Contacts of the helix formed by residues 132 - 157 (chain C) in PDB entry 2RD9
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 VAL 132 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 3.8 31.9 - - + -
64C ILE* 3.9 19.2 - - + +
65C LEU* 4.1 11.9 - - + -
112C VAL* 3.9 9.0 - - + -
117C ASP 3.4 27.4 - - - +
118C LEU* 3.5 8.0 + - + +
120C ARG* 2.9 18.9 + - + +
131C LYS* 1.3 71.3 - - - +
133C ARG* 1.3 63.8 + - - +
135C LEU* 3.1 10.1 + - - +
136C LEU* 3.0 37.8 + - + +
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Residues in contact with ARG 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.1 42.5 - - - +
3C PHE* 4.2 24.6 - - + -
118C LEU* 3.1 32.8 + - + +
119C GLU* 3.2 28.0 + - - -
131C LYS* 3.4 30.6 - - + +
132C VAL* 1.3 78.6 - - - +
134C GLU* 1.3 77.2 + - - +
136C LEU* 3.7 6.2 - - - +
137C SER* 2.7 39.5 + - - +
161D ASP* 4.4 6.9 + - - +
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C VAL 4.4 1.7 - - - +
130C VAL* 3.5 11.4 - - - +
131C LYS* 3.0 35.8 + - + +
133C ARG* 1.3 93.9 + - - +
135C LEU* 1.3 60.2 + - - +
137C SER* 3.8 1.4 - - - -
138C ALA* 2.9 28.4 + - - +
160D THR 4.8 1.6 - - - +
161D ASP 3.2 22.9 - - - +
162D VAL* 4.0 8.7 - - - +
163D GLY* 3.4 22.4 - - - -
164D PRO* 4.1 7.3 - - - +
165D TRP* 3.9 9.7 - - + -
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASN* 4.9 0.2 - - - +
57C TRP* 3.6 39.3 - - + +
60C ARG* 4.2 18.6 - - + -
61C LEU* 3.6 44.4 - - + +
64C ILE* 3.9 15.7 - - + -
73C PHE* 5.5 0.2 - - + -
131C LYS 3.1 9.5 + - - +
132C VAL 3.1 8.6 + - - +
134C GLU* 1.3 75.0 - - - +
136C LEU* 1.3 64.6 + - + +
138C ALA* 3.4 3.8 + - - +
139C TRP* 3.0 25.6 + - - +
165D TRP* 3.8 31.0 - - + -
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.8 12.6 - - + -
5C MSE 3.5 31.6 - - + -
8C ALA* 5.8 0.4 - - + -
12C LEU* 5.1 2.8 - - + +
61C LEU* 4.4 13.0 - - + -
108C LEU* 3.8 25.4 - - + -
112C VAL* 4.7 0.7 - - + -
118C LEU* 3.8 21.1 - - + -
132C VAL* 3.0 27.0 + - + +
133C ARG 3.7 4.3 - - - +
135C LEU* 1.3 81.4 - - + +
137C SER* 1.3 65.4 + - - +
139C TRP* 3.2 28.5 + - + +
140C VAL* 3.2 25.6 + - - +
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Residues in contact with SER 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.2 21.3 - - - +
133C ARG 2.7 23.9 + - - -
134C GLU 3.8 0.9 - - - -
136C LEU* 1.3 77.1 - - - +
138C ALA* 1.3 61.8 + - - +
140C VAL* 3.2 4.5 + - - +
141C VAL* 3.1 25.3 + - - +
158D TYR* 3.9 12.5 - - - -
161D ASP* 3.2 43.2 + - - +
162D VAL* 3.8 5.8 - - - -
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TRP* 3.6 14.4 - - + -
134C GLU 2.9 20.0 + - - +
135C LEU 3.6 5.4 - - - +
137C SER* 1.3 77.9 - - - +
139C TRP* 1.3 52.0 + - - +
141C VAL* 3.7 1.0 - - - +
