Contacts of the helix formed by residues 88 - 117 (chain D) in PDB entry 1JI5
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 88 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLY 4.7 1.9 + - - -
87D GLU* 1.3 75.1 - - - +
89D ALA* 1.3 68.4 + - + +
90D GLU* 3.4 29.2 - - + +
91D GLY* 3.5 15.3 - - - -
92D MET* 2.7 36.5 + - - +
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 4.0 20.9 - - + -
31D LYS 3.5 26.8 + - - +
34D GLN* 5.2 12.1 - - + -
38D LEU* 5.2 3.5 - - + +
42D PHE* 4.8 0.7 - - - -
88D THR* 1.3 76.8 - - + +
90D GLU* 1.3 78.5 + - - +
92D MET* 3.3 5.8 + - - +
93D VAL* 3.1 27.1 + - - +
143D PHE* 5.9 1.6 - - + -
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLN* 5.4 7.7 - - - +
88D THR* 3.4 19.8 - - + +
89D ALA* 1.3 93.2 - - - +
91D GLY* 1.3 53.4 + - - +
93D VAL* 3.2 8.2 + - - +
94D GLU* 2.7 42.3 + - - +
143D PHE* 5.0 11.8 - - - -
144D LEU* 4.4 16.3 - - + +
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Residues in contact with GLY 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D GLU* 4.9 6.5 - - - -
88D THR* 3.1 23.1 + - - -
90D GLU* 1.3 79.8 - - - +
92D MET* 1.3 50.5 + - - +
94D GLU* 3.4 12.3 - - - +
95D ALA* 2.6 37.2 + - - +
98D LYS* 5.8 0.2 + - - -
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Residues in contact with MET 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ASN* 4.5 1.8 - - - +
26D PHE* 3.2 64.0 - - + -
29D TYR* 3.8 17.3 - - + +
30D VAL* 3.8 41.1 - - - +
42D PHE* 3.7 7.6 - - + -
87D GLU* 3.8 28.5 - - + +
88D THR 2.7 23.1 + - - +
89D ALA* 3.5 4.7 - - - +
91D GLY* 1.3 71.3 - - - +
93D VAL* 1.3 62.4 + - - +
95D ALA* 3.0 2.8 + - - +
96D ILE* 2.9 29.9 + - - +
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 3.9 28.7 - - + -
42D PHE* 4.4 6.3 - - + -
89D ALA 3.1 16.0 + - - +
90D GLU* 3.6 5.2 - - - +
92D MET* 1.3 75.6 - - - +
94D GLU* 1.3 61.0 + - - +
96D ILE* 2.7 24.9 - - - +
97D MET* 3.0 14.0 - - - +
140D LEU* 3.6 30.3 - - + +
143D PHE* 3.9 23.1 - - + -
144D LEU* 3.7 22.2 - - + -
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Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU* 2.7 21.2 + - - +
91D GLY* 3.4 11.7 - - - +
93D VAL* 1.3 77.9 - - - +
95D ALA* 1.3 60.8 + - - +
97D MET* 3.5 10.0 - - + +
98D LYS* 3.1 48.2 + - + +
144D LEU* 4.2 20.7 - - + +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS* 4.8 9.0 + - - +
26D PHE* 3.8 20.0 - - + -
87D GLU* 5.6 3.6 - - + -
91D GLY 2.6 22.2 + - - +
92D MET* 3.0 6.4 + - - +
94D GLU* 1.3 73.6 - - - +
96D ILE* 1.3 62.3 + - + +
98D LYS* 3.3 18.0 + - - +
99D ASP* 3.1 25.4 + - - +
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 5.3 4.5 - - + -
22D LYS* 5.1 5.6 - - + -
23D LEU* 4.1 23.6 - - + -
26D PHE* 3.4 31.4 - - + -
42D PHE* 4.4 9.9 - - + -
45D LEU* 4.9 3.1 - - + -
92D MET 2.9 18.4 + - - +
93D VAL* 2.7 38.1 - - - +
95D ALA* 1.3 70.0 - - - +
97D MET* 1.3 62.0 + - - +
99D ASP* 3.3 15.7 - - + +
100D TYR* 2.8 46.7 + - + -
140D LEU* 4.1 19.3 - - + -
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Residues in contact with MET 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D VAL 3.0 21.3 + - - +
94D GLU* 3.5 13.7 - - + +
96D ILE* 1.3 81.5 - - - +
98D LYS* 1.3 71.5 + - + +
100D TYR* 3.3 6.3 + - - +
101D GLU* 3.1 47.5 + - - +
137D ALA* 4.2 9.1 - - - +
140D LEU* 4.1 19.7 - - + -
