Contacts of the helix formed by residues 113 - 139 (chain A) in PDB entry 2QE9
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 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU 5.2 0.7 - - - -
101A LEU* 3.9 22.0 - - + +
102A VAL* 4.6 0.9 - - - -
112A TYR* 1.3 76.2 - - - +
114A ARG* 1.3 65.0 + - - +
115A ASP* 3.7 10.7 + - - +
116A GLU* 3.0 33.2 + - - +
117A ILE* 3.2 13.5 + - - +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3A TYR* 6.4 1.1 - - - -
56A ILE* 3.4 47.8 + - + +
89A VAL* 3.7 25.5 + - - +
90A LEU* 5.0 7.5 - - - +
92A THR* 4.2 14.7 + - - -
93A HIS* 4.3 28.2 + - - -
100A GLU 4.5 14.6 + - - +
102A VAL* 4.3 16.4 - - + +
112A TYR 3.9 0.6 + - - -
113A THR* 1.3 72.0 - - - +
115A ASP* 1.3 57.8 + - - +
117A ILE* 3.1 6.6 + - - +
118A LEU* 2.9 44.0 + - + +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3A TYR* 2.5 41.3 + - + +
113A THR* 3.1 10.1 + - - +
114A ARG* 1.3 78.2 - - - +
116A GLU* 1.3 63.0 + - - +
118A LEU* 3.3 3.3 + - - +
119A HIS* 2.9 54.4 + - - -
0B GLY* 4.6 1.8 - - - -
3B LYS* 3.5 27.5 - - - +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 4.3 14.3 - - + -
113A THR* 3.0 29.5 + - - +
115A ASP* 1.3 78.2 + - - +
117A ILE* 1.3 62.4 + - - +
119A HIS* 3.4 6.0 + - - +
120A HIS* 3.1 21.7 + - - +
3B LYS* 4.4 14.6 - - - +
148B PHE* 3.5 32.3 - - - +
149B ILE* 4.0 27.7 - - + +
150B GLY 4.8 2.3 + - - -
151B ARG 5.8 0.2 + - - -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 3.7 53.4 - - + +
56A ILE* 3.6 24.9 - - + -
102A VAL* 3.6 44.4 - - + -
112A TYR* 3.9 15.9 - - + -
113A THR 3.2 8.3 + - - +
114A ARG 3.1 7.9 + - - +
116A GLU* 1.3 73.4 - - - +
118A LEU* 1.3 58.2 + - - +
120A HIS* 3.1 7.8 + - - +
121A ILE* 2.9 30.7 + - + +
149B ILE* 4.9 1.8 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3A TYR* 4.0 20.2 - - + +
-2A PHE* 6.2 1.6 - - + -
1A MSE 3.6 30.5 - - + -
2A MSE 4.4 12.1 - - + -
5A PHE* 4.0 22.9 - - + -
53A ILE* 4.4 3.6 - - + -
56A ILE* 4.0 22.0 - - + -
90A LEU* 4.3 13.7 - - + -
93A HIS* 6.4 0.4 - - - +
114A ARG* 2.9 34.7 + - + +
115A ASP 3.7 3.6 - - - +
117A ILE* 1.3 74.2 - - - +
119A HIS* 1.3 63.6 + - - +
121A ILE* 3.5 5.0 + - + +
122A ILE* 3.1 28.8 + - - +
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.4 12.7 - - + +
115A ASP* 2.9 52.0 + - - +
116A GLU* 3.5 9.6 - - - +
118A LEU* 1.3 76.8 - - - +
120A HIS* 1.3 56.6 + - - +
122A ILE 3.5 0.2 + - - -
123A ALA* 3.0 31.4 + - - +
0B GLY* 2.6 35.7 + - - -
3B LYS* 3.5 10.7 - - + +
4B PHE* 3.3 42.8 - + - -
148B PHE* 3.5 34.5 - + + -
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 5.1 4.9 - - + +
52A TRP* 3.7 41.9 + + - -
116A GLU 3.1 13.7 + - - +
117A ILE* 3.1 8.3 + - - +
119A HIS* 1.3 73.3 - - - +
121A ILE* 1.3 60.5 + - - +
123A ALA* 3.6 1.2 + - - +
124A HIS* 3.0 41.5 + + + +
147B SER* 3.4 25.6 - - - -
148B PHE* 3.6 16.8 + - + +
149B ILE* 3.3 39.6 + - + +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.6 27.6 - - + -
8A ASN* 4.8 0.8 + - - +
48A VAL* 5.9 1.3 - - - -
49A GLU* 3.8 27.6 - - + +
52A TRP* 3.8 33.2 - - + -
53A ILE* 3.7 35.9 - - + -
117A ILE* 2.9 24.8 + - + +
118A LEU* 3.7 6.7 - - + +
120A HIS* 1.3 74.0 - - - +
122A ILE* 1.3 67.8 + - - +
124A HIS* 3.3 6.4 + - - +
125A GLU* 3.2 24.4 + - + +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.8 28.3 - - + +
4A PHE* 3.6 46.9 - - + -
5A PHE* 3.8 26.7 - - + -
8A ASN* 3.5 13.9 + - - +
