Contacts of the helix formed by residues 113 - 145 (chain W) 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 W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 4.3 3.8 + - - +
128A GLU* 4.6 3.5 - - - +
4W ASP* 5.8 1.3 + - + -
7W VAL* 3.5 28.7 - - + +
61W ARG* 3.0 24.4 + - - -
65W LEU* 4.1 8.1 - - - +
108W CYS* 2.9 24.1 + - + +
111W VAL* 3.3 5.0 - - + +
112W HIS* 1.3 71.9 - - - +
114W TYR* 1.3 57.3 + - - +
115W VAL* 3.6 1.6 + - - +
116W SER* 2.7 31.2 + - - -
117W ARG* 3.1 18.7 + - - +
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Residues in contact with TYR 114 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 4.0 14.0 - - + +
105A ILE* 3.5 43.3 - - + +
106A VAL* 3.2 29.5 + - - +
117A ARG* 3.8 18.8 + - - +
121A LYS* 4.5 16.1 - - + +
124A LEU* 4.0 17.0 - - + -
109W GLU* 3.7 32.9 + - - -
112W HIS* 3.2 39.3 + - + -
113W ASP* 1.3 71.8 + - - +
115W VAL* 1.3 61.0 + - - +
117W ARG* 3.3 9.0 + - + +
118W ASP* 2.9 28.9 + - - +
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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
----------------------------------------------------------
121A LYS* 4.8 5.2 - - + +
124A LEU* 3.9 13.9 - - + -
125A GLU* 3.8 43.1 - - + +
128A GLU* 3.4 32.5 + - + +
61W ARG* 3.6 25.1 - - - +
113W ASP* 3.4 0.8 + - - -
114W TYR* 1.3 72.7 - - - +
116W SER* 1.3 66.0 + - - +
118W ASP* 3.1 8.5 + - + +
119W LEU* 3.0 22.4 + - + +
----------------------------------------------------------
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Residues in contact with SER 116 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W VAL* 4.0 9.6 - - - +
11W LEU* 4.3 7.5 - - - +
61W ARG* 2.9 29.1 + - - +
65W LEU* 4.0 1.2 - - - +
108W CYS* 3.8 15.3 - - - -
113W ASP* 2.7 36.5 + - - -
115W VAL* 1.3 78.4 - - - +
117W ARG* 1.3 61.4 + - - +
119W LEU* 3.2 7.3 + - - +
120W LEU* 3.0 26.2 + - - +
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Residues in contact with ARG 117 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 4.3 14.2 - - - +
109H GLU* 2.5 42.6 + - - -
114H TYR* 3.9 18.4 + - - +
117H ARG* 4.1 18.3 - - - +
105W ILE* 3.6 25.3 - - + +
108W CYS* 3.9 17.9 - - + +
109W GLU* 2.8 41.3 + - - +
113W ASP 3.1 14.7 + - - +
114W TYR* 3.6 11.9 - - + +
115W VAL 3.3 0.4 - - - -
116W SER* 1.3 75.5 - - - +
118W ASP* 1.3 59.6 + - - +
120W LEU* 3.2 7.3 + - - +
121W LYS* 2.8 33.1 + - + +
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Residues in contact with ASP 118 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASP* 5.6 1.0 - - - +
121A LYS* 3.9 26.8 - - + +
122A ASP* 5.4 1.6 - - - +
125A GLU* 4.1 13.4 - - - +
114W TYR 2.9 14.0 + - - +
115W VAL* 3.1 11.6 + - + +
117W ARG* 1.3 76.4 - - - +
119W LEU* 1.3 64.3 + - - +
121W LYS* 3.4 22.6 + - - +
122W ASP* 3.1 36.2 + - - +
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Residues in contact with LEU 119 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W LEU* 5.6 1.3 - - + -
57W LYS* 3.8 36.1 - - + +
58W LEU* 3.7 17.3 - - + -
61W ARG* 4.0 25.4 - - + -
115W VAL* 3.0 12.2 + - + +
116W SER* 3.5 9.4 - - - +
118W ASP* 1.3 77.0 - - - +
120W LEU* 1.3 67.1 + - + +
122W ASP* 3.3 9.6 + - - +
123W ILE* 3.1 44.9 + - + +
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Residues in contact with LEU 120 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W LEU* 3.9 27.1 - - + -
14W ILE* 4.1 9.2 - - + -
58W LEU* 4.1 16.8 - - + -
101W LEU* 3.9 24.1 - - + +
104W ALA* 3.8 29.4 - - + -
105W ILE* 3.7 15.7 - - + +
108W CYS* 3.9 20.2 - - - -
