3 15.9 + - + +
149W TYR* 3.8 24.9 - - + +
----------------------------------------------------------
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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