118A LEU 3.1 19.6 + - - +
119A HIS 3.7 3.8 - - - +
120A HIS 3.4 0.2 - - - -
121A ILE* 1.3 83.4 - - - +
123A ALA* 1.3 62.1 + - - +
126A ILE* 3.3 32.5 + - + +
4B PHE* 3.8 18.2 - - + -
126B ILE* 5.7 0.4 - - + -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS 3.0 17.2 + - - +
120A HIS 4.1 2.2 - - - +
122A ILE* 1.3 76.4 - - - +
124A HIS* 1.3 57.1 + - - +
126A ILE 3.4 0.3 + - - -
127A HIS* 2.9 34.0 + - - +
4B PHE* 4.7 2.7 - - + -
7B TYR* 4.0 34.1 - - + +
126B ILE* 3.7 20.9 - - + +
146B ALA 4.9 2.5 - - - +
148B PHE* 4.6 10.8 - - + +
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Residues in contact with HIS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS* 3.1 14.8 + + - -
45A ILE* 4.5 8.8 + - - +
48A VAL* 3.5 35.5 - - + +
49A GLU 5.4 0.2 + - - -
120A HIS* 3.0 31.6 + + + +
121A ILE* 3.5 8.7 + - - +
123A ALA* 1.3 77.1 - - - +
125A GLU* 1.3 63.7 + - - +
127A HIS* 3.6 5.8 - + - +
128A HIS* 3.3 33.2 + + - -
200A NI 2.2 43.2 - - + +
201A CIT 3.1 11.4 + - - -
146B ALA 5.7 1.8 + - - -
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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
----------------------------------------------------------
8A ASN* 3.6 38.4 + - - +
12A ARG* 2.9 58.2 + - - +
45A ILE* 3.3 30.0 - - + +
49A GLU* 4.3 6.3 - - + +
121A ILE* 3.2 10.5 + - + +
122A ILE 3.5 0.2 + - - -
123A ALA 3.3 0.2 - - - -
124A HIS* 1.3 77.7 + - - +
126A ILE* 1.3 66.1 + - - +
128A HIS* 3.2 3.3 + - - +
129A ILE* 2.9 40.1 + - + +
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.6 5.8 - - + -
7A TYR* 4.0 14.4 - - + +
8A ASN* 3.2 24.0 - - - +
122A ILE* 3.3 30.0 + - + +
125A GLU* 1.3 75.3 - - - +
127A HIS* 1.3 62.7 + - - +
129A ILE* 3.8 7.6 - - + +
130A GLY* 3.0 20.8 + - - -
123B ALA* 3.7 37.2 - - + +
126B ILE* 3.7 19.5 - - + -
127B HIS* 3.7 30.6 + - + +
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA 2.9 19.3 + - - +
124A HIS* 3.6 5.8 - + - +
126A ILE* 1.3 76.2 - - - +
128A HIS* 1.3 83.3 + + - +
130A GLY 3.2 9.0 + - - -
131A GLN* 3.3 24.1 + - - +
201A CIT 3.8 19.9 + - - -
7B TYR* 5.5 0.2 - - - +
126B ILE* 3.6 17.9 + - + +
129B ILE* 5.1 3.8 - - + +
130B GLY* 3.6 20.6 + - - -
133B SER* 3.8 28.5 - - - -
144B VAL 5.5 2.5 - - - -
146B ALA* 3.2 33.8 - - + +
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY* 4.7 3.6 - - - -
35A VAL* 4.4 9.1 + - + -
41A THR* 3.8 14.4 - - + +
44A HIS* 3.2 12.5 + + - -
45A ILE* 3.8 22.0 - - + -
124A HIS* 3.3 28.8 + + - +
125A GLU 3.2 1.8 + - - +
127A HIS* 1.3 86.6 - + - +
129A ILE* 1.3 66.1 + - - +
131A GLN* 2.7 42.8 + - - +
132A LEU* 3.2 14.6 + - - +
200A NI 2.2 43.5 - - + +
201A CIT 3.0 12.6 + - - -
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 6.0 0.2 - - - +
11A VAL* 3.9 17.7 - - + -
12A ARG* 4.8 4.3 - - - -
15A TRP* 3.4 33.8 - - + +
42A LEU* 4.5 7.0 - - + -
45A ILE* 3.6 19.1 - - + -
125A GLU* 2.9 40.2 + - + +
126A ILE* 3.8 8.3 - - + +
128A HIS* 1.3 75.8 - - - +
130A GLY* 1.3 61.9 + - - +
132A LEU* 3.1 32.8 + - + +
133A SER* 3.3 11.4 + - - -
146A ALA* 5.7 4.7 - - + -
127B HIS* 5.0 6.4 + - + +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ILE 3.0 13.8 + - - -
127A HIS 3.2 5.6 + - - -
128A HIS 3.2 0.4 - - - -
129A ILE* 1.3 77.4 - - - +
131A GLN* 1.3 59.0 + - - +
133A SER* 2.6 21.8 + - - -
134A VAL 3.7 1.2 + - - -
127B HIS* 3.5 33.0 + - - -
130B GLY* 4.0 7.4 - - - -