116W SER 3.0 20.1 + - - +
117W ARG* 3.7 4.0 - - - +
119W LEU* 1.3 80.0 - - + +
121W LYS* 1.3 57.1 + - - +
123W ILE* 3.2 6.3 + - + +
124W LEU* 2.8 29.1 + - - +
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Residues in contact with LYS 121 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 4.5 22.9 - - + +
115H VAL* 5.0 3.2 - - + +
118H ASP* 2.6 48.3 + - + +
105W ILE* 4.1 10.2 - - + +
117W ARG* 2.8 23.3 + - + +
118W ASP* 3.7 19.9 + - - +
120W LEU* 1.3 75.5 - - - +
122W ASP* 1.3 86.9 + - - +
124W LEU* 3.1 8.0 + - + +
125W GLU* 2.8 37.1 + - - +
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Residues in contact with ASP 122 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54W HIS* 4.9 1.3 + - - -
118W ASP* 3.1 22.2 + - - +
119W LEU* 3.5 10.7 - - - +
121W LYS* 1.3 100.4 + - - +
123W ILE* 1.3 66.6 + - + +
125W GLU* 3.3 11.4 + - - +
126W SER* 3.2 21.3 + - - -
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Residues in contact with ILE 123 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14W ILE* 4.9 0.7 - - + -
18W GLU* 3.4 24.2 - - - +
54W HIS* 3.8 36.1 - - + +
57W LYS* 5.6 2.2 - - + -
58W LEU* 3.8 28.0 - - + -
101W LEU* 4.3 13.0 - - + -
119W LEU* 3.1 36.8 + - + +
120W LEU* 3.6 11.0 - - + +
122W ASP* 1.3 76.4 - - + +
124W LEU* 1.3 63.8 + - - +
126W SER* 3.2 3.8 + - - -
127W GLU* 2.9 35.8 + - + +
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Residues in contact with LEU 124 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 4.1 13.7 - - + -
115H VAL* 4.0 17.3 - - + -
98W THR* 3.2 28.5 - - - +
101W LEU* 4.1 26.7 - - + +
102W ARG* 3.7 27.8 - - + +
105W ILE* 4.0 21.1 - - + -
120W LEU 2.8 17.4 + - - +
121W LYS* 3.4 6.5 - - + +
123W ILE* 1.3 78.3 - - - +
125W GLU* 1.3 57.2 + - - +
127W GLU* 3.2 1.5 + - - -
128W GLU* 2.8 42.8 + - - +
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Residues in contact with GLU 125 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H VAL* 3.9 31.9 - - + +
118H ASP* 4.5 16.5 - - - +
121W LYS* 2.8 18.3 + - - +
122W ASP* 3.6 17.1 - - - +
124W LEU* 1.3 75.8 - - - +
126W SER* 1.3 64.3 + - - +
128W GLU* 3.2 4.2 + - - +
129W GLU* 3.0 39.8 + - + +
----------------------------------------------------------
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Residues in contact with SER 126 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W ASP* 5.1 7.6 + - - +
54W HIS* 3.1 30.6 + - - -
122W ASP 3.2 10.3 + - - -
123W ILE 3.2 8.6 + - - -
125W GLU* 1.3 82.0 - - - +
127W GLU* 1.3 61.4 + - - +
129W GLU* 3.3 19.0 + - - +
130W HIS* 3.1 19.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 127 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W GLU* 2.8 18.2 - - - +
51W GLU* 2.7 29.3 - - - +
54W HIS* 3.6 4.3 + - - -
94W GLU* 2.6 41.3 - - - +
97W ALA* 5.1 5.8 - - + -
98W THR* 4.3 14.1 - - - +
101W LEU* 3.9 20.2 - - + -
123W ILE* 2.9 26.2 + - - +
124W LEU* 3.8 4.5 - - - +
126W SER* 1.3 78.0 + - - +
128W GLU* 1.3 64.1 + - - +
130W HIS* 3.1 6.4 + - - +
131W ILE* 3.0 25.9 + - + +
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Residues in contact with GLU 128 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H ARG* 2.7 43.1 + - - +
64H PHE* 3.7 22.1 - - + -
113H ASP* 4.7 0.2 - - - +
115H VAL* 3.5 18.9 - - + +
98W THR* 4.4 5.4 - - - +
102W ARG* 2.9 33.8 + - - +
124W LEU* 2.8 26.9 + - + +
125W GLU* 3.2 6.3 + - - +
127W GLU* 1.3 79.0 - - - +
129W GLU* 1.3 62.1 + - - +
131W ILE* 3.2 14.0 + - + +
132W ASP* 3.0 18.7 + - - +