142C HIS* 2.8 35.3 + - - +
162D VAL* 3.8 11.8 - - + +
165D TRP* 4.0 33.2 - - + -
169D LEU* 4.1 8.0 - - + +
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Residues in contact with TRP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.6 31.1 - - + +
53C GLU* 3.4 16.8 + - - -
57C TRP* 3.4 49.1 - + + -
58C ILE* 3.9 30.5 - - + -
101C ARG* 3.3 39.5 - - - +
104C ASN* 4.0 18.8 - - + -
105C LEU* 4.5 4.5 - - + -
108C LEU* 4.3 13.2 - - + -
135C LEU* 3.0 12.8 + - + +
136C LEU* 3.3 30.1 - - + +
138C ALA* 1.3 72.6 - - - +
140C VAL* 1.3 63.8 + - - +
142C HIS* 3.2 2.5 + - + +
143C ASP* 3.2 21.2 + - - +
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ALA* 3.8 38.6 - - + +
11C LEU* 3.6 33.7 - - + -
12C LEU* 3.9 17.0 - - + -
136C LEU 3.2 13.1 + - - +
137C SER 3.6 6.5 - - - +
139C TRP* 1.3 76.0 - - - +
141C VAL* 1.3 64.6 + - - +
143C ASP* 3.3 7.7 + - - +
144C LEU* 3.2 27.7 + - + +
30D TRP* 4.6 0.9 - - + -
158D TYR* 3.9 20.4 - - + -
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C SER 3.1 15.9 + - - +
138C ALA 4.0 3.4 - - - +
140C VAL* 1.3 74.5 - - + +
142C HIS* 1.3 57.7 + - - +
144C LEU* 3.7 5.9 - - - +
145C THR* 2.7 48.7 + - - +
155D ALA* 3.7 28.0 - - + +
158D TYR* 3.7 29.8 - - + +
162D VAL* 3.7 7.9 - - + -
169D LEU* 4.0 23.3 - - + -
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Residues in contact with HIS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-9B HIS* 3.0 15.5 + + - -
48C HIS* 3.4 10.8 - + - -
49C LEU* 4.0 10.2 - - + +
52C ALA* 4.0 16.7 - - + +
57C TRP* 3.4 22.6 + + + -
138C ALA 2.8 19.0 + - - +
139C TRP 3.4 6.7 - - - +
140C VAL 3.2 0.2 - - - -
141C VAL* 1.3 76.7 - - - +
143C ASP* 1.3 64.4 + - - +
145C THR* 3.3 2.0 + - - -
146C HIS* 3.1 35.2 + + - -
300C NI 2.1 43.8 - - + +
302C IMD 3.1 14.8 - + - -
169D LEU* 4.0 11.6 - - + +
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Residues in contact with ASP 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.6 8.0 - - - +
15C THR* 2.7 36.4 + - + +
49C LEU* 4.1 18.1 - - - +
57C TRP* 5.7 0.2 + - - -
101C ARG* 2.8 40.2 + - - -
139C TRP* 3.2 13.2 + - - +
140C VAL* 3.4 9.6 - - - +
142C HIS* 1.3 77.7 + - - +
144C LEU* 1.3 61.1 + - + +
146C HIS* 3.3 3.5 + - - +
147C ILE* 2.9 35.1 + - + +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.0 16.4 - - + -
15C THR* 5.9 0.9 - - - +
140C VAL* 3.2 32.6 + - + +
141C VAL* 3.7 6.5 - - + +
143C ASP* 1.3 79.7 - - + +
145C THR* 1.3 60.3 + - - +
147C ILE* 3.3 6.8 + - + -
148C ALA* 2.9 25.8 + - - +
22D PHE* 3.8 33.4 - - + -
151D VAL* 3.0 28.2 - - + +
154D MSE 3.9 9.2 - - + +
155D ALA* 3.6 38.1 - - + +
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Residues in contact with THR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 2.7 35.8 + - - +
