Contacts of the helix formed by residues 113 - 144 (chain D) in PDB entry 3E1N
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 5.9 1.1 - - - +
3D GLY* 5.9 0.2 - - - -
4D ASP* 5.5 4.0 + - + +
7D VAL* 3.4 29.0 - - + +
61D ARG* 2.9 23.0 + - - -
65D LEU* 3.8 10.6 - - - +
108D ALA* 2.9 16.5 + - + +
111D VAL* 3.3 5.6 - - + +
112D HIS* 1.3 72.5 - - - +
114D TYR* 1.3 56.6 + - - +
115D VAL* 3.8 2.4 + - - +
116D SER* 2.6 29.4 + - - -
117D ARG* 3.0 26.9 + - - +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ASP* 3.3 41.4 + - - -
112D HIS* 2.8 64.3 + + + -
113D ASP* 1.3 73.2 + - - +
115D VAL* 1.3 60.8 + - + +
117D ARG* 3.5 9.8 - - - +
118D ASP* 2.8 28.8 + - - +
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ARG* 3.1 35.0 - - - +
113D ASP* 3.3 2.5 + - - +
114D TYR* 1.3 77.1 - - + +
116D SER* 1.3 65.4 + - - +
118D ASP* 3.2 6.9 + - + +
119D MET* 2.9 25.4 + - + +
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.1 11.8 - - - +
11D LEU* 4.3 6.0 - - - +
61D ARG* 2.9 30.9 + - - +
65D LEU* 3.7 5.7 - - - +
108D ALA* 4.7 0.7 - - - -
113D ASP* 2.6 36.8 + - - -
115D VAL* 1.3 74.7 - - - +
117D ARG* 1.3 64.0 + - - +
119D MET* 3.4 7.0 + - - +
120D MET* 2.9 35.7 + - - +
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ILE* 3.3 38.9 + - + +
106D GLY* 4.3 4.2 - - - -
108D ALA* 4.1 5.4 - - + -
109D ASP* 3.1 43.9 + - - +
113D ASP 3.0 15.9 + - - +
114D TYR* 3.5 15.9 - - - +
116D SER* 1.3 76.7 - - - +
118D ASP* 1.3 64.4 + - - +
120D MET* 2.9 14.4 + - - +
121D ILE* 2.9 42.6 + - + +
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Residues in contact with ASP 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR 2.8 19.1 + - - +
115D VAL* 3.2 8.7 + - + +
117D ARG* 1.3 72.2 - - - +
119D MET* 1.3 65.3 + - - +
121D ILE* 3.2 12.2 + - - +
122D GLU* 3.1 42.3 + - - +
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Residues in contact with MET 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 5.7 1.8 - - - -
57D ARG* 3.4 68.1 + - + +
58D TYR* 4.6 14.4 - - - -
60D GLU* 6.2 0.2 - - + -
61D ARG* 3.8 32.3 - - + +
115D VAL* 2.9 17.4 + - + +
116D SER* 3.6 6.3 - - - +
118D ASP* 1.3 79.1 + - - +
120D MET* 1.3 62.0 + - - +
122D GLU* 3.4 3.3 + - - +
123D ILE* 3.2 30.6 + - + +
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Residues in contact with MET 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 5.5 1.6 - - + -
10D TYR* 6.2 0.2 - - + -
11D LEU* 3.9 15.3 - - + -
14D LEU* 3.6 26.2 - - - -
58D TYR* 4.4 14.1 - - + -
101D LEU* 3.8 14.0 - - + +
104D ALA* 3.7 26.0 - - + +
105D ILE* 3.6 14.6 - - + -
108D ALA* 3.7 29.2 - - + -
116D SER* 2.9 28.6 + - - +
117D ARG* 2.9 6.9 + - - +
119D MET* 1.3 77.9 - - + +
121D ILE* 1.3 58.0 + - - +
123D ILE* 3.2 7.9 + - - +
124D LEU* 2.8 27.9 + - - +
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ILE* 4.0 22.9 - - + -
117D ARG* 2.9 49.9 + - + +
118D ASP* 3.2 12.1 + - - +
120D MET* 1.3 72.6 - - - +
122D GLU* 1.3 67.5 + - + +
124D LEU* 3.3 7.4 + - + +
125D ARG* 3.0 25.2 + - + +
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Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ARG* 3.3 29.8 + - - +
118D ASP* 3.1 35.9 + - - +
119D MET 3.8 6.7 - - - +
121D ILE* 1.3 76.9 - - + +
123D ILE* 1.3 63.6 + - - +
125D ARG* 3.3 14.0 + - - +
126D ASP* 3.1 23.9 + - - +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 4.0 2.9 - - - +
54D HIS* 3.7 39.9 - - + +
57D ARG* 4.0 15.0 - - + +
58D TYR* 3.6 42.0 - - + +
101D LEU* 4.0 7.6 - - + -