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Residues in contact with GLU 129 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125W GLU* 3.0 32.0 + - + +
126W SER* 3.6 20.8 + - - +
127W GLU 3.3 0.2 - - - -
128W GLU* 1.3 76.0 - - - +
130W HIS* 1.3 62.3 + - - +
132W ASP* 3.3 10.1 + - - +
133W TYR* 3.0 21.8 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W TYR* 3.7 27.2 - + - -
44W GLU* 4.6 2.8 + - - -
47W GLU* 3.3 48.1 + - + +
51W GLU* 5.1 0.2 + - - -
90W ASP* 4.5 4.3 - - - -
94W GLU* 2.7 28.2 + - - +
126W SER 3.1 12.1 + - - +
127W GLU* 3.1 11.5 + - - +
129W GLU* 1.3 74.6 - - - +
131W ILE* 1.3 64.5 + - - +
133W TYR* 3.2 14.7 + + - -
134W LEU* 3.0 48.2 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H PHE* 4.2 11.2 - - + -
91W LEU* 4.0 14.6 - - + -
94W GLU* 3.6 35.9 - - + +
95W LEU* 4.3 15.3 - - + -
98W THR* 4.0 23.1 - - + +
127W GLU 3.0 17.2 + - - +
128W GLU* 3.2 14.3 + - + +
130W HIS* 1.3 74.9 - - - +
132W ASP* 1.3 57.4 + - - +
134W LEU* 3.2 7.1 + - - +
135W GLU* 2.8 55.9 + - - +
----------------------------------------------------------
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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 ASP* 4.2 13.5 - - - +
64H PHE* 3.7 32.4 - - + +
128W GLU 3.0 11.5 + - - +
129W GLU* 3.3 15.0 - - - +
131W ILE* 1.3 76.8 - - - +
133W TYR* 1.3 58.3 + - - +
135W GLU* 4.0 3.3 - - - +
136W THR* 2.7 42.7 + - - -
----------------------------------------------------------
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Residues in contact with TYR 133 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40W LEU* 3.6 26.5 - - - +
43W HIS* 3.4 56.1 - + + +
44W GLU* 5.4 3.8 - - - -
47W GLU* 5.0 1.1 - - - +
87W LEU* 4.6 3.6 - - + -
129W GLU 3.0 10.1 + - - +
130W HIS* 3.6 23.3 - + + +
132W ASP* 1.3 80.1 - - - +
134W LEU* 1.3 72.9 + - + +
136W THR* 3.2 5.5 + - - -
137W GLN* 2.9 70.4 + - + +
153W HIS* 5.2 2.1 + - - -
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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
----------------------------------------------------------
44W GLU* 5.5 0.4 - - - +
87W LEU* 3.7 39.8 - - + +
90W ASP* 3.9 27.1 - - + +
91W LEU* 4.0 19.7 - - + +
94W GLU* 4.3 4.3 - - + -
130W HIS* 3.0 56.5 + - + +
131W ILE* 3.5 6.7 - - - +
133W TYR* 1.3 83.0 - - + +
135W GLU* 1.3 67.2 + - - +
137W GLN* 3.1 5.0 + - - +
138W LEU* 3.0 31.0 + - + +
----------------------------------------------------------
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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
----------------------------------------------------------
2H LYS 5.6 3.6 + - - -
64H PHE* 4.2 16.3 - - - +
66H GLU* 3.8 21.8 - - - +
91W LEU* 4.2 20.2 - - + +
95W LEU* 5.7 2.9 - - - +
131W ILE* 2.8 38.9 + - + +
132W ASP* 4.1 2.8 - - - +
134W LEU* 1.3 78.2 - - - +
136W THR* 1.3 62.4 + - - +
138W LEU* 3.5 7.9 + - - +
139W GLY* 3.1 19.6 + - - -
----------------------------------------------------------
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Residues in contact with THR 136 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ASN 5.0 1.1 - - - +
34G ASP* 3.4 14.6 + - - +
35G TRP* 3.8 5.3 - - - +
36G GLY* 3.6 35.4 - - - +
132W ASP* 2.7 31.6 + - - -
133W TYR* 3.4 6.5 - - - -
135W GLU* 1.3 78.6 - - - +
137W GLN* 1.3 72.1 + - - +
139W GLY* 3.3 3.0 + - - -
140W LEU* 3.0 24.7 + - + +
----------------------------------------------------------
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Residues in contact with GLN 137 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87W LEU* 4.1 14.6 - - + -