131B GLN* 3.3 10.3 - - - +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY* 3.3 34.5 - - - +
35A VAL 4.5 0.9 + - - -
41A THR* 4.7 3.1 - - - +
127A HIS* 3.3 23.9 + - - +
128A HIS* 2.7 37.1 + - - +
130A GLY* 1.3 75.5 - - - +
132A LEU* 1.3 61.9 + - - +
134A VAL* 3.1 15.1 + - - +
135A TRP* 3.4 25.0 + - + -
130B GLY 3.4 16.6 + - - +
133B SER* 2.9 19.0 + - - +
134B VAL* 3.6 21.8 - - + +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 3.8 34.8 - - + -
18A TRP* 5.2 1.5 - - + -
38A ILE* 4.2 20.4 - - + +
41A THR* 3.9 19.1 - - + -
42A LEU* 4.2 18.4 - - + -
128A HIS 3.2 10.8 + - - +
129A ILE* 3.1 33.4 + - + +
131A GLN* 1.3 75.6 - - - +
133A SER* 1.3 57.1 + - - +
135A TRP* 3.2 33.5 + - + +
136A ALA* 2.9 28.8 + - - +
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 3.9 13.0 - - - -
129A ILE 3.3 6.3 + - - -
130A GLY 2.6 21.1 + - - -
132A LEU* 1.3 79.8 - - - +
134A VAL* 1.3 58.5 + - - +
136A ALA* 3.6 2.5 - - - +
137A ARG* 3.4 25.8 + - - +
143A PRO* 3.9 20.3 - - - +
144A VAL 5.6 0.7 - - - -
33B GLY* 4.4 2.4 - - - -
34B GLY 5.0 0.8 + - - -
127B HIS* 3.7 13.7 - - - -
131B GLN* 2.9 26.9 + - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY 4.1 1.6 - - - +
131A GLN 3.1 9.2 + - - +
133A SER* 1.3 73.8 + - - +
135A TRP* 1.3 67.1 + - - +
137A ARG* 3.1 5.9 + - - +
138A GLU* 3.0 34.3 + - - +
32B LEU 3.5 16.3 - - - +
33B GLY* 4.1 11.2 - - - -
131B GLN* 3.5 47.6 - - + +
134B VAL* 3.6 26.7 - - + -
135B TRP* 3.7 13.5 - - + +
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Residues in contact with TRP 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.6 34.1 + - + +
32A LEU 3.1 21.0 + - - +
33A GLY* 3.2 30.5 - - - -
35A VAL 4.9 1.1 - - - -
36A GLU* 3.8 19.1 - - - -
37A ASN* 3.9 9.4 - - - -
38A ILE* 3.9 17.7 - - + -
41A THR* 3.4 27.1 - - + -
131A GLN* 3.4 15.2 + - + -
132A LEU* 3.2 33.5 + - + +
134A VAL* 1.3 76.7 - - - +
136A ALA* 1.3 56.1 + - - +
138A GLU* 3.1 25.1 + - - +
139A LEU* 2.9 35.3 + - - +
134B VAL* 3.7 16.3 - - + +
138B GLU* 5.0 0.2 + - - -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TRP* 4.0 2.0 - - + -
18A TRP* 3.5 32.8 - - + -
132A LEU 2.9 15.7 + - - +
133A SER 3.6 7.2 - - - +
135A TRP* 1.3 75.4 - - - +
137A ARG* 1.3 59.7 + - - +
139A LEU* 3.1 10.6 + - - +
140A LYS 3.3 0.2 + - - -
141A LEU* 3.0 25.6 + - - +
143A PRO* 3.9 28.0 - - + -
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER 3.4 12.3 + - - +
134A VAL 3.1 6.0 + - - +
136A ALA* 1.3 78.6 - - - +
138A GLU* 1.3 57.7 + - - +
140A LYS* 3.0 20.3 + - - +
141A LEU 3.6 11.0 + - - +
142A SER* 3.7 26.1 + - - +
143A PRO* 3.5 21.7 - - + +
32B LEU* 4.0 18.1 - - + +
33B GLY* 3.5 32.8 - - - +
34B GLY 4.6 6.8 + - - +
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 5.4 10.8 + - - +
134A VAL* 3.0 27.9 + - + +
135A TRP* 3.1 26.2 + - - +
137A ARG* 1.3 75.0 - - - +
139A LEU* 1.3 61.0 + - - +
140A LYS* 3.2 6.4 + - - +
32B LEU* 3.9 31.5 + - + +
138B GLU* 2.6 37.5 - - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 4.0 8.7 - - + -
22A LEU* 3.9 23.3 - - + -
26A GLU* 3.9 25.6 - - + +
31A ARG* 3.6 38.1 - - - +
38A ILE* 4.0 17.7 - - + -
135A TRP 2.9 15.5 + - - +
136A ALA 3.1 8.5 + - - +
138A GLU* 1.3 75.7 - - - +
140A LYS* 1.3 69.2 + - - +
141A LEU* 3.5 16.3 + - + +
----------------------------------------------------------
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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