119D MET* 3.2 33.1 + - + +
120D MET* 3.2 7.4 + - - +
122D GLU* 1.3 73.6 - - - +
124D LEU* 1.3 58.8 + - - +
126D ASP* 2.8 21.6 + - - +
127D GLU* 2.9 30.2 + - - +
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA* 4.0 26.9 - - + +
101D LEU* 3.7 22.6 - - + +
102D ARG* 4.1 26.5 - - + +
105D ILE* 3.8 23.1 - - + -
120D MET 2.8 16.4 + - - +
121D ILE* 3.3 10.5 + - + +
123D ILE* 1.3 75.5 - - - +
125D ARG* 1.3 57.0 + - - +
127D GLU* 2.9 5.6 + - + +
128D GLU* 2.8 48.6 + - - +
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Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ILE* 3.0 16.2 + - + +
122D GLU* 3.3 16.8 - - - +
124D LEU* 1.3 76.6 - - - +
126D ASP* 1.3 65.0 + - - +
128D GLU* 3.5 7.4 + - - +
129D GLY* 3.2 16.3 + - - -
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Residues in contact with ASP 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ASP* 4.8 9.0 - - - +
54D HIS* 3.0 32.0 + - + +
57D ARG* 5.4 3.6 + - - -
122D GLU 3.1 12.9 + - - +
123D ILE* 2.8 13.5 + - - +
125D ARG* 1.3 75.3 - - - +
127D GLU* 1.3 63.2 + - - +
129D GLY* 3.1 4.6 + - - -
130D HIS* 3.0 31.5 + - + +
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 3.2 7.1 - - - +
54D HIS* 3.1 11.8 + - - -
94D GLU* 3.6 7.7 - - - +
97D GLY* 5.7 1.3 - - - -
98D ALA* 5.1 6.3 - - + +
101D LEU* 3.7 23.7 - - + +
123D ILE* 2.9 17.9 + - - +
124D LEU* 2.9 10.9 + - + +
126D ASP* 1.3 76.5 - - - +
128D GLU* 1.3 58.3 + - - +
130D HIS* 2.8 20.9 + - - +
131D ILE* 2.8 37.4 + - + +
300D FE2 1.9 28.7 - - - -
301D FE2 2.0 29.2 - - - -
400D UNK 3.3 5.5 + - - -
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA* 5.3 1.2 - - - +
102D ARG* 2.5 35.7 + - - -
124D LEU* 2.8 26.4 + - - +
125D ARG* 3.7 9.4 - - - +
127D GLU* 1.3 78.0 - - - +
129D GLY* 1.3 56.8 + - - +
131D ILE* 3.3 16.3 + - + +
132D ASP* 2.9 27.6 + - - +
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Residues in contact with GLY 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLU* 5.3 0.4 - - - -
125D ARG 3.2 10.4 + - - -
126D ASP 3.1 8.7 + - - -
128D GLU* 1.3 72.6 - - - +
130D HIS* 1.3 65.0 + - - +
132D ASP* 3.1 9.9 + - - +
133D TRP* 3.0 22.5 + - - +
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Residues in contact with HIS 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR* 4.0 4.7 - - - +
47D GLU* 3.1 39.0 + - + +
50D ASP* 2.9 36.0 + - + +
51D GLU* 3.1 25.6 - - - -
54D HIS* 4.2 5.6 - + - -
94D GLU* 2.9 18.1 + - - +
126D ASP 3.0 16.9 + - - -
127D GLU* 2.8 16.1 + - - +
129D GLY* 1.3 73.7 - - - +
131D ILE* 1.3 62.4 + - - +
133D TRP* 3.1 3.4 + - - +
134D LEU* 3.0 30.4 + - - +
301D FE2 2.4 23.3 - - - -
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 3.9 14.8 - - + -
94D GLU* 3.6 31.4 - - + +
95D LEU* 3.8 24.7 - - + -
98D ALA* 4.2 13.9 - - + -
102D ARG* 5.9 0.7 - - - +
127D GLU* 2.8 24.6 + - + +
128D GLU* 3.4 18.2 - - + +
129D GLY 3.3 0.2 - - - -
130D HIS* 1.3 73.2 - - - +
132D ASP* 1.3 66.5 + - - +
134D LEU* 3.3 3.8 + - - +
135D GLU* 2.9 47.3 + - - +
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLU 2.9 14.8 + - - +
129D GLY* 3.1 12.8 + - - +
131D ILE* 1.3 75.2 - - - +
133D TRP* 1.3 62.6 + - - +
135D GLU* 3.3 10.6 + - - +
136D THR* 2.8 41.7 + - - -
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Residues in contact with TRP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ARG* 4.1 11.8 - - - +
40D LEU* 4.0 17.0 - - + -
43D VAL* 3.4 40.7 - - + +
44D GLU* 3.7 19.5 - - + -
47D GLU* 4.1 19.7 - - - +
