Contacts of the helix formed by residues 127 - 158 (chain J) in PDB entry 3A9Q
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 GLY 127 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ASP* 4.9 0.7 - - - -
123J HIS* 2.7 23.7 + - - -
124J ALA 4.0 1.8 + - - -
125J ASP 3.5 2.0 - - - -
126J LYS* 1.3 75.1 - - - +
128J ASP* 1.3 66.4 + - - -
129J ALA 3.4 2.6 + - - -
130J LEU 4.2 0.4 - - - -
131J HIS* 3.1 23.4 + - - +
193J LYS* 3.9 17.0 - - - +
197J VAL* 6.5 0.7 - - - -
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Residues in contact with ASP 128 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG* 3.4 37.1 + - - -
69J TYR* 4.0 8.5 + - + -
70J PHE* 3.6 15.6 - - + -
75J VAL* 3.7 15.8 - - - +
77J LEU* 3.8 2.3 - - - +
121J PHE 3.5 22.7 - - - +
122J ASP* 3.8 21.5 + - - +
123J HIS 4.4 1.1 - - - +
127J GLY* 1.3 72.6 - - - +
129J ALA* 1.3 64.6 + - - +
131J HIS* 3.7 0.5 - - - +
132J ALA* 2.9 32.7 + - - +
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Residues in contact with ALA 129 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J PHE* 4.3 0.9 - - - -
77J LEU* 4.2 3.4 - - + -
80J LEU* 3.8 28.3 - - + +
127J GLY 3.4 0.6 - - - -
128J ASP* 1.3 85.6 + - - +
130J LEU* 1.3 63.0 + - - +
132J ALA* 3.3 2.1 + - - +
133J MET* 3.0 24.8 + - - +
188J LEU* 3.8 17.1 - - + +
197J VAL* 3.7 32.5 - - + -
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Residues in contact with LEU 130 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J LYS* 3.5 36.1 - - + +
127J GLY 3.6 1.6 + - - -
128J ASP 3.4 0.2 - - - -
129J ALA* 1.3 77.7 - - - +
131J HIS* 1.3 64.8 + - - +
133J MET 3.2 1.0 + - - -
134J GLU* 2.9 53.5 + - + +
185J VAL* 3.9 29.4 - - + +
188J LEU* 4.1 19.6 - - + +
189J ARG* 3.9 22.0 - - + +
197J VAL* 5.6 2.6 - - + +
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Residues in contact with HIS 131 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J LEU* 6.1 2.0 - - - +
120J ASP 5.6 0.6 + - - -
121J PHE* 3.5 30.4 - - + -
122J ASP 4.1 2.7 + - - -
123J HIS* 3.5 42.2 + + + -
126J LYS* 4.0 15.9 - - + +
127J GLY 3.1 19.1 + - - +
128J ASP 3.7 2.5 - - - +
130J LEU* 1.3 77.8 - - - +
132J ALA* 1.3 57.2 + - - +
134J GLU* 3.3 2.4 + - - +
135J LEU* 3.0 63.2 + - + +
25N LEU* 5.3 10.2 - - + +
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Residues in contact with ALA 132 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J MET* 4.4 8.0 - - - +
70J PHE* 3.4 40.6 - - + -
80J LEU* 4.7 0.2 - - + -
84J PHE* 4.1 14.2 - - + -
121J PHE* 4.7 7.6 - - + -
128J ASP 2.9 9.5 + - - +
129J ALA 3.8 2.2 - - - +
131J HIS* 1.3 78.6 - - - +
133J MET* 1.3 58.2 + - - +
135J LEU* 3.3 10.7 + - - +
136J ALA* 2.9 28.2 + - - +
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Residues in contact with MET 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J LEU* 4.3 15.3 - - + -
83J PHE* 4.0 28.7 - - + -
84J PHE* 4.3 7.4 - - + -
129J ALA 3.0 16.9 + - - +
130J LEU 3.8 3.1 - - - +
132J ALA* 1.3 77.1 - - - +
134J GLU* 1.3 57.5 + - - +
136J ALA* 3.3 2.1 + - - -
137J LEU* 2.9 24.4 + - - +
181J ILE* 3.5 21.3 - - + +
184J TYR* 3.5 48.5 - - + -
185J VAL* 3.8 15.3 - - + +
188J LEU* 3.9 12.1 - - + -
200J PHE* 4.5 6.5 - - + -
204J LEU* 4.2 15.7 - - + -
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Residues in contact with GLU 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J LYS* 2.8 38.7 + - - -