141D ARG* 3.8 41.3 - - + +
144D LEU* 4.2 14.1 - - + -
145D ASN* 6.3 0.7 - - - +
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Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU* 3.1 39.6 + - + +
95D ALA* 3.6 14.7 - - - +
96D ILE 3.2 0.2 - - - -
97D MET* 1.3 82.7 - - + +
99D ASP* 1.3 61.0 + - - +
101D GLU* 3.2 16.5 + - - +
102D MET* 2.8 50.2 + - + +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.1 11.0 - - + +
22D LYS* 2.8 38.7 + - - +
80D ILE* 3.9 33.3 - - + +
81D GLN 4.9 2.8 + - - -
95D ALA 3.1 16.1 + - - +
96D ILE* 3.1 15.6 + - - +
98D LYS* 1.3 77.2 - - - +
100D TYR* 1.3 64.2 + - + +
102D MET* 3.4 21.6 + - - +
103D MET* 3.1 23.8 + - - +
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Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D TRP* 4.3 19.1 - + - -
19D LEU* 4.7 12.3 - - + -
23D LEU* 4.5 7.4 - - + +
45D LEU* 3.0 36.3 + - + +
48D GLU* 5.1 1.6 + - - -
96D ILE* 2.8 29.3 + - + -
97D MET* 3.5 7.9 - - - +
99D ASP* 1.3 78.2 - - + +
101D GLU* 1.3 58.2 + - + +
103D MET* 2.9 10.6 + - - +
104D LEU* 2.9 30.5 + - + +
133D LEU* 4.1 41.4 - - + +
136D HIS* 3.8 36.8 - + + -
137D ALA* 4.7 5.4 - - + -
140D LEU* 4.2 17.7 - - + -
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Residues in contact with GLU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D MET* 3.1 32.9 + - - +
98D LYS* 3.6 18.9 - - - +
100D TYR* 1.3 75.4 - - - +
102D MET* 1.3 64.2 + - + +
103D MET 3.0 0.2 - - - -
104D LEU* 3.0 30.7 + - + +
105D VAL* 3.5 11.1 + - - +
137D ALA* 4.5 10.5 - - + -
141D ARG* 2.4 36.6 + - - +
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Residues in contact with MET 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ILE* 6.0 2.9 - - + -
98D LYS* 2.8 40.9 + - + +
99D ASP* 3.4 29.8 - - - +
101D GLU* 1.3 76.4 - - + +
103D MET* 1.3 58.2 + - - +
104D LEU 3.4 0.2 - - - -
105D VAL* 3.0 29.5 - - + +
106D GLU* 3.7 8.7 + - - +
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Residues in contact with MET 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLN* 2.9 44.4 - - - +
15D ASP* 4.5 15.7 - - + +
16D TRP* 3.3 38.4 - - + +
19D LEU* 4.4 16.6 - - - -
80D ILE* 5.2 4.7 - - + -
99D ASP 3.1 11.8 + - - +
100D TYR* 2.9 14.0 + - - +
102D MET* 1.3 77.2 - - - +
104D LEU* 1.3 64.2 + - - +
105D VAL 3.2 1.8 - - - -
106D GLU* 3.3 10.1 + - + +
107D LEU* 2.9 37.4 + - + +
129D ILE* 4.4 0.9 - - + -
133D LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D TYR 2.9 16.3 + - - +
101D GLU* 3.0 24.0 + - + +
103D MET* 1.3 78.4 - - - +
105D VAL* 1.3 62.4 + - + +
107D LEU* 3.1 8.4 + - + +
108D LYS* 2.9 27.1 + - - +
130D TYR* 3.3 57.0 - - + +
133D LEU* 4.0 15.5 - - + -
134D GLU* 3.8 27.1 - - + +
137D ALA* 5.4 3.8 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLU 3.7 12.1 - - - +
102D MET* 3.0 23.1 - - + +
104D LEU* 1.3 78.3 - - + +
106D GLU* 1.3 82.4 + - + +
107D LEU 3.1 0.3 + - - -
108D LYS* 3.1 13.1 + - + +
109D LYS* 3.0 39.9 + - - +
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.8 5.2 - - - +
11D LYS* 2.8 46.7 - - - +
12D GLN* 5.4 5.7 + - - +
15D ASP* 3.5 9.0 - - - +
79D SER* 3.5 7.3 + - - -
102D MET 4.0 11.6 - - - +
103D MET* 3.3 15.6 + - + +
105D VAL* 1.3 86.6 - - + +
107D LEU* 1.3 56.5 + - - +
109D LYS* 3.6 14.0 - - + +
110D GLY* 2.9 23.4 + - - -
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 6.1 0.4 - - + -