87D LEU* 4.9 5.4 - - + -
129D GLY 3.0 13.1 + - - +
130D HIS 3.1 6.5 + - - +
132D ASP* 1.3 79.8 - - - +
134D LEU* 1.3 88.4 + - + +
136D THR* 3.3 5.4 + - - -
137D GLU* 3.0 60.0 + - + +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR* 3.6 23.6 - - - +
44D GLU* 4.2 5.6 - - - +
47D GLU* 4.6 2.2 - - - +
87D LEU* 3.9 26.2 - - + +
90D ASP* 4.1 9.2 - - + -
91D LEU* 3.9 32.5 - - + +
94D GLU* 4.0 12.6 - - + -
130D HIS* 3.0 28.8 + - + +
131D ILE* 3.9 3.6 - - - +
133D TRP* 1.3 103.3 - - + +
135D GLU* 1.3 62.8 + - - +
137D GLU* 3.2 4.0 + - - +
138D LEU* 2.9 28.6 + - + +
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 4.2 23.6 - - + +
95D LEU* 5.3 3.6 - - - +
131D ILE* 2.9 37.7 + - - +
132D ASP* 3.8 10.8 - - - +
134D LEU* 1.3 77.0 - - - +
136D THR* 1.3 63.0 + - - +
138D LEU* 3.8 5.3 - - - +
139D ASP* 3.0 32.0 + - - +
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ASP* 2.8 29.7 + - - -
133D TRP* 3.7 7.0 - - + -
135D GLU* 1.3 76.9 - - - +
137D GLU* 1.3 59.9 + - - +
139D ASP* 3.2 7.4 + - + +
140D LEU* 2.9 45.8 + - + +
143D LYS* 5.5 0.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ARG* 3.0 32.9 + - - -
87D LEU* 4.2 11.0 - - + -
133D TRP* 3.0 56.2 + - + +
134D LEU* 3.7 5.2 - - - +
136D THR* 1.3 79.4 - - - +
138D LEU* 1.3 62.6 + - - +
140D LEU* 3.0 28.3 + - - +
141D ILE* 3.0 19.0 + - - +
149D TYR* 2.5 39.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLU* 3.9 30.7 - - + +
87D LEU* 3.7 32.1 - - + +
88D ARG* 3.8 41.8 + - + +
91D LEU* 3.8 29.8 - - + -
134D LEU 2.9 18.3 + - - +
135D GLU* 3.8 4.7 - - - +
137D GLU* 1.3 76.3 - - - +
139D ASP* 1.3 65.4 + - - +
141D ILE* 3.4 18.6 + - + +
142D GLN* 3.5 12.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 3.0 23.4 + - - +
136D THR* 3.6 6.4 - - - +
138D LEU* 1.3 75.6 - - - +
140D LEU* 1.3 69.1 + - - +
142D GLN* 3.0 10.2 + - - +
143D LYS* 2.9 49.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ARG* 5.0 7.6 - - - +
136D THR* 2.9 30.9 + - + +
137D GLU* 3.0 32.5 + - - +
139D ASP* 1.3 75.4 - - - +
141D ILE* 1.3 62.3 + - - +
143D LYS* 4.4 15.3 - - + +
144D MET* 2.9 55.1 + - + +
149D TYR* 4.3 9.9 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D VAL* 4.6 3.6 - - + -
84D GLU* 4.2 31.0 - - + +
87D LEU* 4.3 15.7 - - + -
137D GLU 3.0 14.9 + - - +
138D LEU* 3.5 11.7 - - + +
139D ASP 3.1 0.4 - - - -
140D LEU* 1.3 77.6 - - - +
142D GLN* 1.3 70.7 + - - +
145D GLY* 2.9 29.8 + - - -
146D LEU* 4.4 28.5 - - + +
149D TYR* 3.6 41.5 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLU* 3.7 27.2 + - - -
88D ARG* 4.9 7.4 - - - +
138D LEU 3.5 10.8 + - - +
139D ASP* 3.0 10.9 + - - +
141D ILE* 1.3 88.6 + - - +
143D LYS* 1.3 69.5 + - + +
144D MET 3.5 0.2 + - - -
145D GLY* 3.7 5.5 + - - -
----------------------------------------------------------
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ASP* 2.9 43.8 + - + +
140D LEU* 4.0 17.7 - - + +
142D GLN* 1.3 80.2 - - + +
144D MET* 1.3 59.6 + - + +
----------------------------------------------------------
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Residues in contact with MET 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 2.9 52.9 + - + +
143D LYS* 1.3 77.1 - - + +
145D GLY* 1.3 66.9 + - - +
148D ASN* 3.4 34.8 + - + +
149D TYR* 3.7 28.5 - - + +
152D ALA* 4.8 8.3 - - - -
250D SO4 4.6 1.6 + - - -
----------------------------------------------------------
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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