130J LEU* 2.9 38.9 + - + +
131J HIS* 3.7 4.3 - - - +
133J MET* 1.3 73.9 - - - +
135J LEU* 1.3 61.2 + - - +
137J LEU* 3.4 6.2 + - - +
138J SER* 3.0 30.7 + - - -
185J VAL* 3.9 16.2 - - + -
189J ARG* 2.7 36.5 + - - +
25N LEU* 3.9 16.6 - - + +
28N VAL* 4.4 12.8 - - + +
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Residues in contact with LEU 135 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J MET* 4.0 10.5 - - + -
118J LEU* 5.6 3.4 - - + -
121J PHE* 4.0 25.1 - - + -
131J HIS* 3.0 54.6 + - + +
132J ALA* 3.6 4.9 - - - +
134J GLU* 1.3 74.7 - - - +
136J ALA* 1.3 60.1 + - - +
138J SER* 3.2 3.4 + - - -
139J LEU* 2.9 36.3 + - + +
18N PHE* 4.7 12.8 - - + -
21N VAL* 4.5 17.9 - - + +
25N LEU* 3.9 26.2 - - + -
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J TYR* 3.8 30.3 - - + +
66J MET* 4.7 1.7 - - - +
83J PHE* 5.2 0.7 - - + -
84J PHE* 4.1 12.6 - - + -
132J ALA 2.9 16.5 + - - +
133J MET* 3.6 8.7 - - - +
135J LEU* 1.3 73.4 - - - +
137J LEU* 1.3 66.1 + - - +
139J LEU* 3.2 5.2 + - - +
140J GLU* 2.9 29.6 + - - +
181J ILE* 4.2 13.9 - - + -
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J MET 2.9 17.5 + - - +
134J GLU* 3.6 6.3 - - - +
136J ALA* 1.3 74.2 - - - +
138J SER* 1.3 58.8 + - - +
140J GLU* 3.2 3.8 + - - +
141J LYS* 2.9 40.5 + - + +
178J ILE* 3.8 28.9 - - + +
181J ILE* 3.6 12.7 - - + +
182J SER* 3.3 30.7 - - - +
185J VAL* 4.4 13.9 - - + -
28N VAL* 4.6 22.4 - - + -
36N LEU* 3.9 23.3 - - + +
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Residues in contact with SER 138 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J GLU 3.0 18.0 + - - -
135J LEU 3.6 3.8 - - - -
137J LEU* 1.3 78.0 - - - +
139J LEU* 1.3 57.5 + - - +
141J LYS* 3.3 1.8 + - - -
142J LEU* 2.9 31.7 + - - +
21N VAL* 3.5 21.3 - - - -
24N GLU* 3.5 16.7 + - - +
25N LEU* 3.2 35.0 + - - +
28N VAL* 3.6 6.3 - - - +
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Residues in contact with LEU 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J VAL* 4.7 17.5 - - + +
62J VAL* 3.6 31.4 - - + -
63J TYR* 4.3 18.2 - - + +
66J MET* 4.0 13.5 - - + -
135J LEU* 2.9 21.7 + - + +
136J ALA* 3.6 4.5 - - - +
138J SER* 1.3 77.4 - - - +
140J GLU* 1.3 58.8 + - - +
142J LEU* 3.4 8.3 + - + +
143J THR* 2.8 31.9 + - - -
15N PHE* 6.2 1.3 - - + -
17N PRO* 4.1 26.7 - - + +
18N PHE* 5.5 4.7 - - + -
21N VAL* 3.9 20.6 - - + -
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Residues in contact with GLU 140 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J VAL* 4.1 5.4 - - - +
63J TYR* 2.5 32.9 + - - +
91J GLU* 3.6 14.9 - - - +
136J ALA 2.9 20.6 + - - +
137J LEU* 3.7 5.2 - - - +
139J LEU* 1.3 76.7 - - - +
141J LYS* 1.3 58.9 + - - +
143J THR* 3.3 4.8 + - - +
144J ASN* 2.9 18.0 + - - +
174J GLN* 2.7 50.6 + - - +
177J ALA* 4.2 11.8 - - + +
178J ILE* 3.9 16.6 - - + -
181J ILE* 3.6 21.1 - - + -
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Residues in contact with LYS 141 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU* 2.9 35.7 + - + +
138J SER* 3.8 4.0 - - - +
140J GLU* 1.3 73.4 - - - +
142J LEU* 1.3 61.3 + - - +
144J ASN* 3.3 0.9 + - - +
145J GLU* 3.0 16.6 + - - +
178J ILE* 4.1 9.4 - - + -
24N GLU* 3.9 26.2 + - + +
28N VAL* 6.0 3.8 - - + +
29N PRO* 5.1 9.1 - - - +
35N SER 5.3 0.4 + - - -
36N LEU 2.7 30.0 + - - -
37N ALA* 3.7 13.9 - - - +
38N ARG 3.2 20.3 + - - -
