Contacts of the helix formed by residues 94 - 123 (chain I) in PDB entry 2BKC
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 94 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I LYS* 1.3 75.9 - - - +
95I MET* 1.3 62.5 + - - +
96I ASP* 3.2 28.3 - - + +
97I GLN* 2.9 31.7 + - + +
98I LEU* 3.1 23.1 + - - +
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Residues in contact with MET 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G HIS* 6.0 2.7 - - + -
34I MET* 3.5 45.8 - - + -
35I ARG 3.6 25.6 + - - +
36I GLY* 4.7 1.6 - - - +
38I ASN* 3.9 32.5 - - + +
39I PHE* 3.9 3.6 - - - +
42I LEU* 3.8 19.1 - - + -
93I LYS 4.1 0.2 + - - -
94I THR* 1.3 73.3 + - - +
96I ASP* 1.3 65.3 + - - +
98I LEU* 3.3 8.6 + - - +
99I MET* 3.1 34.5 + - + +
149I PHE* 4.2 22.2 - - + -
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Residues in contact with ASP 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G HIS* 3.2 33.8 + - - -
94I THR* 3.2 13.6 - - + +
95I MET* 1.3 77.2 - - - +
97I GLN* 1.3 57.3 + - + +
99I MET* 3.1 4.6 + - - +
100I GLU* 2.9 35.9 + - - +
149I PHE* 3.8 12.6 - - - -
150I LEU* 3.8 25.6 - - + +
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Residues in contact with GLN 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I PRO 4.2 3.6 + - - -
93I LYS* 3.5 36.3 + - + +
94I THR* 2.9 46.8 + - + +
96I ASP* 1.3 78.4 - - + +
98I LEU* 1.3 61.4 + - - +
100I GLU* 3.3 17.8 + - - +
101I ASP* 3.3 20.3 + - - +
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Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I GLN* 5.5 5.6 - - + +
30I ILE* 3.5 44.2 - - + +
33I TYR* 4.7 3.8 - - + +
34I MET* 3.9 36.6 - - + +
35I ARG 5.2 0.2 - - - +
89I TYR* 4.2 17.0 - - + -
93I LYS* 3.9 27.8 - - + +
94I THR 3.1 20.3 + - - +
95I MET* 3.7 11.7 - - - +
97I GLN* 1.3 73.0 - - - +
99I MET* 1.3 66.1 + - + +
101I ASP* 3.4 9.2 + - + +
102I LEU 3.1 16.1 + - - -
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Residues in contact with MET 99 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ILE* 3.5 33.4 - - + -
34I MET* 4.4 1.6 - - + -
42I LEU* 3.4 26.2 - - + -
46I MET* 3.7 15.5 - - + -
95I MET* 3.1 28.2 + - + +
96I ASP 3.7 4.3 - - - +
98I LEU* 1.3 75.2 - - + +
100I GLU* 1.3 60.2 + - - +
102I LEU* 3.3 6.7 + - + +
103I VAL* 2.9 33.7 + - + +
146I PHE* 3.9 22.9 - - + -
149I PHE* 4.1 19.3 - - + -
150I LEU* 4.1 16.6 - - + -
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Residues in contact with GLU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I ASP* 2.9 23.6 + - - +
97I GLN* 3.6 21.6 - - - +
98I LEU 3.2 0.2 - - - -
99I MET* 1.3 74.3 - - - +
101I ASP* 1.3 61.3 + - - +
103I VAL* 3.9 6.0 - - + +
104I GLY* 2.9 26.9 + - - -
150I LEU* 4.1 20.2 - - + +
152I LYS* 5.3 11.2 + - + +
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Residues in contact with ASP 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LYS* 2.9 41.1 + - - +
29I GLN* 4.7 5.7 + - - -
30I ILE* 4.8 4.3 - - - +
97I GLN 3.3 10.5 + - - +
98I LEU* 3.6 14.2 - - + +
99I MET 3.3 0.2 - - - -