142C HIS* 3.6 7.6 - - - -
144C LEU* 1.3 78.0 - - - +
146C HIS* 1.3 56.9 + - - +
148C ALA* 3.5 7.3 + - - +
149C GLN* 3.1 23.7 + - - +
152C ARG* 4.9 1.9 + - - -
302C IMD 3.9 8.5 - - + +
155D ALA* 5.1 4.2 - - - +
169D LEU* 3.5 25.7 + - - +
172D LEU* 3.8 22.1 - - + +
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 4.3 9.4 - + - -
45C VAL* 3.6 18.7 - - + +
48C HIS* 3.1 13.0 - + - -
49C LEU* 3.9 14.4 - - + -
142C HIS* 3.1 44.2 + + - +
143C ASP 3.9 2.9 - - - +
145C THR* 1.3 74.5 - - - +
147C ILE* 1.3 64.3 + - - +
148C ALA 3.3 0.2 - - - -
149C GLN* 2.8 29.5 + - - +
150C ILE* 3.0 29.3 + - - +
300C NI 2.3 34.4 - - + +
302C IMD 3.2 12.0 + + - -
172D LEU* 4.5 4.7 - - + +
173D ASN 5.5 2.9 - - - -
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C THR* 4.1 29.2 - - + +
18C THR* 5.1 8.5 - - + -
19C LEU* 4.0 24.7 - - + -
22C PHE* 6.1 2.2 - - + -
49C LEU* 5.6 0.4 - - + +
143C ASP 2.9 23.7 + - - +
144C LEU* 3.3 12.8 + - + +
146C HIS* 1.3 74.8 - - - +
148C ALA* 1.3 62.5 + - - +
150C ILE* 3.1 12.4 + - - +
151C VAL* 3.0 30.9 + - + +
22D PHE* 4.1 27.4 - - + -
147D ILE* 5.2 2.0 - - + -
151D VAL* 3.8 22.0 - - + -
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU 2.9 12.9 + - - +
145C THR* 3.6 10.5 - - - +
146C HIS 3.3 0.2 - - - -
147C ILE* 1.3 78.0 - - - +
149C GLN* 1.3 56.8 + - - +
151C VAL* 3.3 7.0 + - - +
152C ARG* 2.9 49.6 + - - +
148D ALA* 5.1 8.9 - - + +
151D VAL* 4.0 15.9 - - + +
152D ARG* 5.0 13.9 - - + +
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Residues in contact with GLN 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 4.0 13.6 + - + +
39C THR* 5.2 1.2 - - - -
40C TRP* 4.3 8.3 + - - +
45C VAL* 3.6 22.5 - - + +
145C THR 3.1 15.5 + - - +
146C HIS* 2.8 38.9 + - - +
148C ALA* 1.3 75.0 - - - +
150C ILE* 1.3 62.0 + - - +
152C ARG* 3.6 15.5 + - - +
153C SER* 2.8 35.3 + - - +
172D LEU* 4.1 14.7 - - + +
173D ASN* 2.8 37.4 + - - +
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.9 28.0 - - + -
22C PHE* 4.4 7.4 - - + -
23C LEU* 4.3 8.7 - - + -
42C VAL* 3.6 35.2 - - + +
45C VAL* 3.8 30.5 - - + -
46C VAL* 4.3 18.2 - - + -
49C LEU* 5.1 0.7 - - + -
146C HIS 3.0 18.8 + - - +
147C ILE* 3.4 7.4 - - - +
149C GLN* 1.3 79.3 - - - +
151C VAL* 1.3 63.0 + - - +
153C SER* 3.3 3.4 + - - -
154C MSE 3.1 35.1 + - - +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.7 24.5 - - + -
147C ILE* 3.0 25.1 + - + +
148C ALA* 3.8 6.3 - - - +
150C ILE* 1.3 76.2 - - - +
152C ARG* 1.3 58.9 + - - +
154C MSE 3.3 9.3 + - - +
155C ALA* 2.9 25.2 + - + +
144D LEU* 2.8 44.6 - - + +
147D ILE* 3.6 23.3 - - + -
148D ALA* 3.9 14.8 - - + +