39N GLN* 2.8 46.2 + - + +
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Residues in contact with LEU 142 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J SER 2.9 18.7 + - - +
139J LEU* 3.6 9.6 - - + +
140J GLU 3.3 0.2 - - - -
141J LYS* 1.3 74.9 - - - +
143J THR* 1.3 58.3 + - - +
145J GLU* 3.2 20.0 + - - +
146J LYS* 2.9 37.1 + - + +
15N PHE* 5.5 8.7 - - + -
17N PRO* 4.2 4.5 - - + +
20N GLU* 3.1 47.1 - - + +
21N VAL* 3.3 24.5 - - + +
23N LYS* 5.1 4.7 - - + -
24N GLU* 3.2 27.1 - - + +
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Residues in contact with THR 143 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J GLN* 4.0 5.2 - - - +
55J VAL* 4.3 6.5 - - + +
56J GLU* 3.6 26.9 - - - +
59J VAL* 3.6 23.1 - - + +
91J GLU* 5.3 0.2 + - - -
139J LEU 2.8 21.4 + - - -
140J GLU* 3.5 8.2 + - - -
142J LEU* 1.3 76.2 - - - +
144J ASN* 1.3 53.0 - - - +
146J LYS* 3.2 9.1 + - - +
147J LEU* 2.8 43.2 + - + +
174J GLN* 3.9 13.2 - - - +
214J CA 4.1 8.3 - - - -
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Residues in contact with ASN 144 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J GLU 2.9 14.0 + - - +
141J LYS 3.4 8.5 - - - +
142J LEU 3.2 0.2 - - - -
143J THR* 1.3 77.4 - - - +
145J GLU* 1.3 56.4 + - - +
147J LEU* 3.2 2.4 + - - +
148J LEU* 2.9 49.6 + - - +
171J LEU* 4.1 15.1 - - - +
174J GLN* 3.4 30.3 - - + +
175J VAL* 5.2 10.7 + - - +
178J ILE* 3.9 8.8 - - + +
39N GLN* 3.1 30.9 + - - +
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Residues in contact with GLU 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J LYS 3.0 13.1 + - - +
142J LEU* 3.2 25.8 + - - +
144J ASN* 1.3 75.4 - - - +
146J LYS* 1.3 59.7 + - + +
148J LEU* 3.3 3.2 + - - +
149J ASN* 2.9 49.0 + - - +
23N LYS* 5.2 9.3 + - - +
24N GLU* 4.4 5.1 - - - +
39N GLN* 4.1 6.2 - - - +
40N LYS* 3.3 36.2 + - - +
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Residues in contact with LYS 146 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J GLU* 3.9 21.7 + - - +
52J GLN* 3.5 22.3 - - - +
55J VAL* 4.1 16.6 - - + +
142J LEU* 2.9 23.3 + - - +
143J THR* 3.5 8.3 - - - +
145J GLU* 1.3 79.0 - - + +
147J LEU* 1.3 55.8 + - - +
149J ASN* 3.2 17.7 + - + +
150J LEU* 2.9 25.1 + - - +
15N PHE* 3.7 26.2 - - + -
20N GLU* 2.7 33.8 + - - -
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Residues in contact with LEU 147 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J GLN* 3.4 30.5 + - + +
56J GLU* 3.9 6.7 - - - +
98J LEU* 5.3 0.2 - - + -
143J THR* 2.8 28.6 + - + +
144J ASN* 3.7 4.0 - - - +
146J LYS* 1.3 71.8 - - - +
148J LEU* 1.3 58.8 + - - +
150J LEU* 3.2 8.8 + - + +
151J HIS* 2.9 27.7 + - - +
166J VAL* 3.8 12.2 - - + +
170J TYR* 3.8 39.3 - - + +
171J LEU* 3.8 15.5 - - + -
174J GLN* 3.8 35.7 - - + +
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Residues in contact with LEU 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J ASN* 2.9 39.6 + - - +
145J GLU* 3.7 4.0 - - - +
147J LEU* 1.3 75.7 - - - +
149J ASN* 1.3 58.5 + - - +
151J HIS* 3.3 5.8 + - + +
152J SER* 2.9 26.9 + - - -
171J LEU* 3.9 30.3 - - + -
40N LYS* 3.7 34.1 - - + -
160N VAL* 4.1 23.3 - - + +
161N GLN* 5.2 4.7 - - + +
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Residues in contact with ASN 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J GLU* 2.9 34.4 + - - +
146J LYS* 3.4 21.8 - - + +