100I GLU* 1.3 76.8 - - - +
102I LEU* 1.3 60.5 + - - +
104I GLY* 3.5 1.5 + - - -
105I THR* 2.9 31.2 + - - -
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Residues in contact with LEU 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE* 3.4 38.4 - - + -
26I LYS* 5.3 1.3 - - - -
27I ILE* 4.6 5.2 - - + -
30I ILE* 4.2 17.2 - - + +
46I MET* 4.4 9.2 - - + -
49I LEU* 3.8 15.3 - - + -
98I LEU 3.1 13.4 + - - +
99I MET* 3.4 13.5 - - - +
100I GLU 3.2 0.2 - - - -
101I ASP* 1.3 77.4 - - - +
103I VAL* 1.3 56.0 + - - +
105I THR* 2.9 8.9 + - - -
106I LEU* 2.9 36.9 + - + +
146I PHE* 3.7 49.4 - - + -
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Residues in contact with VAL 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I MET 2.9 19.8 + - - +
100I GLU* 3.9 6.5 - - - +
102I LEU* 1.3 74.7 - - + +
104I GLY* 1.3 57.2 + - - +
106I LEU* 3.4 12.5 + - + +
107I GLU* 3.1 47.6 + - + +
142I HIS 5.4 0.2 - - - +
143I ILE* 4.7 6.9 - - + +
146I PHE* 3.4 36.3 - - + -
147I LYS* 3.8 24.0 - - + +
150I LEU* 4.2 13.2 - - + -
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Residues in contact with GLY 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I GLU 2.9 17.3 + - - -
101I ASP* 3.8 2.5 - - - -
102I LEU 3.1 0.2 - - - -
103I VAL* 1.3 78.8 - - - +
105I THR* 1.3 56.9 + - - +
107I GLU* 3.4 14.9 + - - +
108I LEU* 3.2 24.9 + - - +
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Residues in contact with THR 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE* 3.4 35.4 - - + -
26I LYS* 3.5 18.6 - - - -
84I VAL* 3.6 31.7 - - + +
85I GLU 5.8 0.2 + - - -
101I ASP* 2.9 15.0 + - - -
102I LEU 2.9 9.0 + - - -
104I GLY* 1.3 73.5 - - - +
106I LEU* 1.3 64.8 + - - +
108I LEU* 3.4 8.7 + - + +
109I LEU* 3.2 23.7 + - + +
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Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE* 3.9 16.4 - - + -
49I LEU* 5.3 2.0 - - + -
53I PHE* 3.9 31.2 - - + -
102I LEU* 2.9 36.2 + - + +
103I VAL* 3.5 14.8 - - + +
105I THR* 1.3 77.1 - - - +
107I GLU* 1.3 57.6 + - - +
109I LEU* 3.2 6.1 + - + +
110I ARG* 3.0 24.3 + - - +
139I ILE* 3.5 22.5 - - + +
142I HIS* 4.2 25.4 - - + +
143I ILE* 3.8 19.3 - - + -
146I PHE* 4.3 6.3 - - + -
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Residues in contact with GLU 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I VAL* 3.1 24.6 + - - +
104I GLY* 3.7 13.3 - - - +
105I THR 3.3 0.2 - - - -
106I LEU* 1.3 73.1 - - - +
108I LEU* 1.3 65.8 + - - +
110I ARG* 3.4 26.7 + - - +
111I ASP* 3.0 31.7 + - - +
143I ILE* 3.8 19.2 - - + +
147I LYS* 3.4 31.4 + - - -
154I PRO 4.6 4.0 - - - +
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Residues in contact with LEU 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ASN* 4.4 2.2 - - - +
83I SER* 3.7 30.1 - - - +
84I VAL* 4.2 21.1 - - + -
85I GLU* 5.3 2.2 - - + +
104I GLY 3.2 13.4 + - - +
105I THR* 3.6 11.2 - - + +
106I LEU 3.3 0.2 - - - -
107I GLU* 1.3 77.6 - - - +
109I LEU* 1.3 60.5 + - - +
111I ASP* 4.0 4.8 - - - +
112I GLU* 3.0 54.0 + - + +