133W TYR* 2.9 67.6 + - + +
134W LEU* 3.1 5.6 + - - +
136W THR* 1.3 89.1 - - - +
138W LEU* 1.3 63.4 + - - +
140W LEU* 3.1 14.1 + - - +
141W ILE* 3.0 27.1 + - - +
149W TYR* 2.8 44.4 + - + +
153W HIS* 3.9 10.1 + - - -
----------------------------------------------------------
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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 GLN* 4.0 27.2 + - + +
87W LEU* 3.8 32.8 - - + +
88W GLN* 4.0 28.9 - - + +
91W LEU* 4.1 19.1 - - + -
134W LEU 3.0 21.8 + - - +
135W GLU* 3.9 5.6 - - - +
137W GLN* 1.3 81.4 - - - +
139W GLY* 1.3 60.0 + - - +
140W LEU 3.4 0.2 + - - -
141W ILE* 3.4 21.4 + - + +
142W GLN* 3.5 18.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TRP 5.5 0.9 - - - -
135W GLU 3.1 15.5 + - - -
136W THR* 3.6 4.7 - - - -
137W GLN 3.2 0.2 - - - -
138W LEU* 1.3 75.8 - - - +
140W LEU* 1.3 60.6 + - - +
142W GLN* 3.3 9.0 + - - +
143W LYS* 3.0 41.7 + - - +
----------------------------------------------------------
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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 3.3 21.8 - - - +
36G GLY* 4.1 12.3 - - - +
37G LEU* 4.0 14.6 - - + -
154G MET* 3.9 33.0 - - + -
136W THR* 3.0 20.4 + - + +
137W GLN* 3.1 33.8 + - - +
139W GLY* 1.3 73.9 - - - +
141W ILE* 1.3 62.5 + - - +
143W LYS* 2.9 7.1 + - + +
144W VAL* 2.8 43.7 + - + +
149W TYR* 3.9 13.9 - - + -
----------------------------------------------------------
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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 THR* 5.0 1.6 - - + -
84W GLN* 3.8 35.0 - - - +
87W LEU* 4.0 23.6 - - + -
137W GLN 3.0 18.3 + - - +
138W LEU* 3.5 19.7 - - + +
139W GLY 3.3 0.2 - - - -
140W LEU* 1.3 77.7 - - - +
142W GLN* 1.3 61.9 + - - +
145W GLY* 3.0 28.1 + - - -
146W LEU* 4.2 25.6 - - + -
149W TYR* 3.6 34.3 - - + -
----------------------------------------------------------
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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 GLU* 4.6 4.9 - - - +
84W GLN* 3.5 26.5 + - - +
138W LEU 3.5 13.6 + - - +
139W GLY* 3.3 10.0 + - - +
140W LEU 3.1 0.6 - - - -
141W ILE* 1.3 80.8 - - - +
143W LYS* 1.3 64.6 + - + +
145W GLY* 4.1 3.1 + - - -
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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 59.8 + - + +
37G LEU* 4.5 14.1 - - + -
146G LEU* 5.5 1.4 - - - +
147G GLU* 3.7 15.1 - - - +
150G LEU* 3.8 27.0 - - + +
139W GLY* 3.0 29.5 + - - +
140W LEU* 2.9 8.7 + - + +
142W GLN* 1.3 79.6 - - + +
144W VAL* 1.3 64.3 + - + +
145W GLY 3.5 0.2 - - - -
----------------------------------------------------------
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Residues in contact with VAL 144 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 5.1 0.2 - - + -
147G GLU* 3.4 26.1 - - - +
150G LEU* 3.8 12.8 - - + -
151G GLN* 3.7 26.0 - - + +
154G MET* 4.3 16.6 - - - -
140W LEU* 2.8 30.4 + - + +
143W LYS* 1.3 80.0 - - + +
145W GLY* 1.3 71.1 + - - +
148W ASN* 3.3 26.9 + - + +
149W TYR* 3.6 23.8 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G GLU* 3.6 15.0 + - - -
141W ILE 3.0 17.1 + - - -
142W GLN 4.1 1.7 + - - -
143W LYS 3.5 1.8 - - - -
144W VAL* 1.3 82.4 - - - +
146W LEU* 1.3 65.9 + - - -
147W GLU 3.3 2.5 - - - -
148W ASN 3.3 1.9 + - - -
149W TYR* 3.0 19.6 + - - +
----------------------------------------------------------
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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