151D VAL* 5.8 0.2 - - + -
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Residues in contact with ARG 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 2.8 41.7 + - - +
145C THR 4.9 1.4 + - - -
148C ALA* 2.9 41.8 + - - +
149C GLN* 3.6 9.2 - - - +
151C VAL* 1.3 73.7 - - + +
153C SER* 1.3 66.4 - - - +
155C ALA* 3.2 7.8 + - - +
156C LYS* 3.0 24.8 + - - +
148D ALA* 4.8 14.6 - - + -
152D ARG* 5.6 11.2 - - - +
172D LEU* 3.3 26.1 - - - +
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Residues in contact with SER 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C CYS* 3.6 17.3 - - - +
34C ASN* 3.5 39.0 - - - +
35C GLU* 3.6 15.9 + - - +
40C TRP 4.1 6.9 + - - -
42C VAL* 4.1 8.8 + - - +
149C GLN* 2.8 28.3 + - - +
150C ILE* 3.4 6.1 - - - -
152C ARG* 1.3 74.9 - - - +
154C MSE 1.3 64.2 + - - +
156C LYS* 3.3 8.5 + - - +
157C ARG* 3.6 6.2 + - - +
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Residues in contact with MSE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.9 18.4 - - + -
23C LEU* 3.8 21.8 - - - -
26C LEU* 3.5 24.7 - - + -
30C TRP* 3.5 33.2 - - + +
33C CYS* 3.9 6.7 - - - -
42C VAL* 4.0 12.8 - - + -
150C ILE* 3.1 17.5 + - - +
151C VAL* 3.6 7.6 - - - +
152C ARG 3.2 0.2 - - - -
153C SER* 1.3 78.1 - - - +
155C ALA* 1.3 60.4 + - - +
157C ARG* 3.3 19.1 - - - +
158C TYR* 4.4 2.4 + - - -
11D LEU* 3.4 40.4 - - + -
144D LEU* 3.8 9.9 - - + +
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Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C VAL 2.9 15.7 + - - +
152C ARG* 3.2 10.1 + - - +
154C MSE 1.3 76.9 - - - +
156C LYS* 1.3 61.9 + - - +
158C TYR* 3.2 12.6 + - - -
159C ASP* 3.8 8.7 + - - +
141D VAL* 3.9 27.8 - - + +
144D LEU* 3.5 25.5 - - + +
145D THR* 5.1 3.6 - - - +
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Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 2.8 29.2 + - - -
34C ASN 3.9 6.1 - - - +
35C GLU* 3.6 43.3 - - + +
36C GLY* 4.1 5.3 - - - +
152C ARG 3.0 16.4 + - - +
153C SER* 3.6 6.7 - - - +
154C MSE 3.2 0.2 - - - -
155C ALA* 1.3 71.5 - - - +
157C ARG* 1.3 65.7 + - - +
158C TYR 3.0 3.5 + - - -
159C ASP* 3.1 28.9 + - - +
-1D GLN* 2.7 49.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER* 3.5 31.2 + - - -
30C TRP* 3.9 25.9 - - + -
33C CYS* 3.3 28.5 - - - -
34C ASN 5.5 0.2 + - - -
153C SER 3.6 2.6 + - - +
154C MSE 3.3 15.8 + - - +
155C ALA 3.2 0.2 - - - -
156C LYS* 1.3 78.0 - - - +
158C TYR* 1.3 65.4 + - + +
161C ASP* 3.4 7.4 - - - +
-1D GLN* 3.7 5.8 + - - +
0D GLY 4.8 0.2 - - - +
2D ASN* 2.9 62.3 + - + +
4D GLN* 5.3 1.2 - - - +
7D GLU* 2.8 31.7 + - - -
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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