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Residues in contact with LEU 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I GLN* 3.5 24.0 - - - +
19I ASN* 4.1 21.1 - - + +
20I LEU* 4.3 14.6 - - + -
23I PHE* 3.9 35.9 - - + -
53I PHE* 4.6 7.6 - - + -
84I VAL* 4.5 7.4 - - + -
105I THR* 3.2 19.0 + - + +
106I LEU* 3.2 8.0 + - + +
107I GLU 3.2 0.6 - - - -
108I LEU* 1.3 75.0 - - + +
110I ARG* 1.3 57.4 + - - +
112I GLU* 4.6 2.0 - - - -
113I TYR* 2.7 50.7 + - + +
139I ILE* 4.2 11.4 - - + -
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Residues in contact with ARG 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I LEU 3.0 17.0 + - - +
107I GLU* 3.5 31.9 + - - +
109I LEU* 1.3 75.5 - - - +
111I ASP* 1.3 82.9 + - - +
113I TYR* 3.7 5.6 - - - +
114I LYS* 3.0 27.1 + - + +
136I LYS* 4.3 20.7 - - + +
139I ILE* 4.0 17.1 - - + +
140I ASP* 3.3 26.7 + - - +
143I ILE* 3.7 21.7 - - + +
154I PRO 4.9 0.8 + - - -
155I LEU* 3.8 25.8 - - - +
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Residues in contact with ASP 111 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I GLU* 3.0 20.3 + - - +
108I LEU* 4.1 3.9 - - - +
110I ARG* 1.3 103.7 + - - +
112I GLU* 1.3 67.1 + - + +
114I LYS* 3.3 18.2 - - - +
115I GLN* 3.0 21.3 - - - +
----------------------------------------------------------
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Residues in contact with GLU 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 3.3 9.1 - - + -
15I HIS* 3.2 10.3 + - - -
16I GLN* 2.9 29.7 + - - +
19I ASN* 3.1 10.7 + - - -
83I SER* 2.4 28.9 + - - -
108I LEU* 3.0 33.7 + - + +
109I LEU* 4.0 4.9 - - - +
111I ASP* 1.3 73.4 - - + +
113I TYR* 1.3 66.2 + - - +
115I GLN* 3.0 21.9 + - - +
116I GLY 3.0 17.8 + - - -
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Residues in contact with TYR 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 4.1 10.1 - + - -
16I GLN* 3.5 37.6 - - + +
20I LEU* 3.5 23.0 - - - +
56I GLN* 2.8 22.7 + - - -
60I VAL* 5.0 1.8 - - + +
109I LEU* 2.7 34.1 + - + +
110I ARG* 3.7 6.1 - - - +
112I GLU* 1.3 73.2 - - + +
114I LYS* 1.3 57.1 + - - +
116I GLY* 3.2 0.9 + - - -
117I ILE* 2.8 39.5 + - + +
132I LEU* 4.3 15.0 - - + +
135I PHE* 3.6 37.1 - + + -
136I LYS* 4.3 13.0 - - + -
139I ILE* 3.7 21.5 - - + -
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Residues in contact with LYS 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E GLY 4.3 11.0 - - - -
126E ASP* 2.6 29.8 + - - -
110I ARG* 3.0 13.4 + - + +
111I ASP* 3.3 15.7 - - - +
113I TYR* 1.3 76.2 - - - +
115I GLN* 1.3 62.7 + - - +
117I ILE* 3.2 21.0 + - - +
118I GLU* 3.1 49.8 + - - +
136I LYS* 4.1 21.5 - - + +
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Residues in contact with GLN 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 4.8 4.9 - - + -
111I ASP* 3.0 27.3 + - - +
112I GLU* 3.0 20.9 + - - +
114I LYS* 1.3 76.5 - - - +
116I GLY* 1.3 59.7 + - - +
118I GLU* 3.3 12.5 + - - +
119I LEU* 3.0 29.8 + - - +
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Residues in contact with GLY 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PHE* 3.5 35.7 - - - -