12D GLN* 3.9 23.1 - - + +
103D MET* 2.9 39.7 + - + +
104D LEU* 3.3 10.5 - - - +
106D GLU* 1.3 75.2 - - - +
108D LYS* 1.3 59.4 + - - +
110D GLY* 2.7 20.4 + - - +
111D MET* 2.8 22.0 + - + +
126D LEU* 3.6 39.2 - - + +
129D ILE* 4.4 5.4 - - + -
130D TYR* 3.9 35.2 - - + +
133D LEU* 4.3 8.3 - - + -
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 2.9 13.0 + - + +
105D VAL* 3.6 11.9 - - + +
107D LEU* 1.3 73.3 - - - +
109D LYS* 1.3 64.6 + - + +
111D MET* 3.1 17.0 + - + +
112D GLU* 3.0 24.3 + - - +
130D TYR* 3.2 39.5 + - + +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL* 3.0 31.9 + - - +
106D GLU* 3.6 14.4 - - + +
108D LYS* 1.3 76.4 - - + +
110D GLY* 1.3 60.4 + - - +
112D GLU* 3.1 18.9 + - - +
113D ILE* 2.8 22.8 - - + +
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Residues in contact with GLY 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 5.5 0.5 - - - +
8D VAL* 3.7 24.2 - - - +
106D GLU 2.9 13.9 + - - -
107D LEU 2.7 9.4 + - - -
109D LYS* 1.3 76.6 - - - +
111D MET* 1.3 54.8 + - - -
113D ILE* 3.4 10.3 - - - +
114D ALA* 3.1 27.4 + - - +
126D LEU* 3.8 11.0 - - - +
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Residues in contact with MET 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 2.8 17.2 + - + +
108D LYS* 3.6 31.4 - - + +
110D GLY* 1.3 70.2 - - - +
112D GLU* 1.3 61.0 + - - +
114D ALA* 3.5 4.6 - - - +
115D GLN* 2.8 43.1 + - - +
123D SER* 3.5 19.5 - - - +
126D LEU* 3.8 17.7 - - + -
127D LEU* 3.8 31.2 - - + +
130D TYR* 3.7 31.2 - - + -
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS 3.0 13.0 + - - +
109D LYS* 3.1 15.7 + - - +
111D MET* 1.3 78.7 - - - +
113D ILE* 1.3 58.5 + - - +
115D GLN* 3.1 14.0 + - - +
116D ASN* 2.8 54.6 + - - +
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN* 4.1 7.6 - - - +
5D VAL* 3.4 39.9 - - + +
8D VAL* 3.7 17.9 - - + -
109D LYS 2.8 20.2 - - - +
110D GLY* 3.4 13.9 - - - +
112D GLU* 1.3 71.7 - - - +
114D ALA* 1.3 63.2 + - - +
116D ASN* 3.6 10.1 + - - +
117D SER* 2.8 43.1 + - - +
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 4.2 12.1 - - + -
110D GLY 3.1 21.4 + - - +
111D MET* 3.5 6.7 - - - +
113D ILE* 1.3 81.4 - - - +
115D GLN* 1.3 60.9 + - - +
117D SER 3.2 7.1 + - - -
118D ASP 3.3 0.2 + - - -
119D ASP* 2.8 44.0 + - - +
122D THR* 4.5 9.4 - - + -
123D SER* 4.0 16.8 - - - +
126D LEU* 5.2 0.2 - - + -
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D MET* 2.8 32.4 + - - +
112D GLU* 3.4 15.4 + - - +
114D ALA* 1.3 79.0 - - - +
116D ASN* 1.3 61.4 + - - +
118D ASP* 3.0 19.2 + - - -
119D ASP 4.4 5.4 - - - +
120D GLU* 4.9 10.7 - - + +
123D SER* 3.9 19.5 - - - +
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Residues in contact with ASN 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D GLU* 2.8 43.5 + - - +
113D ILE* 3.6 9.8 + - - +
115D GLN* 1.3 80.9 - - - +
117D SER* 1.3 59.0 + - - +
118D ASP* 3.1 3.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN* 4.5 8.4 + - - -
5D VAL* 3.8 23.8 - - - +
113D ILE* 2.8 24.9 + - - +
114D ALA 3.2 1.5 + - - -
115D GLN 3.2 0.2 - - - -
116D ASN* 1.3 76.4 - - - +
118D ASP* 1.3 71.3 + - - +
119D ASP* 3.4 4.3 + - - +
----------------------------------------------------------
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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