148J LEU* 1.3 75.3 - - - +
150J LEU* 1.3 58.8 + - - +
152J SER* 3.0 10.1 + - - -
153J VAL* 2.9 32.7 + - + +
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Residues in contact with LEU 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J ALA* 3.6 38.6 - - + +
49J VAL* 3.9 14.8 - - + +
52J GLN* 3.9 31.6 - - + +
98J LEU* 4.6 11.7 - - + -
146J LYS 2.9 12.0 + - - +
147J LEU* 3.4 10.8 - - + +
149J ASN* 1.3 75.3 - - - +
151J HIS* 1.3 64.4 + - - +
153J VAL* 3.1 9.3 + - + +
154J ALA* 3.0 20.6 + - - +
162J LEU* 4.5 8.7 - - + -
166J VAL* 3.7 29.6 - - + -
170J TYR* 6.4 0.2 - - + -
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Residues in contact with HIS 151 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J LEU 2.9 14.2 + - - +
148J LEU* 3.5 13.7 + - + +
150J LEU* 1.3 76.6 - - - +
152J SER* 1.3 58.8 + - - +
154J ALA* 3.3 6.6 + - - +
155J THR* 2.9 51.2 + - - -
163J ALA* 3.4 30.6 + - + +
166J VAL* 4.2 13.0 - - + +
167J GLU* 2.8 35.0 + - + +
171J LEU* 4.2 5.8 - - + -
160N VAL* 3.4 35.1 - - + +
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Residues in contact with SER 152 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J LEU 2.9 13.7 + - - -
149J ASN* 3.0 13.4 + - - -
151J HIS* 1.3 77.2 + - - +
153J VAL* 1.3 59.6 + - - +
155J THR* 3.8 5.6 - - - -
156J LYS* 2.8 33.1 + - - +
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Residues in contact with VAL 153 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLU* 3.9 40.4 - - + +
45J SER* 4.2 5.8 - - - +
48J ALA* 4.0 20.2 - - + -
149J ASN* 2.9 20.0 + - + +
150J LEU* 3.1 8.3 + - + +
152J SER* 1.3 75.6 - - - +
154J ALA* 1.3 57.9 + - - +
156J LYS* 3.6 7.2 - - + +
157J ASN* 2.9 47.2 + - - +
162J LEU* 5.8 0.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J SER* 4.7 2.5 - - - -
150J LEU 3.0 9.8 + - - +
151J HIS* 3.5 9.9 - - - +
153J VAL* 1.3 78.0 - - - +
155J THR* 1.3 62.7 + - - +
157J ASN 3.2 1.7 + - - -
158J GLY 2.9 4.9 + - - -
159J ASP* 2.8 35.5 + - - +
162J LEU* 3.6 37.2 - - + +
163J ALA* 3.7 19.3 - - + +
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Residues in contact with THR 155 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J HIS* 2.9 39.1 + - - -
152J SER* 3.8 6.5 - - - -
154J ALA* 1.3 74.4 - - - +
156J LYS* 1.3 65.4 + - - +
158J GLY* 3.0 14.8 + - - +
159J ASP 5.0 0.7 - - - +
163J ALA* 4.3 7.2 - - - +
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Residues in contact with LYS 156 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLU* 2.8 38.6 + - - +
152J SER* 2.8 24.1 + - - +
153J VAL* 3.6 5.4 - - + +
155J THR* 1.3 75.6 - - - +
157J ASN* 1.3 73.2 + - - +
158J GLY 3.5 0.5 + - - -
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Residues in contact with ASN 157 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J VAL* 3.6 37.0 - - + +
44J GLU* 2.7 36.0 + - - +
45J SER* 4.2 7.2 - - - +
153J VAL* 2.9 26.2 + - - +
154J ALA 3.2 2.4 + - - +
156J LYS* 1.3 86.9 + - - +
158J GLY* 1.3 61.1 + - - +
159J ASP* 3.3 4.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY 158 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ALA 2.9 3.0 + - - -
155J THR* 3.0 14.8 + - - -
156J LYS 3.2 1.4 + - - -
157J ASN* 1.3 79.1 - - - +
159J ASP* 1.3 58.4 - - - +
160J VAL* 3.2 16.8 + - - +
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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