112I GLU 3.0 10.7 + - - -
113I TYR 3.2 1.3 + - - -
115I GLN* 1.3 76.2 - - - +
117I ILE* 1.3 56.8 + - - +
119I LEU* 3.8 5.9 - - - +
120I THR* 2.8 33.8 + - - +
132I LEU* 3.7 7.6 - - - +
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Residues in contact with ILE 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ASP* 3.7 28.5 - - + +
113I TYR 2.8 21.6 + - - +
114I LYS* 3.4 14.4 - - - +
115I GLN 3.2 0.4 - - - -
116I GLY* 1.3 76.4 - - - +
118I GLU* 1.3 57.4 + - - +
120I THR* 3.1 5.5 - - - +
121I ASP* 3.0 25.1 + - + +
129I ASN* 3.0 24.9 + - - +
132I LEU* 3.6 27.6 - - + +
133I ILE* 3.8 22.9 - - + -
136I LYS* 3.8 29.2 - - + -
----------------------------------------------------------
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Residues in contact with GLU 118 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I LYS* 3.1 44.4 + - - +
115I GLN* 3.3 11.5 + - - +
117I ILE* 1.3 74.5 - - + +
119I LEU* 1.3 63.2 + - - +
121I ASP* 3.4 7.8 + - - +
122I LYS* 3.1 26.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 4.1 29.2 - - - +
8I ASP* 3.5 32.1 - - - +
9I THR* 4.3 4.7 - - - +
12I PHE* 3.9 24.7 - - + -
115I GLN 3.0 16.5 + - - +
116I GLY* 3.8 4.3 - - - +
117I ILE 3.3 0.2 - - - -
118I GLU* 1.3 76.6 - - - +
120I THR* 1.3 59.0 + - - +
122I LYS* 3.4 6.6 + - + +
123I GLU* 3.1 43.1 + - + +
----------------------------------------------------------
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Residues in contact with THR 120 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I THR* 4.3 15.9 - - - -
116I GLY 2.8 26.2 + - - +
117I ILE* 3.1 15.0 - - - +
119I LEU* 1.3 74.8 - - - +
121I ASP* 1.3 61.7 + - - +
123I GLU* 4.0 1.6 - - - +
124I GLY* 3.3 2.6 + - - -
125I ASP* 2.9 60.4 + - - +
128I THR* 3.8 5.8 - - - -
129I ASN* 3.2 33.1 + - - +
132I LEU* 4.2 6.7 - - + -
----------------------------------------------------------
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Residues in contact with ASP 121 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ILE* 3.0 20.0 + - + +
118I GLU* 3.5 9.6 - - - +
120I THR* 1.3 77.2 - - - +
122I LYS* 1.3 63.4 + - + +
124I GLY* 3.2 13.3 + - - -
126I ASP* 5.8 0.5 - - - +
129I ASN* 4.1 15.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I GLU 3.1 15.1 + - - +
119I LEU* 3.4 7.4 + - + +
121I ASP* 1.3 79.9 - - - +
123I GLU* 1.3 60.9 + - + +
124I GLY 3.3 1.0 + - - -
----------------------------------------------------------
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Residues in contact with GLU 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL 4.0 4.7 - - - +
8I ASP* 3.6 25.0 - - - +
9I THR* 3.3 34.0 + - - +
119I LEU* 3.1 25.0 + - + +
120I THR 4.5 2.2 - - - +
121I ASP 3.4 0.2 - - - -
122I LYS* 1.3 76.7 - - + +
124I GLY* 1.3 62.8 + - - +
125I ASP* 3.3 4.1 + - + +
----------------------------------------------------------
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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